10.1101/2020.07.06.20140285

We use a global metapopulation transmission model to study the establishment of sustained and undetected community transmission of the COVID-19 epidemic in the United States. The model is calibrated on international case importations from mainland China and takes into account travel restrictions to and from international destinations. We estimate widespread community transmission of SARS-CoV-2 in February, 2020. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 in the West and East Coast metropolitan areas that could have been seeded as early as late-December, 2019. For most of the continental states the largest contribution of imported infections arrived through domestic travel flows.

Estimating the establishment of local transmission and the cryptic phase of the COVID-19 pandemic in the USA

10.31234/osf.io/z4puv

The spreading of the COVID-19 virus has a devastating impact on patients with psychiatric illnesses. Here, we highlight the potential consequences of the COVID-19 pandemic for psychiatric patients of old age, based on several patients that we have treated in the past months (2020). We not only elaborate on the challenging conditions of old age psychiatric patients but also provide potential solutions to optimize patient care for this vulnerable group.

Challenging COVID-19 times for older psychiatric patients: potential implications and solutions

Many countries imposed stringent lockdowns in response to the COVID-19 pandemic. Sweden, however, adopted a ‘soft’ approach of self-imposed social precautions without state regulation. This evoked extensive criticism within and outside the country, especially in view of its high death rates in comparison to its Nordic neighbours. The Swedish government, however, has been steadfast with its strategy. As countries emerge from lockdowns and begin to reopen their societies, there are many lessons to learn from Sweden’s soft COVID-19 strategy.

Sweden’s ‘Soft’ COVID19 Strategy: An Appraisal

10.31234/osf.io/6wdaz

A Registered Reports system is key to preventing questionable research practices. Under this system, manuscripts, including their detailed protocols (i.e., hypothesis, experimental design, sample size, and methods of statistical analysis), are reviewed prior to data collection. If a protocol manuscript is accepted, publication of the full manuscript including the results and discussion is guaranteed in principle regardless of whether the collected data support the registered hypothesis. However, this assurance of publication might be broken under the impact of the COVID-19 pandemic. The present paper reports the first author’s real-life experience related to the collapse of the assurance of publication in the Registered Reports system and discusses the disbenefits of this collapse. Furthermore, we propose the implementation of a journal section specific to protocol manuscripts as a solution to the crisis of the Registered Reports system.

The pandemic threatens the Registered Reports system as well as human lives

The latest coronavirus news updated every day including coronavirus cases, the latest news, features and interviews from New Scientist and essential information about the covid-19 pandemic

Covid-19 news: UK could eliminate coronavirus entirely, say scientists

2007.03287

Networks provide a mathematically rich framework to represent social contacts sufficient for the transmission of disease. Social networks are often highly clustered and fail to be locally tree-like. In this paper, we study the effects of clustering on the spread of sequential strains of a pathogen using the generating function formulation under a complete cross immunity coupling. We derive conditions for the epidemic threshold of the first strain and the threshold of coexistence of the second strain. We find that clustering has a dual affect on the first strain, reducing the epidemic threshold but also decreasing the final outbreak size at large transmissibilities. Clustering reduces the coexistence threshold of the second strain and its outbreak size. We apply our model to the study of multilayer clustered networks and observe the fracturing of the residual graph experimentally.

Two-pathogen model with competition on clustered networks

2007.03443

How can the birth and evolution of ideas and communities in a network be studied over time? We use a multimodal pipeline, consisting of network mapping, topic modeling, bridging centrality, and divergence to analyze Twitter data surrounding the COVID-19 pandemic. We use network mapping to detect accounts creating content surrounding COVID-19, then Latent Dirichlet Allocation to extract topics, and bridging centrality to identify topical and non-topical bridges, before examining the distribution of each topic and bridge over time and applying Jensen-Shannon divergence of topic distributions to show communities that are converging in their topical narratives.

Cultural Convergence: Insights into the behavior of misinformation networks on Twitter

Provisional counts of the number of deaths registered in England and Wales, including deaths involving the coronavirus (COVID-19) pandemic, by age, sex and region, in the latest weeks for which data are available.

Deaths registered weekly in England and Wales, provisional: week ending 26 June 2020

Pubs, restaurants and cafes in England welcomed customers back through their doors on 4 July, sparking warnings of a second wave of covid-19 infections. Yet there have been warnings of another wave since the country began easing restrictions, and one hasn’t materialised. Will this time be different? Scientists on an independent advisory panel on coronavirus called Independent SAGE have repeatedly warned that the relatively swift easing of lockdown restrictions in England risks cases rising again.

Why hasn't the UK seen a second wave of the coronavirus?

Primeiro dia do webinário internacional "Pensando a Pandemia", com tópicos em filosofia da mente e psicologia. 14:00 - Bahar Tuncgenc: What motivates people to do social distancing? A comprehensive analysis on a global sample 15:00 - Short break 15:15 - Ernesto Perini: Quando duas crises se encontram - a pandemia de covid-19 e o negacionismo científico

Pensando a Pandemia: Tópicos em Filosofia da Mente e Psicologia

Stopgap measures are keeping renters in their apartments, even as their bills stack up.

NYC Rental Market Pushed to Breaking Point by Tenant Debts

Decisions on fitness for employment that entails a risk of contracting Covid-19 require an assessment of the workers personal vulnerability should infection occur. Using recently published UK data, we have developed a risk model that provides estimates of personal vulnerability to Covid-19 according to sex, age, ethnicity, and various comorbidities. Vulnerability from each risk factor is quantified in terms of its equivalence to added years of age. Addition of the impact from each risk factor to an individuals true age generates their Covid-age, a summary measure representing the age of a healthy UK white male with equivalent vulnerability. We discuss important limitations of the model, including current scientific uncertainties and limitations on generalisability beyond the UK setting and its use beyond informing assessments of individual vulnerability in the workplace. As new evidence becomes available, some of these limitations can be addressed. The model does not remove the need for clinical judgement or for other important considerations when managing occupational risks from Covid-19.

10.1101/2020.05.21.20108969

ASSESSMENT OF WORKERS PERSONAL VULNERABILITY TO COVID-19 USING COVID-AGE

10.1186/s12911-016-0342-z

In communicating chronic risks, there is increasing use of a metaphor that can be termed ‘effective-age’: the age of a ‘healthy’ person who has the same risk profile as the individual in question. Popular measures include ‘real-age’, ‘heart-age’, ‘lung-age’ and so on.Here we formally define this concept, and illustrate its use in a variety of areas. We explore conditions under which the years lost or gained that are associated with exposure to risk factors depends neither on current chronological age, nor the period over which the risk is defined. These conditions generally hold for all-cause adult mortality, which enables a simple and vivid translation from hazard-ratios to years lost or gained off chronological age. Finally we consider the attractiveness and impact of this concept.Under reasonable assumptions, the risks associated with specific behaviours can be expressed in terms of years gained or lost off your effective age. The idea of effective age appears a useful and attractive metaphor to vividly communicate risks to individuals.

How old are you, really? Communicating chronic risk through ‘effective age’ of your body and organs

No one wants to pay $30,000 per semester for the current experience.

College Courses Online Are Disappointing. Here’s How to Fix Them.

New York's subway is trying to convince commuters that it is safe to ride. Recently, it has added vending machines with personal protective equipment at 10 of the busiest stations.

New York's Subway Installs Vending Machines With Personal Protective Equipment

UK neurologists publish details of mildly affected or recovering Covid-19 patients with serious or potentially fatal brain conditions

Warning of serious brain disorders in people with mild coronavirus symptoms

Playing a starring role in this thread is Board of Trade adviser and @trussliz fan Andrew Mills (who has just changed his twitter handle). Nothing at all to see here.

Thank you everyone. So, in addition to the chocolatier and the pest controller contracts, shall we go after the:tiny employment agency14.2%Mauritian family office85.8%20,110 votes · Final results

We have litigation in train in respect of the chocolatier and the pest control company. We can probably take on one more - if you'd like to support it.

Anyway, as Ayanda Capital's contract is by far the biggest I've seen; and its business lines don't include supplying PPE; and it is owned through an especially grim tax haven; and has links to the Tories, this might be one for journalists to take a look at.

A fair bit of White Lives Matter type stuff with the characteristic sprinkling of support for transphobes. But mostly it is RTing support for @trussliz.

And he has a twitter profile which is rather on-brand for the modern Conservative Party.

But his LinkedIn entry describes him as a Senior Board Adviser. Oh, and an Adviser to Liz Truss' Board of Trade (which does contain an Andrew Mills).

This rather interesting man doesn't appear anywhere on Ayanda's website...

Its website says that it is a "family office" focusing on currency trading, etc. Not an obvious place to buy PPE. (A family office is a rather ugly creature of late capitalism. If you have SOO much money you need a business specially to look after it then...)

Its net assets (in its unaudited accounts) look healthy but are swamped by its intangible assets, which could be anything.

So what do we know about Ayanda Capital Limited? Well, it is owned by the Horlick family through an entity based in Mauritius, one of the worst tax havens in the world.

Government does give you the chance to click through and read the contract but (as with every single on I have tried) the link is broken (

But wait, that is nothing. The Government spent a cool quarter of a billion quid buying facemasks from a rather interesting outfit called Ayanda Capital Limited (again it was apparently the only tenderer).

You may think it is not the most obvious place from which to purchase £18.5m worth of facemasks (for which contract it was apparently the only bidder). This Government disagrees.

It's an employment agency with net assets of £322.

We are already pursuing a Government over the £108m PPE contracts it said it entered into with a chocolatier and a supplier of pigeon netting. I know there's only so much of this weirdness you can take but here are two more. First Aventis Solutions Limited.

Novel coronavirus cases in Florida and Texas continue to soar, including nearly 3,800 and 2,700 deaths, respectively. Each state has reported nearly 205,650 to 206,450 infections to date, according to the latest figures from Johns Hopkins University.The combined number of COVID-19-related deaths recorded in both states over the past month is greater than the total hurricane-related deaths reported in the U.S. over the past 20 years.

Coronavirus Kills More in Florida, Texas in One Month Than 20 Years of Hurricanes

This is an update regarding the JASP summer workshop “Theory and Practice of Bayesian Hypothesis Testing” originally scheduled for August 24-25, 2020. Unfortunately, the ongoing outbreak of COVID19 and the associated international travel restrictions make it impossible to proceed with the workshop as planned.We therefore decided to offer an online version of the workshop on the same dates. The online workshop will mainly take place during business hours in our local time zone (CEST). However, we will attempt to accommodate the needs of international participants as well. A detailed plan of this online workshop will follow later.Due to the lower costs of organizing an online workshop, we decided to decrease the workshop fees by 100€ for all price categories. The updated prices can be found on our workshop website.

JASP Workshop Goes Online, Fees Reduced

The @HSELive #CovidTracker app is live from today. Download it to help keep us all more safe. #dubw

10. In the absence of more data on the potential effect of cross-reactive T-cells on the severity of COVID-19, it is dangerous to lower our guard and loose certain measures such as wearing masks and social distancing.

9. These findings indicate, that we do not miss many exposed individuals in the current seroprevalence studies. In conclusion, I think we should not fall back into wishful thinking that an underestimated T-cell immunity will resolve this pandemic.

8. In a recent paper from us, http://tinyurl.com/yb9388be we found only 1 out of 44 mild (outpatient) cases after 21 days post onset that did not mount an antibody response. And all asymptomatic patients in another study http://tinyurl.com/y9f39twv mounted neutralizing antibodies.

7. seroprevalence rates are vastly underestimating the true exposure rate and that we are closer to herd immunity that we think. While I do believe that these patients exist, I don't think that they comprise a large proportion that dramatically changes the exposure rate.

6. Yet, as of today we do not know whether this is true or not and we need to investigate it further. Second, it has been descriped that people exposed to SARS-CoV-2 only mount a T-cell response but do not produce any antibodies. From this, some people like to conclude that

5. if the specific T-cell response cannot prevent infection and transmission, the cross-reactive response against SARS-CoV-2 cannot prevent it either. However, the cross-reactive T-cell response might or might not play a role in the protection of patients against severe disease.

4. get regularly infected by them (every couple of years). So it obviously does not prevent infection in the upper respiratory tract and also not transmission of the common cold CoVs, otherwise they should have died out long time ago. Therefore, I think it is save to assume that

3. While I do trust these studies, as the authors pointed out themselves, it is in my opinion quite unclear what this cross-reactive T-cell response means in terms of protection. We know that despite having this specific T-cell response against common cold CoVs, we do

2. There are 2 different points that are discussed at the moment: First, there are some studies, i.e. http://tinyurl.com/y8zzf8tw, that show a cross-reactive T-cell response in sample taken before the pandemic, due to previous infection with common cold coronaviruses.

1. Since there was a huge discussion about T-cell mediated immunity following the Lancet comment on seroprevalence by @EckerleIsabella and me, I'd like to share my thoughts on this in the following thread:

ObjectivesTo validate the diagnostic accuracy of a Euroimmun SARS-CoV-2 IgG and IgA immunoassay for COVID-19.MethodsIn this unmatched (1:2) case-control validation study, we used sera of 181 laboratory-confirmed SARS-CoV-2 cases and 326 controls collected before SARS-CoV-2 emergence. Diagnostic accuracy of the immunoassay was assessed against a whole spike protein-based recombinant immunofluorescence assay (rIFA) by receiver operating characteristic (ROC) analyses. Discrepant cases between ELISA and rIFA were further tested by pseudo-neutralization assay.ResultsCOVID-19 patients were more likely to be male and older than controls, and 50.3% were hospitalized. ROC curve analyses indicated that IgG and IgA had high diagnostic accuracies with AUCs of 0.990 (95% Confidence Interval [95%CI]: 0.983-0.996) and 0.978 (95%CI: 0.967-0.989), respectively. IgG assays outperformed IgA assays (p=0.01). Taking an assessed 15% inter-assay imprecision into account, an optimized IgG ratio cut-off > 2.5 displayed a 100% specificity (95%CI: 99-100) and a 100% positive predictive value (95%CI: 96-100). A 0.8 cut-off displayed a 94% sensitivity (95%CI: 88-97) and a 97% negative predictive value (95%CI: 95-99). Substituting the upper threshold for the manufacturer’s, improved assay performance, leaving 8.9% of IgG ratios indeterminate between 0.8-2.5.ConclusionsThe Euroimmun assay displays a nearly optimal diagnostic accuracy using IgG against SARS-CoV-2 in patient samples, with no obvious gains from IgA serology. The optimized cut-offs are fit for rule-in and rule-out purposes, allowing determination of whether individuals in our study population have been exposed to SARS-CoV-2 or not. IgG serology should however not be considered as a surrogate of protection at this stage.

10.1016/j.cmi.2020.06.024

Validation of a commercially available SARS-CoV-2 serological immunoassay

With no clear direction from the federal government on how to handle the COVID-19 pandemic, it’s been hard to decide what’s safe and unsafe as states begin to open up. There's no right answer; you just need to know the risks and how much risk you're willing to take. That's why Professor Saskia Popescu, an infectious disease epidemiologist at the University of Arizona, Dr. James P. Phillips, MD, the Chief of Disaster Medicine at GWU Emergency Medicine, and I developed a COVID-19 Risk Index to help you do this, based on four key factors: 1) Enclosed space 2) Duration of interaction 3) Crowds 4) Forceful exhalation   

COVID-19 Activity Risk Levels

The Nature Podcast brings you the best stories from the world of science each week. We cover everything from astronomy to zoology, highlighting the most exciting research from each issue of Nature journal. We meet the scientists behind the results and providing in-depth analysis from Nature's journalists and editors.

Nature Podcast

10.37074/jalt.2020.3.1.7

The Coronavirus 2019 (COVID-19) pandemic has created significant challenges for the global higher education community. Through a desktop analysis leveraging university and government sources where possible, we provide a timely map of the intra-period higher education responses to COVID-19 across 20 countries. We found that the responses by higher education providers have been diverse from having no response through to social isolation strategies on campus and rapid curriculum redevelopment for fully online offerings. We provide in our discussion a typology of the types of responses currently undertaken and assess the agility of higher education in preparing for the pandemic. We believe there are significant opportunities to learn from the pedagogical developments of other universities, in order to strengthen our collective response to COVID-19 now and into the future.

COVID-19: 20 Countries' Higher Education Intra-Period Digital Pedagogy Responses

Critics attack ‘confusing’ tweet about guidance on meeting people from other households

No 10 faces ridicule after tweeting incorrect lockdown rules

The ability to measure argument quality is of central importance not just in our everyday lives, but to scientific endeavors ranging from psychology and philosophy, to computer science and artificial intelligence.Classical logic provides fundamental constraints on argument quality, but most everyday informal argument is already in line with these constraints. This leaves the majority of quality concerns unaddressed.A Bayesian, probabilistic framework significantly expands quality standards for argument evaluation. It not only provides a treatment of the traditional catalogue of logical fallacies, it offers normative guidance that is quantitative, computationally explicit, and can be used for education.Consideration of how both logic and probability work to provide measures of argument quality suggests that ‘consistency’ and ‘relevance’ are two sides of the same coin.The idea of resolving dispute through the exchange of arguments and reasons has been central to society for millennia. We exchange arguments as a way of getting at the truth in contexts as diverse as science, the court room, and our everyday lives. In democracies, political decisions should be negotiated through argument, not deception, or even worse, brute force. If argument is to lead to the truth or to good decisions, then some arguments must be better than others and ‘argument strength’ must have some meaningful connection with truth. Can argument strength be measured in a way that tracks an objective relationship with truth and not just mere persuasiveness? This article describes recent developments in providing such measures.

10.1016/j.tics.2020.01.004

Argument Quality in Real World Argumentation

I don't *love* medium, but I'm voting with my money for a service I'd like to be better. If it doesn't improve, I'll leave.

Hmm. For the sake of argument, that *is* the issue. At least for medium I'm incentivising the content I want in a transparent way. If I pay the NYT I've got no idea whether they'll decide to create more of what I like.

Isn't Medium a flat $5 regardless of how much you read? Who the money goes to changes, but that's not really an issue in a news organisation with salaried staff.

but what reason do we have to believe that those would be the financially most viable ones? Doesn't the history of what happened to traditional media in the last two decades suggests this is unlikely?

Sure but if the % of forward looking articles based on reliable track records increases, I'll take that as a win.

interesting idea, but how would that affect content long-term: puff pieces replace "less popular" serious items seems a rather likely consequence

I refuse to subscribe to every newpaper that I read 3 articles from a month. I'm subscribed to @Blendle @Coil and @Medium for content that I pay per use. If news orgs want my money, let me pay only for what I use.

This is part two of a series on the future of applied behavioural science. You can read part one here.Revisiting the Core ChallengeSolutions to challenges solved in isolation inevitably stumble as they enter the messy, complex reality that they need to exist within

Exploring the Valleys of the Applied Behavioural Science Landscape

10.31235/osf.io/pz9jr

Preregistrations -- records made a priori about study designs and analysis plans and placed in open repositories -- are thought to strengthen the credibility and transparency of research. Different authors have put forth arguments in favor of introducing this practice in qualitative research and made suggestions for what to include in a qualitative preregistration form. The goal of this study was to attain consensus among qualitative researchers on which items to include in a qualitative study preregistration form. We defined consensus as 68% agreement and used an online Delphi study design consisting of two rounds with feedback reports in between. In total, 45 researchers participated (response rate: 15%). In round 1, panelists considered 14 proposed items relevant to include in the preregistration form, but 2 items had a 66% relevance score with mixed argument and were put forth again. We combined items where possible, leading to 11 revised items. In round 2, panelists attained consensus on including the two remaining items. Panelists also reached consensus on suggested terminology and elaborations, with the exception of two terms for which they provided clear arguments. The result is a consensus-based form for the preregistration of qualitative studies that consists of 13 items. The form will be made available as a registration option on Open Science Framework. We believe it is important to assure that the strength of qualitative research, which is its flexibility to adapt, adjust and respond, is not lost in preregistration. The preregistration should provide a systematic starting point.

Preregistering Qualitative Research: A Delphi Study

10.1103/PhysRevE.102.012303

Today's society faces widening disagreement and conflicts among constituents with incompatible views. Escalated views and opinions are seen not only in radical ideology or extremism but also in many other scenes of our everyday life. Here we show that widening disagreement among groups may be linked to the advancement of information communication technology by analyzing a mathematical model of population dynamics in a continuous opinion space. We adopted the interaction kernel approach to model enhancement of people's information-gathering ability and introduced a generalized nonlocal gradient as individuals' perception kernel. We found that the characteristic distance between population peaks becomes greater as the wider range of opinions becomes available to individuals or the more attention is attracted to opinions distant from theirs. These findings may provide a possible explanation for why disagreement is growing in today's increasingly interconnected society, without attributing its cause only to specific individuals or events.

Enhanced ability of information gathering may intensify disagreement among groups

A paper authored jointly by the van der Schaar Lab, the University of Cambridge’s Department of Medicine, and a group of Brazilian researchers has been published in Lancet Global Health (editor-in-chief: Zoë Mullan). The paper, which was first published on May 27, examines ethnicity as a COVID-19 risk factor in Brazil. One of its key findings is that patients who self-identify as belonging to the country’s pardo and preto ethnicities exhibit significantly higher in-hospital mortality risk than those who self-identify as branco (“white”). A Lancet Global Health comment calls the work “a pioneering study,” noting that it “confirms in Brazil findings observed in other countries hit hard by COVID-19: that mortality rates from the pandemic differ by geographical region and ethnicity, with disproportionate impact for Black populations and other ethnic minorities.”

“Pioneering” COVID-19 study published in Lancet Global Health