Online panel on ways that researchers can communicate and engage locally and globally in response to COVID-19 -- even if they're not an expert in the virus.

Responding to COVID-19: Opportunities for all researchers to engage

10.31234/osf.io/4nzc7

Interest in improving reproducibility, replicability and transparency of research has increased substantially across scientific fields over the last few decades. We surveyed 560 empirical, quantitative publications published between 1955 and 2018, to estimate the rate of reproducibility for research on social learning, a large subfield of behavioural ecology. We found supporting materials were available for less than 30% of publications during this period. The availability of data declines exponentially with time since publication, with a half-life of about six years, and this “data decay rate” varies systematically with both study design and study species. Conditional on materials being available, we estimate that a reasonable researcher could expect to successfully reproduce about 80% of published results, based on our evaluating a subset of 40 publications. Taken together, this indicates an overall success rate of 24% for both acquiring materials and recovering published results, with non- reproducibility of results primarily due to unavailable, incomplete, or poorly documented data. We provide recommendations to improve the reproducibility of research on the ecology and evolution of social behaviour.

Reproducibility of social learning research declines exponentially over 63 years of publication

10.1038/d41586-020-01812-9

Pandemic politics highlight how predictions need to be transparent and humble to invite insight, not blame.

Five ways to ensure that models serve society: a manifesto

10.1038/s41562-020-0911-0

The scientific community’s response to COVID-19 has resulted in a large volume of research moving through the publication pipeline at extraordinary speed, with a median time from receipt to acceptance of 6 days for journal articles. Although the nature of this emergency warrants accelerated publishing, measures are required to safeguard the integrity of scientific evidence.

Pandemic publishing poses a new COVID-19 challenge

A town in the UK is about to start testing thousands of people for the coronavirus each week, using easily collected saliva and a cheap, quick way of detecting the virus. If the initial trial in Southampton is successful, the aim is to test the town’s entire population of 250,000 people every week to see if this can rapidly halt the virus’ spread.

Town in UK takes steps to test entire population for coronavirus

How the Coronavirus Recovery Is Changing Cities

Prior research in decisions from experience (DFE) has investigated people's consequential decisions after information search both experimentally and computationally. However, prior DFE research has yet to explore how computational cognitive models and their mechanisms could explain the effects of problem framing in experience. The primary objective of this paper is to address this literature gap and develop Instance-based Learning Theory (IBLT) models on the effects of problem framing. Human data was collected on a modified form of the Asian disease problem posed about the COVID-19 pandemic across two between-subject conditions: gain (N = 40) and loss (N = 40). The COVID-19 problem was presented as "lives saved" in the gain condition and "lives lost" in the loss condition. Results revealed the absence of the classical framing effect, exhibiting no preference reversal between gain and loss conditions in experience. Next, an IBL model was developed and calibrated to the data obtained in the gain and loss problems. The calibrated model was generalized to the non-calibrated conditions (gain to loss and loss to gain). An IBL model with ACT-R default parameters was also generalized. Results revealed that the IBL model with calibrated parameters explained human choices more accurately compared to the IBL model with ACT-R default parameters. Also, participants showed greater reliance on recency and frequency of outcomes and less variability in their choices across both gain and loss conditions. We highlight the main implications of our findings for the cognitive modeling community.

Modeling the Absence of Framing Effect in an Experience-based Covid-19 Disease Problem

BAME & low-paid groups at particular risk as disproportionate number unable to work at home & exposed to greater risk under new rules expected to be announced Tues. Independent SAGE says govt must release underlying evidence so public & businesses can make own risk assessments

Independent SAGE agrees with government’s own SAGE group that current levels of transmission are too high. Reducing rules from 2m to 1m will effectively end all social distancing in UK. It is too soon to do so.

NEW: Independent SAGE has evaluated the scientific evidence on social distancing & concludes it is not safe to reduce it from 2m to 1m indoors as government proposes

In the wake of COVID19, the world is scrambling to figure out how to continue the functions of normal life while confined to a much smaller world of couches and home offices. Work, family and friend relationships, exercise, entertainment, and all the other elements of normalcy have been upended. The effort to maintain productivity (and, to be frank, sanity) has initiated a mass digital migration; a movement from life to e-life.

The Digital Migration: Lessons About Open Science Arising from the COVID19 Crisis

10.1038/d41586-020-01863-y

Results from the inaugural study will reveal crucial information about the deepest worries, hopes and triumphs of postdocs around the world.

Take our postdoctoral-researcher survey

Amazing what a difference four weeks makes since Memorial Day Weekend in #COVID19 New cases/day by U.S. region, adjusted for population

10.1038/nmeth.1416

We demonstrate subassembly, an in vitro library construction method that extends the utility of short-read sequencing platforms to applications requiring long, accurate reads. A long DNA fragment library is converted to a population of nested sublibraries, and a tag sequence directs grouping of short reads derived from the same long fragment, enabling localized assembly of long fragment sequences. Subassembly may facilitate accurate de novo genome assembly and metagenome sequencing.

Parallel, tag-directed assembly of locally derived short sequence reads

Instructions Hover over cells with mouse to reveal additional information. Select site subsets using the drop down menu below the plots. Change which sites are displayed by brushing the zoom bar and dragging the brush. Clear the zoom bar by double clicking it. Structural visualizations of the data are available via dms-view here See the paper describing these data here Raw data available on GitHub

SARS-CoV-2 RBD DMS

10.1101/2020.06.17.157982

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

Now we hope data we generated will help others studying evolution of virus and especially those developing vaccines. It's all publicly available, so if you're curious about a specific mutation to RBD, need a stabilizing mutation, or need to change a surface--go look it up! (14/n)

Allie Greaney jumped on board to help @tylernstarr do the experiments amazingly fast, and Sarah Hilton and @khdcrawford helped with code and validation. (13/n)

@tylernstarr had been optimizing approach for other proteins when #SARS_CoV2 hit. We had as colleagues @veeslerlab @coronalexington who had been building basic knowledge about coronavirus spikes for years. They helped advise @tylernstarr how to adapt his approach to RBD. (12/n)

To enable these deep mutational scanning titration assays to be applied to larger protein like RBD, we leveraged barcoding approach originally developed by @JShendure and subsequently extended to use PacBio by @lea_starita @kmatreyek @dougfowler42: https://nature.com/articles/nmeth.1416… (11/n)

Finally, how we were able to characterize so many mutations to this important protein? We leveraged great prior work. In 2016, @jbkinney, Walczak, & Mora showed yeast display & deep mutational scanning could measure dissociation constants at scale: https://elifesciences.org/articles/23156 (10/n)

Lots of other observations about natural mutations, structure-function, and sarbecovirus evolution in the paper itself, so take a look. (9/n)

Key finding from that comparison is that no antibodies have epitopes as constrained as actual ACE2. So epitope focusing can elicit more escape-resistant antibodies. And our data help point the way, as we show what mutations would be tolerated in resurfaced immunogens! (8/n)

We can examine mutational tolerance of epitopes of different antibodies, and compare it to mutational tolerance of actual ACE2 binding interface (here are some antibodies, see paper for more). (7/n)

We can map tolerance to mutations with respect to RBD folding / expression & ACE2 binding on structure (red = intolerant in images below). As expected, most selection for binding in ACE2 interface--but again, lots of mutations still tolerated (again see heat maps or paper) (6/n)

Some observations: While many mutations to RBD are deleterious, lots are tolerated--including a surprising number that increase ACE2 affinity (blue in heat map in prior Tweet). But no evidence that strong affinity enhancing mutations are being selected in human isolates. (5/n)

If you're interested in the evolution of the virus or are studying antibodies / vaccines, you can go to this interactive heatmap (https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS/…) and simply look up the *experimentally measured* effect of any mutation. (4/n)

Before our study, the structure of the RBD protein was known but we didn't know how mutations affected it's function. Now we've measured how virtually all (3800 of 3819) amino-acid mutations affect binding to ACE2 and expression of the folded protein. (3/n)

The RBD (receptor binding domain) enables #SARSCoV2 to bind to human cells. Evolution to bind human ACE2 was key to the emergence of this virus. Now it's also key to mitigating the virus: the most potent antibodies bind to RBD, and most vaccine candidates contain RBD. (2/n)

We've experimentally measured how all amino-acid mutations to the #SARSCoV2 spike RBD affect ACE2 binding and expression of folded protein in a deep mutational scanning study led by @tylernstarr & Allie Greaney: https://biorxiv.org/content/10.1101/2020.06.17.157982v1… Why is this important? (1/n)

Given the significant uptake in the incentives and use of preprints and registered reports, a few early analyses have used those to document the phenomenon: women economists were shown to have a drop in production of preprints and registered reports in March and April and were less likely to work on COVID-related topics. Similarly, over the last three months male authors on arXiv and bioRxiv increased at a greater rate than women authors. Our own analysis builds on data from 11 pre-print repositories and three platforms, for a total of 327,902 documents. This work demonstrates the disproportionate effect on early career researchers (using authorship position as a proxy for seniority in science). We have created this dynamic and interactive website to allow policy makers, scientists, and administrators to monitor this evolving situation. As of May 18th 2020, the data covers 284,842 pre-prints and registered reports, which will be updated on a regular basis.

Monitoring women's scholarly production during the COVID-19 pandemic

and last. government needs to use expertise on the ground. patient voices and organisations are really important here. yet seem scarcely used as a resource to help get this right. trust is not bought, is built. off to work

the second is false advertising. this should always been a red flag and needs to stop. no one in the NHS should trust any org/ provider who makes surreal claims about their stuff or who gets shirty when ask for evidence. yes, am talking about you @babylonhealth

the best tech has grown stuff from ground up and found out what is needed and wanted and what works. humility to know there's stuff you don't yet know. understanding that NHS staff can't be left fixing your botched rubbish.

Replying to @mgtmccartneythe first is belief that the private sector should get massive contracts for stuff that hasn't been done, and who work from top down. healthcare is really complicated. rests on trust and relationships. the gov approach starts off wrong.

profound disconnect between the government belief about what benefits technology will provide, and the later (after ££) evidence for benefit. tech in health=vital, but if not fit for purpose ends up wasting resources better spent elsewhere- time+money. what needs to change?

Months into the pandemic, Vermont’s governor says the state is “the envy of the nation,” with little more than 1,100 confirmed covid-19 infections and 56 deaths. Perhaps most remarkable is that Vermont has been relatively spared the effects of the disease even though a huge swath of the nation’s cases are mere hours from its borders; neighboring New York and Massachusetts have approximately half a million confirmed cases between them, and more than 37,000 deaths.

Vermont borders states with major covid-19 outbreaks, but you won’t find that here

10.1136/bmj.m2255

Illness related to the novel coronavirus has driven a global crisis, and many clinicians are facing unexpected and challenging conversations. This guide is a graphic medicine adaptation of text that was created to provide a practical introduction on how to talk about difficult topics related to covid-19. During early spread of the pandemic, the written text and subsequent illustrations were created to promote rapid sharing of communication skills with clinicians across diverse disciplines. The primary text was produced by non-profit organisation VitalTalk, which gives training to support conversations around serious illness.This guide is not meant to be comprehensive, but it is a starting place for improving conversations with those facing this illness.

Covid-19 communication aids

Infectious diseases have been largely pushed to the wayside by big pharma because they are unable to bring the same profits as other conditions, such as cancer and chronic diseases. Octopus Ventures’ Uzma Choudry explains the reasons behind the failure and why she is hopeful the current Covid-19 pandemic will change attitudes towards the serious public health threats infectious diseases cause.

Covid-19 pandemic: overcoming big pharma’s infectious disease market failure

Charities call on government to rebuild care system to support carers and their families

Coronavirus: 4.5m people in UK forced to become unpaid carers

As shops re-opened in the UK this week, social media users were quick to pour scorn on the hundreds of eager shoppers who queued up to get in. Yes, it’s unclear whether it was a good decision to re-open businesses — but there was a certain snobbishness to many of these posts. Most of the ire was directed at those lining up outside Primark, which sells clothes at prices more affordable to those on low incomes than most other high street stores. Meanwhile, queues also formed outside high-end shops like Selfridges and Harrods — but these shoppers somehow escaped the wrath of most social media commentators.

Why Are We So Quick To Scrutinise How Low-Income Families Spend Their Money?

Over the last few years, memes have played an increasingly important part in online political discussion: in 2016, the Washington Post dubbed the 2016 presidential election “the most-memed election in U.S. history”, and CNN has already christened the 2020 race “the meme election”. But politicians may want to pause for thought before they hit send on that jokey tweet. New research in Communication Research Reports, from Ohio State University’s Olivia Bullock and Austin Huber, suggests that humour doesn’t always go down well online — and that this can impact what voters think of particular candidates and potentially how they vote.

For Political Candidates, Making Jokes Online Might Backfire

A Letter to Grown-UpsChildhood is an amazing time of discovery. Nearly every moment of a child’s life offers opportunities to teach important emotional intelligence skills, such as caring, listening, empathy, problem-solving, self-regulation, and resilience. That holds particularly true in challenging times such as these.During the current pandemic, families have been thrust into extraordinary circumstances that may be life-changing, with short- and long-term effects on children’s well-being. Past experience during global crises has taught us that caring grown-ups in children’s lives can make an enormous difference by providing safety, comforting reassurance, age-appropriate information, and helpful guidance. Helping children learn to be smart about feelings can help alleviate their emotional stress, improve concentration, boost their immune system, and enhance brain development. This First Aid for Feelingsworkbook for children was designed to help you do just that. By using the simple coping strategies found in this workbook, you can encourage children to express thoughts, questions, and feelings. These life skills may help reduce and manage children’s stress or anxiety, and provide some sense of control within their changing lives.

A Workbook to Help Kids Cope During the Coronavirus Pandemic

10.1016/j.jclinepi.2020.06.007

A cautionary note on the use of the missing indicator method for handling missing data in prediction research

10.1073/pnas.2007658117

In response to the coronavirus disease 2019 (COVID-19) pandemic, several national governments have applied lockdown restrictions to reduce the infection rate. Here we perform a massive analysis on near–real-time Italian mobility data provided by Facebook to investigate how lockdown strategies affect economic conditions of individuals and local governments. We model the change in mobility as an exogenous shock similar to a natural disaster. We identify two ways through which mobility restrictions affect Italian citizens. First, we find that the impact of lockdown is stronger in municipalities with higher fiscal capacity. Second, we find evidence of a segregation effect, since mobility contraction is stronger in municipalities in which inequality is higher and for those where individuals have lower income per capita. Our results highlight both the social costs of lockdown and a challenge of unprecedented intensity: On the one hand, the crisis is inducing a sharp reduction of fiscal revenues for both national and local governments; on the other hand, a significant fiscal effort is needed to sustain the most fragile individuals and to mitigate the increase in poverty and inequality induced by the lockdown.

Economic and social consequences of human mobility restrictions under COVID-19