I tracked down the original source of the graph: https://mdedge.com/pediatrics/article/228682/coronavirus-updates/children-and-covid-19-new-cases-may-be-leveling… Coupled with the headline, this is atrocious data presentation from @AmerAcadPeds / @AAPNews. (Cases may be indeed leveling off somewhat, but this graph sure doesn't let you make that assessment.)

To illustrate what is wrong with the original, @JasonSalemi overlays percentage change in cumulative plot with the cumulative plot itself, for Florida data on pediatric cases. The red line falls away precipitously even during the duration of peak growth in cumulative cases.

Plotting the percentage increase in the cumulative total: for all but a few very specialized applications, this is a remarkably misleading form of data visualization because the ever-increasing denominator masks changes in the numerator.

Not so much. Here's a regular cumulative plot of my time spent on zoom.

Maybe it's coincidence, but it looks a lot the way that I've been able to bring my time spent on zoom calls under control over the course of the pandemic. Pretty impressive!

Here's a remarkably misleading #dataviz via @BethPathak. Sure looks like the pediatric COVID situation is getting better, right?

Social bubbles in a pandemic: perception vs. reality

NBC News: The United States has surpassed 200,000 coronavirus deaths.

furthermore, there is no risk or probability linked to the 5 points on the Likert scale - any interpretation that assigns lower risk to lower numbers is pretty much as good as any other in terms of what I personally am entitled to think "won't happen to me" means... 5/5

To be biased, judgments must be *at odds with some rational standard* but someone who is hyper-vigilantly not leaving the house, avoiding social interactions + washing their home delivered groceries can entirely realistically indicate they don't think they will be infected 4/5

"The items were rated in a 5-point Likert scale (1=strongly disagree,5= strongly agree) and a mean score was computed with higher values indicating more optimism bias" 3/5

Here the measure: "The participants completed three items to assess optimism bias: “I don’t think it’s going to happen to me”, “I don’t think it’s going to happen to my loved ones”, “I am afraid that someone I love may get infected” (reverse coded) => 2/4

I cannot retweet this without noting that the measure of bias used is not a measure of "bias": 1/4

For those who might think this issue isn't settled yet, the piece include below has further graphs indicating just how much "protecting the economy" is associated with "keeping the virus under control"

I cannot attest to the accuracy of the underlying science/model but the idea of the tool is very cool and seems extremely useful!

Here you go, debunking debunked - though I'm not wasting any more of my time on this twaddle!

RT @KFF: .@DrewAltman discusses two fundamental policy decisions made by the Trump administration that set the U.S. on the controversial an…

This encapsulates the problem nicely. Sure, there’s a paper. But actually read it & what do you find? p-values mostly juuuust under .05 (a red flag) and a sample size that’s FAR less than “25m”. If you think this is in any way compelling evidence, you’ve totally been sold a pup.

One amazing way to do this would be to control the pandemic; Venmo me.

universities and everything else, it becomes more and likely. 13. Yes, most of this is my own opinion, I genuinely hope I'm wrong about the winter...

is good for shielders, the elderly or the economy. 12. No, we can't say for certain that there will be resurgence of infections in the winter. However, without minimising community transmission over the summer combined with increased social mixing involving schools, pubs, work

protect you better. 10. Yes, you CAN get on top of this with non-pharmaceutical interventions combined with rigorous test, trace, isolate, test again... 11. If we don't get on top of it, we'll have cyclical limbo of local lockdowns and confused unlocking. I can't see how this

they are not a conspiracy and yes you should have it when its available. Antivax is an act of self-harm for humanity. 9. Yes, face masks worn properly do help limit spread. No, they won't protect you personally very well, but better than nothing. Surgical masks and respirators

7. Yes, kids can catch SARS2, no they don't often get very unwell, but yes they can certainly spread it. 8. No, we don't know whether any vaccine will work, but there are some amazing efforts ongoing. No, herd immunity is NOT a viable option and it hasn't happened anywhere. No,

pick up "dead RNA" as I've seen mentioned. Honestly... 6. Yes, the NHS is struggling to catch back up after the peak. This is NOT to do with being distracted, wrongly tasked, or overly cautious. It is due to being chronically underfunded and understaffed for a decade. Simple.

lower numbers in parts of UK keep it around 1 (or slightly higher in some parts). R0 is only 3 when you don't intervene! 4. No, the virus is not getting "weaker". It is infecting younger, healthier people better able to cope. 5. No, tests are not wildly inaccurate, they don't

2. Yes, there are fewer hospital cases and fatalities. This is proportionate to infections, plus more younger people infected. Care homes are better protected (finally) and most shielders did NOT pause, I suspect. 3. Cases are increasing, as is R0, but regional variation and

Upsetting to see so many half-truths, dismissive crap and bizarre media conspiracies floating around...sorry, have to get this off my chest. 1. No, of course there aren't as many infections as in spring. We had a lockdown, albeit truncated, and most people still distance...

We can't predict the future. But we know only fools repeat errors of the past over & over without giving consideration to the best evidence available. The next 2 weeks will fill in a lot of details. Be patient. Be vigilant. Be careful. #MaskUp #SocialDistance #TestTestTest 8/end

For those who think we are reopening too slow, look to Sweden: they are not relaxing measures until October. Their Universities remain in hybrid format. Or look to Israel, where they are on the cusp of a full lockdown after throwing caution to the wind. 7/8

College testing skews data. In NYS, Tompkins county(Ithaca/Cornell) is responsible for 0.5% of the population but 4% of the total testing. 0.2% positive rate. OTOH - Oswego (SUNY) -0.5% of pop is responsible for 0.5% of total testing with 5% positive rate. 6/8

We KNOW we have more college testing. We also know testing, overall, is trending lower = non-college-related testing is dropping sharply. Over the last 2 weeks many hot-spots have either already re-opened bars or have announced plans to do so. 5/8

Case counts continue to drift lower. But we have recent experience where average age of cases drifted lower when bars reopened & severe cases showed up much later. Florida, for instance, hit a low for positive rate in late May - 2 weeks later cases started to take off. 4/8

This is reducing the positive rate, giving us a less reliable indicator. We know from hospitalization and death data a lot about infections that happened in early to mid August, and that news is good. But what is happening NOW? I don't think we know enough. 3/8

The national figures that we have come to rely on are more reliable but subject to MUCH more challenging interpretation than at any time. A LARGE percent (20% of Illinois in this article) of current tests are from colleges doing MASSIVE testing, in some cases. 2/8

Thread/ Colleges, testing, & why we need caution. I am FAR LESS worried about the students. I worry about this - "One major risk is that infections could spread to at-risk faculty and staff and those in the surrounding community." 1/8

Our daily update is published. States reported 763k tests, 37k cases, and 663 COVID-19 deaths. Important caveat: this update does not include Texas’s daily data, which is still not in today.

Tried to reproduce your graph with Estonian data - curiously similar (despite of the >100x smaller scale on the X-axis)

Some additional info: We're looking whether approach-training changes behaviour to real spiders (2 groups) and my supervisor says they will ask us to check if a change in behaviour is mediated by a change in approach-bias (on a variation of the training task).

We're writing up a RR We have some analyses that are secondary to the RQs, but are likely to be conducted because reviewers will ask for them. We cannot afford enough participants for these to have sufficient power. Should we mention in Stage 1 anything about these analyses?

Hi @TwitterSupport--I'm an ID epi that does a lot of science communication. Most of the other amazing scientists I do this with are verified. It would be great if the people I'm communicating with could know my account is really me & really trustworthy. Can I get some help?

Testing is broken. So many stories in last 24 hrs of medical colleagues trying to get tests because kids have a fever or cough. They can’t get one. They can’t work until they get one. How long is this farce going to continue. This was entirely predictable.

I’ve again updated my chart of COVID-19 hospital admissions to include the latest numbers. Admissions in England are rising. The 7-day moving average has increased by 70% since its low point on 26 August. This is the first sustained increase in admissions since March/April.

Matt Hancock tells Radio 4 that on average people only have to travel ten miles to get a nasal swab test for Covid using his failing private system. Yet every GP surgery can do nasal swabs...but are not allowed to for Covid.

This is why you need to download the @BotSentinel extension, folks

A powerful image. These girls are sitting their university entrance exams in Afghanistan ...under a heat of 37C...on the ground...social distant...during a pandemic...because they know that only education will make them free

18. Disclosure: There are IHME doubters and disciples. I’m neither. I am a long-time ally of the GBD, which is vital work that's improved by transparency and honest criticism. In my view the IHME COVID-19 models don't yet meet that standard, but I'd like to see them to get there.

17. Bottom line: This model is getting lots of attention, from the public and (presumably) policy-makers. Trust in science and public health has been badly damaged during this pandemic. Transparency and good communication are essential to any hope for a science-driven response.

16. Provide more scenario analyses that allow some unpacking of the forecasts. What if the expected effects of seasonality are less pronounced than in the base model? How about running the best-fitting predictive model that excludes seasonal effects, for comparison?

15. Make it easier to find these methods. They should be one click away from the forecasts here: https://covid19.healthdata.org/united-states-of-america… Publish the forward projections of all predictors. The forecasted trends are driven by these. People need to see them.

14. So, hoping @IHME can confirm whether I've got all this right. I’ll leave it to others to weigh in on the strength of evidence for seasonal effects on SARS-CoV-2 transmission. Meantime, I have some suggestions for things that @IHME could do to elicit constructive input.

13. Which brings us to seasonality. Seasonality is captured using weekly, state-specific vital statistics data on pneumonia mortality from 2013 to 2019. So, as far as I can surmise, the estimated rise from 900 to 2900 daily deaths derives entirely from this seasonal effect.

12. It’s not behavior. The main projection expects distancing behavior to improve in response to a worsening epidemic. It’s the purple dotted line diving down in the figure, meaning reduced contacts. It’s not mask use, which is held constant ... …nor testing, which goes up.

11. So, this is the key: projections for the next four months depend on projections of the independent variables. In the main projection, daily deaths rise from <900 now to almost 2900 by December 1. What in the model drives things to get much worse?

10. Step 5: Make forward projections of the predictors, which leads to forward projections of beta. These are then plugged into the SEIR model to produce forecasts of all the other outcomes including cases and deaths.

9. Step 4: It’s all about that beta. Here’s the heart of the projection model: a linear regression of beta on a bunch of covariates, including several time varying ones: - social distancing mandates - changes in mobility - testing per capita - mask use - pneumonia seasonality

8. Step 3: More back-calculation! Here, a pretty standard deterministic SEIR model is fit to the estimated series on new infections. Key output in this step is estimated time series on beta, the transmission rate. [Aside: yep, this is a LOT of estimates on estimates ...]

7. Step 2: Back-calculate a time series on new infections from the smoothed death time series, based on … - assumed age pattern of mortality - assumed lag from infection to death - assumed age-specific infection fatality rates

6. Step 1: Estimate smoothed mortality time series using splines. First, cases and hospitalizations used as leading indicators to predict deaths. Then, a 2nd model synthesizes deaths from direct observation with the death series predicted from cases & hospitalizations.

5. The current approach is described as a hybrid ‘mortality spline + SEIR’ model. Let’s have a look at the components. Here’s the schematic from the July preprint. I believe it’s pretty self-explanatory. [Narrator: It isn’t.]

4. So, what’s in the model? There have been a few major renovations. The last one, I believe, was rolled out in July. All remnants of the much-maligned mortality CurveFit were excised in the July release. This CurveFit-ectomy was a welcome advance.

3. After some digging, I think the current IHME forecast model is described here: https://medrxiv.org/content/10.1101/2020.07.12.20151191v1… @IHME: if this is the current model, every estimates update and the FAQ need to point here, and not just to the March and April preprints.

2. First observation: the methods really need to be easier to find and vet. Optimally, publish all code. At least, have every update point clearly to the technical document with full model details. Right now, the FAQ and results updates point to old model versions.

1. Did the latest @IHME mortality forecasts making the media rounds - 410,000 deaths - seem high to you? Yeah, me too. I wanted to understand what’s driving projections of 220K more deaths by New Years. So, I tried to peek under the hood, as best I could. Buckle in. A thread.

The majority (68%) in ICU care had one or more underlying condition considered as one of the risk groups, most prevalent being hypertension (37%), diabetes (25%), chronic pulmonary heart disease (24%), chronic respiratory disease (14%) and chronic cardiovascular disease (11%).

Interesting numbers when I used the death certificate audit data from two Swedish regions where C-19 was established as a direct cause of death and excluded C-19 as a minor contributing factor only.

#India has passed #Brazil to move into the # 2 spot in the world.

Oh, so THAT'S how you describe this feeling.

A lot has gone wrong in the response to COVID. I would have done things differently in economic policy too. But overall the massive response from the Federal Reserve and even more importantly from Congress has been working and should be continued as long as needed.

Action should be based on circumstances. The $600 a week boost to weekly unemployment checks may have made sense when the economy has shutdown but with an UR of 8.4% it should change. The President's $400 is reasonable--but the Senate needs to actually pass it for it to be real.

Further action is needed. We're still in a bad recession. State/local job creation has been weak/negative in recent months & will get worse without aid. And households will run through their cushions soon, consumption growth will start to slow, and that will take a toll on jobs.

The fiscal response has now ended. The "cliff" was at the end of July but given that most households saved a lot in the spring & had healthier balance sheets than pre-crisis they have some ability to smooth. So I would not expect bad macro impacts until Sep or Oct.

The shock to the economy from COVID has in many ways been much larger than the shock that precipitated previous recessions. At the same time, the policy response has also been MUCH larger this time than previous times with a discretionary fiscal stimulus 5X the previous record.

In the double dip recession in the early 1980s the unemployment rate was 8.5% or above for 24 straight months. In the financial crisis it was 34 straight months. This time it will have been 4 months (although it could tick up again).

An unemployment rate of 8.4% is much lower than most anyone would have thought it a few months ago. It is still a bad recession but not a historically unprecedented event or one we need to go back to the Great Depression for comparison.

Employment in industries where people can work from home is still down 3.9%, with little recovery. That's equal to peak-to-trough drop in jobs in those industries during Great Recession. Big red flag for longer-term recovery.

Iowa COVID numbers are spiking. Jodi Ernst says she doesn't believe them, suggests doctors may be inflating figures to get higher reimbursement.

7 #COVID19 deaths on my reservation as of today. Nobody knows how many have the virus bc the numbers are different depending on who you ask. Tribal, IHS, state & federal data systems are spitting out different damn #s. This is ridiculous! Frustrated & angry af. We are dying!

I apologise for any misunderstanding. What I meant was we need to get back to “work as usual” - face to face contact where it is safe to do so as well as online teaching. Buckingham and all universities have been working exceptionally hard all summer to prepare for the new term.

I have always said I think a second wave quite likely. But I believe my own University in particular, but also the sector at large, is very well placed to manage if it occurs. We need to get back to work. The show goes on.

It shouldn’t be hard to know who to trust on coronavirus information. Trust people who’ve been consistently right over the last nine months. Don’t trust people who’ve been repeatedly, unapologetically wrong. That’s it.

The return to workplaces issue, just like the schools, is a perfect example of how we currently have to turn *everything* into a fight. When there are valid & powerful arguments on both ‘sides’, clarity & leadership are crucial. Sadly, our leaders prefer to foment the fighting.

here's the quote from the piece itself: [An example of confirmation bias is...] "...our propensity to interpret declining infection rates as a confirmation that the lockdowns “worked”, when in fact this is a textbook example of the post hoc fallacy.".

why? because it pretends that the temporal cue (falling numbers after lockdown) literally is *the only* evidence being used. Whereas, in actuality, a huge body of evidence *predicts* that lockdowns will bring down numbers and explains *why*

this kind of piece behavioural scientists need to reject! A shallow understanding of the bias literature in an even shallower application to the pandemic- the idea that believing lockdowns brought down infection rates is an example of the "post hoc fallacy" is bizarre 1/3

#Coronavirus tracking from @UNC shows 31% of #SARSCoV2 tests run this week were positive, a dramatic increase from previous wks. Is anyone in #publichealth surprised by these outbreaks? I don't think so. This higher ed experiment is a bad idea in states w/ uncontrolled #COVID19.

Conspiracy theories - The link to COVID-19

RT @BrianNosek: Preprint "conversations about reproducibility have a clear underlying structure, despite the broad scope..of the crisis. ..…

Of course, our plans may still go to hell in a hand basket. From the @CSBS_Illinois vantage point, behavioral and social science could be critical to the situation, but we may need to shift our priorities and consider other perspectives in order to wield more influence 23/

Combining constant testing with comprehensive exposure notification, mask use, and curtailing large gatherings, there is hope that we can keep the outbreaks, which will happen, to a minimum (thanks South Korea and other countries for showing us how it is done, btw). 22/

In the case of @Illinois_Alma, our ability and motivation to test twice a week is a great example of creating conditions where individual differences will hopefully not matter enough to close us down. 21/

The efforts so far have focused on individuals changing their own behavior. While that is 1 solution, another “social science” solution is to create conditions where the individual differences don’t matter. This idea does not seem to be considered as much as one would hope. 20/

Pay students not to party? Gift cards for wearing masks? TikTok threads supporting social distancing? They probably wouldn't hurt, but they are not magic bullets. 19/

Punishment--threatening expulsion and the like--is simple behaviorism. Of course, it is only the stick part of behaviorism. While adding in some carrots would not hurt, I am hard pressed to identify any proactive incentive structure that would magically fix the situation. 18/

The futility of a situationist position is no better demonstrated by the repeated cycle happening at universities where administrators wish their undergrad would simply behave differently and they don’t. I mean how much more of a strong situation do you need than a pandemic? 17/

Situationism assumes that the overriding cause of human behavior is the incentives in any given situation. Change the situation, change the behavior. There is no need to consider prior standing on any attribute or population characteristics. 16/

The idea that college students would miraculously and immediately overcome their well known propensities to be a bit more cavalier than their older patrons is the hallmark of situationism. 15/

The two dominant approaches taken by universities to the need for self-control have been magical thinking or punishment. Interestingly, both magical thinking and punishment do reflect established social and behavioral science paradigms. 14/

Relatedly, many folks, like @dynarski, are appropriately taking universities to task for expecting 19-year olds to get on the COVID-19 behavioral bandwagon and toe the self-control line. HT @sTeamTraen 13/

So, until we start providing data that can help in applied settings, like the one we are facing, I think we should refrain from saying that we should be heard or have more influence. We need to have something to say of value first. 12/

Knowing the compliance % would be rather useful to the modelers right now, but that is applied research. Having hard science envy, we over value “basic science” which is designed to be as useless as possible for applied issues like these. (maybe we can change that too) 11/

Partially, it is because we don’t have much usable knowledge to provide. I know that undergrads are more impulsive and anxious than older populations, but I don’t know how that translates into something useful like the % of students will shirk our requests to comply. 10/

The second reason for our lack of influence is well-worn preference for biological and technical answers to our pandemic problems--the old bias toward the hard sciences issue. While I could complain about this bias, I won’t. Why? 9/

Over time, the student affairs people, given our myopic focus on our own research needs, appropriately began to rely on other social scientists, but not the ones employed as researchers at their own university (maybe we can do things differently going forward...) 8/

The only reasons for us to work with student affairs in the past was to plead with them to selfishly use their data or gain access to the students so we could collect our own data. 7/

First, front line social and behavioral science researchers have seldom helped the units that were charged with the day-to-day activities of undergraduates, like the Vice Chancellor for Student Affairs office. 6/

While I feel like my university has afforded the @CSBS_Illinois the chance to inform the process, for which I am grateful, for the most part, our efforts have not been systematically incorporated into the pandemic planning. I see at least two reasons for that, IMHO. 5/

We posted information on how social and behavioral science knowledge could help. https://csbs.research.illinois.edu/news-events/social-and-behavioral-science-and-covid-19/… Conducted workshops: https://csbs.research.illinois.edu/understandingcontemporarychallenges/… Ran studies: https://csbs.research.illinois.edu/news-events/blog/… and wrote blogs: https://csbs.research.illinois.edu/2020/08/16/what-we-know-about-college-students-to-help-manage-covid-19/… 4/

At the @CSBS_Illinois, we started curating social and behavioral science insights from day 1 in an attempt to provide information to our community. 3/

Being at a University (@Illinois_Alma) that has, to my knowledge, created the most informed and comprehensive system to open safely, and being the director of our social and behavioral science unit (@CSBS_Illinois) I have some thoughts I’d like to share. 2/

Thread alert: There is a lot of back and forth about the use and abuse of behavioral and social science knowledge to help universities and colleges open up to in-person education, or not, in the time of COVID-19. 1/

LIVE now: Independent SAGE's weekly briefing. Please join us for latest analysis & questions from the press & public. All welcome!

How can you safely take off your mask? Simply follow these four easy steps to prevent catching the virus!

Muscaria@conazole·19 AugReplying to @firefoxx66 and @zorinaqThat's probably what we're currently beginning to see in France (+ an increase in hospital and ICU admissions as well in the last few days)... https://raw.githubusercontent.com/rozierguillaume/covid-19/master/images/charts/france/heatmap_cas.jpeg…111markfoodyburton@markfoodyburton·20 AugSince we in France love recipes - maybe this one will appeal. Take population of 67M, Infect in some areas. Now mix for a month- ideally in bars and cafes. When well mixed, redistribute and re-mix all young people together, also turn the temperature down. Yum ...11FakeGregA@GregAlexander8·19 AugReplying to @firefoxx66this tweet is 4 hours old and this data is a month old :(1Beͫvͣaͬnͨd@zorinaq·19 AugMy latest heatmaps are updated on a weekly basis here:mbevand/florida-covid19-line-list-dataAnalyzes line list data for all of Florida's COVID-19 cases - mbevand/florida-covid19-line-list-datagithub.com1131 more replyLaurent Cimasoni@LCimasoni·19 AugReplying to @firefoxx66 and @zorinaqThe updated version is a bit less scary though11markfoodyburton@markfoodyburton·21 AugReplying to @firefoxx66 and @zorinaqI put a little (only) work into generating something similar from the French data set (as we are seemingly hurtling towards the outcome @firefoxx66 is suggesting).2markfoodyburton@markfoodyburton·21 AugLess data than would be nice. 'Middle age' group beginning to expand (as predicted).Tamara Silveira@tammarp·24 AugReplying to @firefoxx66 and @zorinaq@giiventre aqui migs

it's definitely worth considering a broad range of ideas...but does this not run into the same difficulties that plagued "shielding"?Quote TweetMiguel Hernán@_MiguelHernan · 22 Aug1/ Five months ago I asked about a #stratifiedlockdown to handle #COVID19. The idea was to restrict lockdowns to people over age 50 or with preexisting conditions while the rest of society lives a relatively normal life. Time to revisit this approach. https://twitter.com/_MiguelHernan/status/1239227279512829953?s=20

Wouldn't usually share such a big news item without verifying carefully. But @KarenGrepin is a close colleague & top Prof in Hong Kong, and extremely reliable in her tweets.Quote TweetKaren Grepin@KarenGrepin · 24 AugBig news out of Hong Kong: Colleagues at @hkumed claim to have documented first case of COVID-19 re-infection. twitter.com/cwylilian/stat…

UK: far/top right. #COVID19

Convalescent plasma has shown to be beneficial for 35% of patients. This risk reduction figure - shown in chart below - is from @MayoClinic data from expanded access program that was analyzed by FDAA for the emergency use authorization announced today.

How can we navigate daily life during the pandemic? #Publichealth expert & epidemiologist @EpiEllie will be on @reddit_AMA this Thursday (8/27) at 12pm ET to answer all of your #COVID19-related questions. She'll discuss how to safely see friends and family, travel & more. @BUSPH

Calling on retired lawyers! Law students! Bored lawyers! We at @GoodLawProject need your help with some research... we are working on what will be (well, if we win it) seminal litigation to establish the precautionary principle as a freestanding part of E&W common law!

Kids and covid 1. On the rise as proportion of total infections

RT @arthomason: The Atlantic was right. This was always where we were headed.

These NHS & care staff are the same ones who we were standing on our doorsteps clapping not long ago. Many of them are suffering themselves now &, in my opinion, deserve much better recognition, support & rehabilitation than they are currently receiving (6/6)

What shocks me, however, is the apparent lack of attention nationally to the needs of the thousands of NHS staff suffering prolonged symptoms of Covid. How many NHS staff are currently off sick because of Covid? We don’t know. What support are they being offered? Very little. 5/6

Its no surprise that many staff caring for pts with a highly infectious disease, often with inadequate PPE, contracted Covid. In April, @BPSOfficial guidance on Covid recovery predicted a significant % would experience prolonged symptoms. Sadly @LongCovidSOS bears this out (4/6)

The massive increase in sickness could be a) staff contracting Covid or b) stress-related disorders due to working during the pandemic. However, data clearly shows it is the former, in fact, the proportion of sickness absence due to anxiety & depression actually went down. (3/6)

In developing the NHS Covid Recovery programme, I’ve spoken to many people experiencing persistent effects of #Covid_19. I’ve been struck by how many are NHS staff themselves; analysis of newly released data clearly illustrates the scale of the impact of Covid on NHS Staff (1/6)

The sickness rate for NHS Staff in London increased by >100% in April. Of course, the population sickness rate also went up, but the increase was ONLY in frontline NHS organizations & MUCH HIGHER in staff groups that were most likely to be in contact with Covid-19 patients. (2/6)

Now, tell me again. Who commissioned the laboratories? How much attention did they give to what would be needed (other than simply "ramping up testing" for political rather than public health reasons)? 17/17

I'm not blaming the labs for this. The private sector is not a charity. They are doing what they were commissioned to do (and no more) - because they are answerable to their shareholders, to make a profit. 16/17

That's if they decide it's commercially worthwhile at all. If they've set up a system that's making them rich, and it would be tricky and costly to start sharing Ct values, they might decide not to bother. They don't care if key workers are put off work unnecessarily. 15/17

It will be the same with Ct values. "Not in our contract. We can do it if you like. It will cost [now, how much can we sting the suckers for, we know that Hancock will do anything to improve testing numbers, and the NHS and social care are desperate not to lose staff]." 14/17

Instead, they just said "not covered by our contract - come and collect them if you want, otherwise we'll bin them". Which caused huge delays and expense. 13/17

The lighthouse labs are commercial for-profit organisations. When we discovered swabs from a care home had gone to a lighthouse lab when they should have gone to a PHE one, they could easily have run the swabs at minimal cost - & absorbed the cost, or sent us a small bill. 12/17

(Yes, it is PHE doing this work, not local authority public health - LA public health is doing a brilliant job, but not this). 11/17

One of the private lighthouse labs (in Cambridge) apparently does record the Ct - but it won't routinely share it. So the PHE teams have no way of assessing whether these are true cases or prolonged RNA from previous infection - no risk at all. 10/17

Which is where I come to the private "lighthouse" labs. Some of them don't record the Ct. They simply are unable to give use the information, because (they claim) they weren't commissioned to record these data. 9/17

It is *extremely* disruptive otherwise. If we treat these positive cases as new infections, care homes have to be closed all the residents have to self-isolate for 14 days; key health and social care workers have to self-isolate for 10 days, and their contacts for 14. 8/17

So… Now that we are seeing all of these people who had tested positive previously, we need to know if they are currently infected (and infectious), or simply showing residual RNA from a previous infection. 7/17

These aren't "false positives" in the sense of being positive tests in the absence of viral RNA (there is RNA in the swab); but they are "false positives" in the sense that they do not show current infection or infectiousness. 6/17

If there is current infection, there is likely to be a lot of RNA in the sample (and a low Ct value). If somebody has left-over RNA from a previous infection, there'll be less of it, and a high CT value. 5/17

So the Ct value is a way of quantifying the amount of RNA. If there was very little RNA in the sample you'll have to double the amount more often - giving a higher Ct value. If there was a lot of RNA, you'll get a low Ct value. 4/17

tldr: each time you run a "cycle" you double the amount of RNA in the sample. The number of times you do it is called the "cycle threshold" "Ct) ; the more often you have to do this before you can detect it, the less RNA there must have been in the original sample. 3/17

Where these are genuine cases, this is good. The problem is many are being detected in people who had tested positive previously. And we don't know how to interpret them. This helps: https://cebm.net/covid-19/infectious-positive-pcr-test-result-covid-19/… 2/17

A problem with privatisation of testing. Now that we are routinely testing lots of people - including care home staff and residents, and NHS staff - we are picking up positive results in asymptomatic people. 1/17

Videos of talks from July's eBridges conference on "SOCIETY, PSYCHOLOGY AND BEHAVIOUR DURING AND POST COVID-19 LOCKDOWN" are now all available here:

Ellie Murray has spent countless hours of this pandemic providing high quality information on COVID-19 - this AMA is a great opportunity

can I ask, though: schooling was mandatory- were you still meant to go to school when there was an infected household member? or were you specifically *barred* from going to school or work if there was an infected household member? sources would be much appreciated!

"There's no explicit ban on working/going to school when you have an infected family member, that's true." that seems very odd! but, together with the mandatory school policy, if there is *no ban* on going to school, isn't going to school *effectively mandated* in these circs?

I'm familiar with those constraints/arguments- but keeping family members of infected individuals isolated is one of the most basic public health measure - it surely would be legal to mandate, particularly given the role pre/asymptomatic spread? no?

what I am getting at (ex lawyer here, sorry) is that given the conjunction of mandatory schooling and explicit statement that it is ok to go to school if infected it is the *legal* default that the child has to *go to school* (unless an exception is applied for and granted)!?

but that then does not sound to me like a disease control policy- it makes no sense in that way. It would make sense, though, if your goal is to build herd immunity via the least vulnerable.. to be honest, I'm surprised it's actually legal as a policy (has it been challenged?)

That team of authors is not the most dependable, if I may put it that way.

so was that USA today open letter basically misinformation in this regard?

Lots to say, but just quickly: (1) Exceptions are permitted on a case-by-case basis https://skolverket.se/regler-och-ansvar/ansvar-i-skolfragor/skolplikt-och-ratt-till-utbildning… (2) Everyone is encouraged to work from home whenever possible

V. sorry to see a colleague spread what can only be described as conspiracy theories on Twitter. I think academics have a particular duty to keep their heads cool in a moment of crisis.Quote TweetBenjamin L. Jones@BoardshortsBen · 3hIn many other countries, society would be furious and demanding answers to why their children have been used to spread a virus that we now know has potential neurological implications for children. But not in Sweden. https://theguardian.com/world/2020/aug/17/swedens-covid-19-strategist-under-fire-over-herd-immunity-emails

Erik, as people inside and outside Sweden continue to grapple with what exactly the Swedish strategy might have been, there are two aspects that have seemed potentially troubling to me (and only more so in light of the FOI email releases):

2/2 1. mandatory schooling (where there exemptions for immune-compromised parents?) 2. encouraging household members of infected individuals to go to work/school Could you provide more background here and how you see these policies in the wider context?

Are you interested in #preregistration and have experience with either #EEG or #fMRI? We, the MPI CBS #OpenScience initiative, are hosting a hackathon on August 20, 3-6 pm (GMT+2) to continue working on preregistration templates for EEG and fMRI and we need YOUR help! 1/2

Might be of interest. In 2017, @PHE underwent an independent international peer-review from @IANPHIhealth - the International Association of National Public Health Institutes. An organisation that strengthens government agencies responsible for public health. Thread/

11/ I’m continually impressed by the powerful insights that come from epidemiologists who draw from our conceptual and methodology traditions but also tested and validated theory.

10/ When someone in spring 2020 tells @HealthEquityDoc that we are “all in the same boat” re: chances of getting exposed to #SARSCoV2 and dying of #COVID19, she too is going to have some questions... https://iaphs.org/racism-in-the-

9/ When people tell @JuliaLMarcus that shaming folks & involving criminal justice is an effective tool for slowing the spread of #COVID19, she’s going to have a few questions for you...

8/ The problem with data divorced from theory is that statistics can lie. And we humans are fallible and susceptible to suggestion. The theoretical grounding of the researchers that I respect most helps keeps them clear-eyed & ethical.

7/ And the novel coronavirus #SARSCoV2 has presented many novel situations...

6/ The thing is, solid theory gives us a basis for predicting likely outcomes in novel situations...

4/ Future-gazing epidemiologists like @JuliaLMarcus, who has an undergrad double major in sociology and women’s studies...

3/ When I think about the most forward-thinking epidemiologists I know re: #SARSCoV2 and #COVID19, a common bond is a grounding and training in social theory...

2/ Many epidemiologists are not trained in social or health behavior theory. Its value is often overlooked in a field that values quantitative analysis.

1/ An #EpiTwitter about theory...GIFQuote TweetThe Atlantic@TheAtlantic · 13hThe University of North Carolina at Chapel Hill has switched to remote learning after a spike in COVID-19 cases. “Universities have no business reopening if they can’t provide a healthy environment," Julia Marcus and Jessica Gold wrote in July. http://on.theatln.tc/WIHQzDo

How to copy tables directly into your word processor using JASP. #stats #openSource

Many scientists use Twitter to carry on conversations (with varying degrees of formality) about published papers, the good, bad, and ugly. The people in this conversation all do this frequently. None of us are anti-science (cont...)

It’s almost like bringing college kids back to campus is an exceptionally poor idea that we shouldn’t be trying right now

RT @MaartenvSmeden: The lack of rapid sharing of COVID19 patient level data https://t.co/rmEGf6xRXj

In your opinion, what have been the biggest travesties of science during COVID?

Hmmm....these two decisions seem connected somehow

"School children are not the drivers of community spread" of COVID. --@GovRonDeSantis

In this paper we argue that endogenous shifts in private consumption behavior across sectors of the economy can act as a potent mitigation mechanism during an epidemic or when the economy is re-opened after a temporary lockdown. Extending the theoretical framework proposed by Eichenbaum-Rebelo-Trabandt (2020), we distinguish goods by their degree to which they can be consumed at home rather than in a social (and thus possibly contagious) context. We demonstrate that, within the model the "Swedish solution" of letting the epidemic play out without government intervention and allowing agents to shift their sectoral behavior on their own can lead to a substantial mitigation of the economic and human costs of the COVID-19 crisis, avoiding more than 80 of the decline in output and of number of deaths within one year, compared to a model in which sectors are assumed to be homogeneous. For different parameter configurations that capture the additional social distancing and hygiene activities individuals might engage in voluntarily, we show that infections may decline entirely on their own, simply due to the individually rational re-allocation of economic activity: the curve not only just flattens, it gets reversed.

Estimating the COVID-19 Infection Rate: Anatomy of an Inference Problem

I'm optimistic, but this is not an easy task, and there are both commercial forces and forces of inertia and conservatism that are aligned against this, so we need as many people and groups pushing in the right direction in whatever way they think best and possible.

We're doing this @eLife with @PreprintReview - and there are other great efforts including @ReviewCommons @PeerCommunityIn @PREreview_ @peeragescience @WellcomeOpenRes @PubPeer and more that are pushing in a similar direction.

The long-overdue rise of preprinting in biology and medicine gives us a real opportunity. If we can simultaneously encourage preprints to become ubiquitous, and build a system for publicly reviewing preprints, we're a long way there.

It is why I thought - and still think - that steering a journal like @eLife that receives a lot of submissions and has a mission and backing to change is an important part of the solution. But, as I know too well, change from within has its own significant obstacles.

And in order to create, refine and propagate such a new model, we need scientists to participate as authors. But they feel they can't because they will be judged in the incumbent system. This is the rub - and the reason so many excellent ideas and implementations never took off.

We also have to make sure that any system we build doesn't reify - or make worse - the biases and power structures that plague the current science evaluation system and science writ large.

The reason this is important, and hard, is that we have to displace journal titles and impact factors as the way that science and scientists are judged. And as wonderful as it sounds - "everyone should just read the papers and reviews" is not a viable solution.

The question we have always struggled with and that has held back efforts to change - is figuring out what the output of peer review should be if you're not accepting or rejecting papers for a journal, and how - or even if - to distill the results of multiple peer reviews.

It's not like we don't know what a better system would look like - I and others have been advocating it for years. It would couple immediate, author-driven publishing (aka preprints) with ongoing post-publication peer review carried out by multiple individuals and groups.

I loathe this system and the myriad ways it has poisoned science and the ways people navigate their careers in the field. But the pressure on even the most idealistic young scientists to conform to it in order to have a career is so strong that it has proven hard to change.

A core problem in science publishing today is that we have a system where the complex, multidimensional assessment of the rigor, validity, utility, audience and impact of a work that emerges from peer review gets reduced to a single overvalued "accept/reject" decision.

This concerns undergrads. Grad students apparently will still be able to come to campus, given the different circumstances of their life in the university, although that's obviously open to changes as well...

After planning to bring back half of its students to campus in the Fall, Princeton is now deciding to go fully remote. "We cannot provide a genuinely meaningful on-campus experience for our students this fall in a manner that is respectful of public health concerns"

I know it would be unusual for universities to engage in this level of national, coordinated public service. But when orgs are sitting on the expertise & relatively flush resources for this kind of effort, and the gov’t is not doing it, isn’t it time for something extraordinary?

... draw on the tremendous networks of their alumni and their collective wealth and resources to support and amplify this work? Individual academics are doing tremendous work. Institutions seem to be very inwardly focused.

... give them protected time to focus on Covid knowledge consolidation and messaging, host weekly calls for this body of experts to review new data & coordinate public health messaging and serve as a reputable body for policy recommendations and media appearances...

Question for Twitter. Why didn’t academia take the lead on Covid information? Why didn’t schools of med & public health across the US band together, put forth their experienced scientists in epidemiology, virology, emergency & critical care, pandemic and disaster response...

Weirdly, some of the "it's just the flu" folks moved to the opposite end of the spectrum, and are amplifying an exaggerated sense of doom and helplessness. Not saying things are great; just saying groupthink will groupthink. It really is hard to fight.

Anyway, I do wish them luck, honestly, because we need them to do the job right. So much depends on it. At a minimum, I hope there is some reflection on why some people were so wrong. Being wrong is normal and reasonable and even helpful as long as one learns from it, and openly.

I'm NOT saying appoint me. I'm doing what I can already. But just noting that if you're a famous Harvard professor, track record is no barrier. I doubt a woman and/or a person of color would survive such a track record, even if they managed to get the Harvard brand behind them.

Anyway, if I were leading an already battered organization through perhaps the most important phase of its existence, I'd look for people who had a good track-record and were openly critical when necessary but aligned with the mission, to save lives. Then again, famous professor!