One year ago today: The WHO reports 81,454 new cases of COVID-19, and raises €7.4 billion for the Access to COVID-19 Tools Accelerator, an initiative to support development, production, and distribution for COVID-19 treatments and vaccines.

Downgrading the concern on B.1.617, the poorly named "double mutant" —98% effectiveness of mRNA vaccine in an Israeli outbreak @CT_Bergstrom https://twitter.com/CT_Bergstrom/status/1387941641395179524… —Lab studies: minimal immune evasion, expected full protection from vaccine @GuptaR_lab

A new study led by Public Health England and NHS Test and Trace will help increase understanding of how effective daily contact testing could be for people who are contacts of positive COVID-19 cases. It is to be used as an alternative to self-isolation.

Government to launch 40,000 person daily contact testing study

Test results, often required to fly across borders, can be easily manipulated

Fake Covid-19 Certificates Hit Airlines, Which Now Have to Police Them

Covid-19 lockdown has left young children vulnerable to some illnesses

Globally, the end of the pandemic isn't near. More than a million lives depend on improving our response quickly. Don’t be blinded by the light at the end of the tunnel. There isn't enough vaccine and the virus is gathering strength & speed. Global cooperation is crucial. 1/

A few people suggesting the answer is so obvious that the question may have been disingenuous. These sorts of answers say otherwise!

Ask any doctor or nurse in the NHS Why is this even a question?

Just hypothetically, if it were possible, if you could go back to January 2020 would you prefer to do what New Zealand did or what the U.K. did to ‘manage the pandemic’?

Given the dire situation in India and questions regarding the new variant B.1.617, the so called ‘Double Mutant’ we are sharing some prelim analyses on viruses with either or both of the mutations E484Q and L452R in the critical receptor binding domain that our antibodies target

I was very pleased to see Levitt resign yesterday from the science advisory board of the anti-vaxx group PANDA. Previously Sikora had resigned. This press release mentions other resignations. Anyone know if the 3 GBD authors finally resigned? Here's PANDA's views on vaccines:

Ontario is imploding. How can anyone trust this government again?

this seems inevitable when a country accepts doses manufactured abroad while banning the export of doses (and raw materials!) from its own shores... I wonder how long international tolerance of this US policy will last

Meanwhile, in Europe...

Laplace to be for new & veteran Bayesians alike

Welcome to Learning Bayesian Statistics

Fixed version: here's how the Imperial College model of Neil Ferguson performed over 1 year. I used their most conservative R0 assumption, so this is actually generous to them.

2104.06481

Political polarization appears to be on the rise, as measured by voting behavior, general affect towards opposing partisans and their parties, and contents posted and consumed online. Research over the years has focused on the role of the Web as a driver of polarization. In order to further our understanding of the factors behind online polarization, in the present work we collect and analyze Web browsing histories of tens of thousands of users alongside careful measurements of the time spent browsing various news sources. We show that online news consumption follows a polarized pattern, where users' visits to news sources aligned with their own political leaning are substantially longer than their visits to other news sources. Next, we show that such preferences hold at the individual as well as the population level, as evidenced by the emergence of clear partisan communities of news domains from aggregated browsing patterns. Finally, we tackle the important question of the role of user choices in polarization. Are users simply following the links proffered by their Web environment, or do they exacerbate partisan polarization by intentionally pursuing like-minded news sources? To answer this question, we compare browsing patterns with the underlying hyperlink structure spanned by the considered news domains, finding strong evidence of polarization in partisan browsing habits beyond that which can be explained by the hyperlink structure of the Web.

Political Polarization in Online News Consumption

In short: Bayes rule is very useful, and case/vaccine patterns in highly vaccinated populations don't always do what you may assume. 9/9

We can also flip the above equation around, which allows us to use data on % cases vaccinated and % vaccinated to get a rough estimate of vaccine effectiveness: https://twitter.com/AdamJKucharski/status/1382006630997323776?s=20… 8/Quote Tweet

This is an important result, because if cases appear among vaccinated individuals, many people's intuitive response is to ask 'surely the vaccine can't be that effective?' The answer: it may well be effective, just in a highly vaccinated population e.g. https://twitter.com/AdamJKucharski/status/1200329736544759808?s=20… 7/

Now we have something we can apply to real-life situations, because can measure many of these things. For example, if 60% of a population have been vaccinated, and vaccine is 80% effective, above means we'd expect (1-0.8)x0.6/(1-0.6x0.8)= 23% of cases to have been vaccinated. 6/

If we write out the ways in which we could get P(not protected), we end up with below equation (I've labelled the terms on the bottom of the fraction to make it clearer where these come from): 5/

Applying the above to our vaccine question, we therefore have: P(vaccinated | case) = P(case | vaccinated) x P(vaccinated) / P(case) which is equivalent to P(vaccinated | case) = (1–V) x P(vaccinated)/P(not protected) where V is vaccine effectiveness. 4/

If we want to know the probability of event A given event B, or P(A|B) for short, we can calculate this as P(A|B) = P(B|A) P(A)/ P(B) There are a couple more mathsy tweets coming up, so hold on as then we'll get back to the real-life implications. 3/

In above question, there are a lot of things happening conditional on other things happening (e.g. probability cases have been vaccinated), which means we can use Bayes rule (https://en.wikipedia.org/wiki/Bayes%27_theorem…) to work out the proportion of cases that we'd expect to have been vaccinated. 2/

If populations are highly vaccinated, we'd expect a higher proportion of future cases to have been previously vaccinated (because by definition, there aren't as many non-vaccinated people around to be infected). But what sort of numbers should we expect? A short thread... 1/

1/ To delay 2nd doses of the Pfizer and Moderna COVID vaccines (like the UK, Germany, & Canada)? https://usatoday.com/story/opinion/2021/04/08/covid-surge-deliver-first-vaccine-shots-delay-second-doses-column/7122747002/… Or not to delay? https://thinkglobalhealth.org/article/dont-be-seduced-two-shots-are-better-one… That is the question.

After ~10 months of relative quiescence we've started to see some striking evolution of SARS-CoV-2 with a repeated evolutionary pattern in the SARS-CoV-2 variants of concern emerging from the UK, South Africa and Brazil. 1/19

Ben Wakana@benwakana46Replying to @benwakana46"Institutions CAN BE TRUSTED to look out for the public interest." -@celinegounder

Céline Gounder, MD, ScM, FIDSA@celinegounderWith all due respect to @NateSilver538, he is not an expert on the psychology of vaccine confidence. He is a poll aggregator and political pundit. He is not an infectious disease specialist, epidemiologist, vaccinologist, virologist, immunologist, or behavioral scientist.

10.1136/bmj.n913

Improving indoor ventilation and air quality will help us all to stay safeOver a year into the covid-19 pandemic, we are still debating the role and importance of aerosol transmission for SARS-CoV-2, which receives only a cursory mention in some infection control guidelines.12

Covid-19 has redefined airborne transmission

10.31234/osf.io/zu2a3

The COVID-19 pandemic has caused a decrease in both material resources (e.g., jobs, access to healthcare), and socio-psychological resources, triggered by social distancing and lockdowns. It is established that perceived resource scarcity creates a mindset that affects cognitive abilities, including decision-making. Given the importance of social norms compliance in the current climate, we investigated whether perceived material and socio-psychological scarcity experienced during the pandemic predicted cooperation, measured using two Public Good Games (PGGs), where participants contributed money or time (i.e., hours indoors contributed to shorten the lockdown). Material scarcity had no relationship with cooperation. Scarcity of socio-psychological wellbeing (e.g., connecting with family) predicted increased cooperation in both PGGs, suggesting that missing social contact fosters prosociality. On the other hand, perceived scarcity of freedom (e.g., limited movement) predicted decreased willingness to spend time indoors to shorten the lockdown. These results may have implications for message framing when aiming to increase cooperation.

Perceived scarcity and cooperation contextualized to the COVID-19 pandemic.

10.31234/osf.io/zn7vt

In this article, we provide a toolbox of resources and nudges for those who are interested in advancing open scientific practice. Open Science encompasses a range of behaviours that aim to include the transparency of scientific research and how widely it is communicated. The paper is divided into seven sections, each dealing with a different stakeholder in the world of research (researchers, students, departments and faculties, universities, academic libraries, journals, and funders). With two frameworks in mind — EAST and the Pyramid of Culture Change — we describe the influences and incentives that sway behaviour for each of these stakeholders, we outline changes that can foster Open Science, and suggest actions and resources for individuals to nudge these changes. In isolation, a small shift in one person’s behaviour may appear to make little difference, but when combined, these small shifts can lead to radical changes in culture. We offer this toolbox to assist individuals and institutions in cultivating a more open research culture.

Nudging Open Science

10.31234/osf.io/m5zv9

Study Objectives. This study examined associations between average and intraindividual trajectories of stress, sleep duration, and sleep quality in college students before and after transitioning to online learning due to the COVID-19 pandemic. Methods. Two hundred and one first-year college students answered twice-weekly questionnaires assessing stress exposure, sleep duration, and sleep quality from January until May, 2020 (N= 4,278 unique observations). Results. Multilevel growth modeling revealed that prior to distance learning, student stress was increasing and sleep duration and quality were decreasing. After transitioning online, students’ stress immediately and continuously decreased; sleep quality initially increased but decreased over time; and sleep duration increased but then plateaued for the remainder of the semester. Days with higher stress than typical for that student were associated with lower sleep quality, and higher average stress exposure was linked with shorter sleep duration and lower sleep quality. Specific demographics (e.g., females) were identified as at-risk for stress and sleep problems. Conclusions. Although remote learning initially alleviated college students’ stress and improved sleep, these effects plateaued, and greater exposure to academic, financial, and interpersonal stressors predicted worse sleep on both daily and average levels. Environmental stressors may particularly dictate sleep quality during times of transition, but changes in learning modalities may mitigate short-term detrimental health outcomes, even during a developmental period with considerable stress vulnerability. Future studies should examine the longer-term implications of these trajectories on mental and physical health.

Stress and Sleep Across the Onset of the COVID-19 Pandemic: Impact of Distance Learning on U.S. College Students’ Health Trajectories

The UK’s medicines regulatory body has said that no decision has been made on any regulatory action relating to the Oxford/AstraZeneca vaccine following reports it is considering restricting use of the vaccine in younger people.

Report claims watchdog looking into use of AstraZeneca jab for under-30s

Here is a snapshot of the largest producers of vaccines. Much more supply is in the pipeline but all countries will need to share. It is essential to vaccinate the most vulnerable in the world *now* for the benefit of everyone. The pandemic is not over until it is over everywhere

In King County, pollution makes ZIP codes predictors of your health

In Seattle, a ZIP code can predict everything from income to social class to life expectancy. White, wealthy residents of northern neighborhoods such as Laurelhurst live 13 years longer than their poorer neighbors of color in the southern neighborhoods of South Park and Georgetown. Air and soil pollution has disproportionately affected Seattle’s communities of color for decades, but now a group of University of Washington researchers is working with those communities to understand how COVID-19 makes a dire situation worse.

For tickets, please visit: https://eventbrite.co.uk/e/shaping-the-post-covid-19-world-j-idea-one-year-anniversary-symposium-tickets-125904191827… @ImperialSPH @imperialcollege @MRC_Outbreak @AlistairMB #postCOVID19world

Our next #databeers #brussels is tomorrow night and we've got a few tickets left! Don't miss out on some important and exciting talks from: @svscarpino Juami van Gils Joris Renkens Milena Čukić Last tickets here https://eventbrite.com/e/databeers-brussels-16-webinar-edition-tickets-124115565999?aff=twitter

Doing a systematic review? How to prepare, conduct & document a search + manage your results & screening tools https://buff.ly/2HJEGim #phdchat #phdadvice #phdforum #phdlife #ecrchat #acwri

This resonates with my experience: people outside psych commenting on our practices help put pressure on us to improve. And we can also do the same for other fields (looking at you criminology, nutrition, sports science, etc.). Having people watching & commenting helps.

New paper!!! @psmaldino look at what causes the persistence of poor methods in science, even when better methods are available. And we argue that interdisciplinary contact can lead better methods to spread. 1

respectfully, science has not “become politicized” there are not 2 equivalent sides to every issue one side has politicized the science spewing antiscientific garbage

Today was a very, very odd day I testified before @senatehomeland They held a hearing on hydroxychloroquine. Yup, HCQ In the middle of the worst surge of pandemic HCQ It was clear how our information architecture shapes questions of science and medicine of COVID A thread

The 876 intensive care beds certified and recognized by the SGI, which are normally available in Switzerland for the treatment of adults, are currently practically fully occupied.

COVID-19: Full utilization of certified and recognized intensive care bed capacities

alarmism vs denial in Switzerland...or some observations on the Swiss COVID response a monster thread...

Ongoing, an incredibly awesome talk on computational reproducibility by @AdinaKrik. Slides: https://zenodo.org/record/4285927#.X7vjPrMo9OR…. If you are looking for an expert speaker on computational reproducibility, or someone to teach a workshop, look no further!

Our #YSR2020 computational reproducibility symposium just started with @lakens @AdinaKrik @brandmaier organized by @MLSicorello @s_nebe and @z_sazae @bioDGPs and DGPA!

LIVE @WHO @DrMikeRyan says "we have all received death threats" and other hate mail because we are scientists, trying to work in a #pandemic in the "international space."Quote Tweet

Media briefing on #COVID19 with @DrTedros

The campaign against @DrZoeHyde that has involved several scientists targeting her with personal attacks, and trying to misrepresent her is deeply disappointing. She has been referred to as 'evil', 'idiotic', 'sadistic', and a'sociopath'. A few thoughts on these attacks.

All-inclusive authorship on large scientific papers can a be dangerous practice Alert: potential unpopular opinion Thread 1/n

There’s no going back to the old ways. Which technologies could propel the industry forward?

Covid Pushes Real Estate Into the Future

The relationship between pandemics and inequality is of significant interest at the moment. The Black Death in the 14th century is one salient example of a pandemic which dramatically decreased wealth inequality, but this column argues that the Black Death is exceptional in this respect. Pandemics in subsequent centuries have failed to significantly reduce inequality, due to different institutional environments and labour market effects. This evidence suggests that inequality and poverty are likely to increase in the aftermath of the Covid-19 crisis.

Pandemics and inequality: A historical overview

Which is what I will do for the next three nights. But tonight. It’s me and Cliff and Oreo ice cream. And how ironic I have on my “home” Hoodie. The South Dakota I love seems far away right now.

I can’t stop thinking about it. These people really think this isn’t going to happen to them. And then they stop yelling at you when they get intubated. It’s like a fucking horror movie that never ends. There’s no credits that roll. You just go back and do it all over again.

Going to ruin the USA. All while gasping for breath on 100% Vapotherm. They tell you there must be another reason they are sick. They call you names and ask why you have to wear all that “stuff” because they don’t have COViD because it’s not real. Yes. This really happens. And

I have a night off from the hospital. As I’m on my couch with my dog I can’t help but think of the Covid patients the last few days. The ones that stick out are those who still don’t believe the virus is real. The ones who scream at you for a magic medicine and that Joe Biden is

The much-hyped drug sparked a battle between power and knowledge. Let’s not repeat it.

The Strange and Twisted Tale of Hydroxychloroquine

I need to make some preliminary remarks on my report today. The EMS - which is where the positive test data comes from - seems to be having quite a problem. Many cases were reported later today. In Vienna there was according to this

ere is my working definition of a public health expert: someone who is constantly frustrated that people will not act on clear health advice in the interests of their own health. From smoking to diabetes, from eating responsibly and exercising to practicing safe sex, from getting an annual flu shot to wearing face coverings in the time of coronavirus, the literature on public health is awash with tricks, nudges, and sometimes outright bribes to try and get people to take care of themselves. Some progress has been made, but the feeling is often one of disappointment that so many people aren’t following the advice.

A hidden success in the Covid-19 mess: the internet

1. Hospitalizations have hit a new all-time HIGH. 2. Deaths are increasing rapidly, now at 7.1K/week. 3. #SouthDakota on track to reach levels only achieved by NY in hospitalizations/capita. @GovRicketts @KristiNoem @DougBurgum have a lot to answer for.

The increase in hospitalizations and deaths confirms the main pattern we’ve identified in the data—after cases go up, a rise in these figures follows. We explain the relationship between the three metrics in this post.

Deaths are also rising. Today’s death count is the highest since August 19, pushing the 7-day average up to nearly 1,000.

Today’s number of currently hospitalized people—62k—is also a record. A total of 17 states have reported single-day record hospitalizations.

Our daily update is published. States reported 1.2 million tests and 131k cases, the highest single-day total since the pandemic started. There are 62k people currently hospitalized with COVID-19. The death toll was 1,347.

If you are interested in QAnon, QAnonCasualties is a must subreddit to read regularly and to get to know what is happening in QWorld from those closest to QAnon adherents.

If you are interested in QAnon, QAnonCasualties is a must subreddit to read regularly and to get to know what is happening in QWorld from those closest to QAnon adherents.

I am quite sure the "herd immunity" discussion barely exists in parts of East Asia (e.g, Japan, South Korea, Taiwan, Vietnam, Thailand) which have used the strategy @devisridhar has been explaining endlessly and patiently for months now.....

Yet another article packed full of wise words: e.g., "in some ways, the people pushing for “herd immunity” are forcing us into these lockdown-release cycles because you end up in a reactive position by underestimating the spread of the virus and the hospitalisation rate"

(CNN)Wearing a mask can help protect you, not just those around you, from coronavirus transmission, the Centers for Disease Control and Prevention said in new guidance Tuesday. The statement was an update to previous guidance suggesting the main benefit of mask wearing was to help prevent infected people from spreading the virus to others.

CDC now says masks protect both the wearers and those around them from Covid-19

The bigger they are the harder they fall may be true of heavyweight boxers. It's just as true of distinguished figures in public life. And they don't come much more distinguished than Lord Sumption.

JOHN HUMPHRYS: Let's not kid ourselves. The NHS puts a price on ALL our lives