How the UK’s coronavirus testing regime totally unravelled | WIRED UK
The irritation being expressed by microbiologists and their colleagues who are critical of the government is not over the quality of labs or people’s willingness to dig in and help. Rather, it is to do with how testing for Covid-19 has been managed, particularly at a national level. As the chances of reaching 100,000 tests per day by the end of April grow ever slimmer, the UK’s sorry predicament is only becoming clearer.
Muddled thinking punctures plan for British ventilator | Financial Times
Omnishambles.
An insider with direct knowledge of the process said that the basic products are now unlikely to be cleared for use in the UK against Covid-19. “Pretty much all the basic new designs are not going to get through the Covid approval process. The government spin is the ‘clinical need’ changed, but the reality is that it was always misguided to think you could develop and create these ventilators,” the person said. “Starting the process in this way was unwise. It has gradually become more sensible.”
(tags: covid-19 uk fail bureaucracy tories ventilators medicine)
PEPP-PT Data Protection Architecture – Security and privacy analysis
Analysis of the PEPP-PT contact tracing project architecture by the DP-3T project
(tags: architecture pepp-pt security data-privacy contact-tracing covid-19)
Study sees need for some social distancing into 2022 to curb coronavirus
‘A modeling study on the new coronavirus warns that intermittent periods of social distancing may need to persist into 2022 in the United States to keep the surge of people severely sickened by Covid-19 from overwhelming the health care system. The research, published […] in the journal Science, looked at a range of scenarios for how the SARS-CoV-2 virus will spread over the next five years.’
(tags: covid-19 statnews social-distancing harvard medicine health)
COVID-19 Related Advice – Guidance on Regulation EC261/2004
Airlines are required to provide passengers with information on their rights. Where flights are cancelled passengers must be offered the choice of: a refund; or re-routing (alternative flights) at the earliest opportunity; or re-routing at a later date (subject to availability). It is important that airlines assist passengers by clearly setting out these options to them. In addition, it is open to airlines to offer incentives to passengers to encourage them to fly at a later date, for example through providing vouchers of a higher value. We recognise that, at present, it may be difficult for airlines to provide alternative flights, for example, where government advice is to avoid travel to particular destinations affected by COVID-19. A refund for the passenger may therefore be the only practical option available.
More: https://www.flightrights.ie/news/guidance-note-on-airline-flight-cancellations-%e2%80%93-regulation-eu-2612004.1043.html (via Brian Brazil)(tags: airlines travel covid-19 flights refunds consumer rights)
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via Zeynep Tufekci: ‘Amazing study, supporting droplet (rather than aerosol) as key means of transmission. One asymptomatic person infected 10 (out of 91) at restaurant—but *only* if they were in direct line of air pushed by the air conditioning.’
(tags: china covid-19 air-conditioning droplets transmission diseases sars-cov-2 infection)
Rift opens over European coronavirus contact tracing apps – Reuters
The rift has opened up over a German-led initiative, called Pan-European Privacy-Preserving Proximity Tracing (PEPP-PT https://www.pepp-pt.org), which has been criticised for being too centralised and thus prone to governmental mission creep. [….] “Solutions which allow reconstructing invasive information about the population should be rejected without further discussion,” the scientists said in their letter. Among the signatories was Michael Backes, head of Germany’s CISPA Helmholtz Center for Information Security, which pulled out of PEPP-PT at the weekend. Swiss researchers have also publicly dissociated themselves from PEPP-PT, citing concerns over centralisation and privacy. Critics have also questioned PEPP-PT’s assertion that seven European countries – Austria, Germany, France, Italy, Malta, Spain and Switzerland – had come on board. Spain and Switzerland now back rival DP-3T, government and research sources said.
Category: Uncategorized
No matter how you crunch the numbers, this pandemic is only just getting started
Scary op-ed from professor of the evolution and epidemiology of infectious disease at Harvard, William Hanage in The Guardian, on herd immunity:
There have been more than 93,000 cases of Covid-19 identified in the UK. Let’s round that up and say it is 100,000. So if the reports from the BMJ editorial are accurate, the actual number would be that multiplied by five, in which case there would have already been half a million infections in the UK. If this really is the peak and we see as many cases on the way down as on the way up, that would total 1 million infections from the initial surge in the UK – hopefully all of those people would then be immune. That would leave about 65 million people in the UK still without immunity. I am going to be unusually optimistic here, and assume that everyone who has Covid-19 becomes fully immune (not a given), and that the virus is towards the less transmissible end of the range of estimates currently available. If this is the case, you would need half your population to have been infected to achieve a level of population immunity that would stop the epidemic continuing to grow and overwhelming healthcare systems.
(tags: guardian health uk covid-19 pandemics herd-immunity future)
Irish COVID-19 model showing an R0 below 1.0
This is fantastic news — our lockdown is working! ‘The April 16 2020 modelling data on COVID-19 in Ireland from the Irish Epidemiological Modelling Advisory Group, part of the National Public Health Emergency Team (NPHET).’
PEPP-PT closes down the decentralised protocol option
The EU-wide PEPP-PT COVID-19 contact tracing project is quietly switching to a protocol built around a centralised database; better to stick with the still-decentralised, fully open source DP3T protocol, which has published its open source apps and SDKs: https://twitter.com/mikarv/status/1251044870367690753
(tags: pepp-pt dp3t protocols ios android contact-tracing covid-19 pandemics)
Sarah Owens’ Table Loaf Recipe
recommended by Colette
CT scans might offer a more accurate way to diagnose Covid-19
Jaysus. RT-PCR swab tests have a 30% false negative rate!
A positive result on the swab tests is usually reliable. “If you get a positive test result, looking for the RNA of the virus with the current methods that we have, it’s very likely to be a true positive,” said Jana Broadhurst, an infectious disease doctor and director of the Nebraska Biocontainment Unit Clinical Laboratory at the University of Nebraska Medical Center. But “if you get a negative test result, [the chance that it’s wrong is] about 30%.” Of every 100 symptomatic people who test negative for Covid-19, 30 are actually infected. The test missed them.
(tags: rt-pcr covid-19 medicine swab-tests false-negatives)
Solution Scan of non-pharmaceutical options to reduce SARS-CoV-2 transmission
‘Informing management of lockdowns and a phased return to normality: a Solution Scan of non-pharmaceutical options to reduce SARS-CoV-2 transmission’. This is a pretty exhaustive list of possible approaches to lower the R0.
(tags: covid-19 r0 transmission diseases lockdowns social-distancing)
EDPB on COVID-19 contact tracing apps
European Data Protection Board: Letter concerning the European Commission’s draft Guidance on apps supporting the fight against the COVID-19 pandemic
(tags: edpb data-privacy privacy covid-19 eu ec contact-tracing)
The other kind of contact tracing tools
Farzad Mostashari on Twitter: “Last week I posted about automated digital contact tracing apps- lots of discussion since. now lemme talk about the other kind of contact tracing app, tools that increase the efficiency & ease of contact tracing: enhanced directories, multichannel messaging applications, real-time translation services, symptom reporting & isolation monitoring”
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Turn your favourite regex into FAT32. ‘Haha OS-driven regex engine go brrrrr’
(tags: insane stupid funny fat32 drivers filesystems regexps regex)
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on 12 March, the government alarmed many public health experts by abruptly abandoning containment and announcing that community case-finding and contact-tracing would stop. The aim was no longer to stop people getting it, but to slow it down while protecting the vulnerable. The evidence underpinning the government’s decision appears in a report from 9 March summarising the potential impact of behavioural and social interventions. The report did not consider the impact of case-finding and contact-tracing, but it did suggest that the biggest impact on cases and deaths would come from social distancing and the protection of vulnerable groups. And yet social distancing was not recommended then. That day, 12 March, after hearing with disbelief the government announcement that didn’t include widespread social distancing, I recommended to my team at Imperial that they should work from home for the foreseeable future. Indeed, I have not been to my office since. Neither the advice nor the science were followed that week. My colleagues, led by Neil Ferguson, published a report on 16 March estimating that without strong suppression, 250,000 people could die in the UK. The government responded that day with a recommendation for social distancing, avoiding pubs and working from home if possible. But there was still no enforcement, and it was left up to individuals and employers to decide what to do. Many people were willing but unable to comply as we showed in a report on 20 March. It was only on 23 March that a more stringent lockdown and economic support was announced. Between 12 and 23 March, tens, if not hundreds of thousands, of people will have been infected. Boris Johnson himself may well have been infected that week, and his stay in the intensive care unit may have been avoided if the government had shifted to remote working on 12 March. The current best estimate is that around 1% of those infected will die.
(tags: nhs health uk politics covid-19 pandemics predictions)
Nature paper on COVID-19 and RT-PCR detection rates over time
‘measures to contain viral spread should aim at droplet-, rather than fomite-based transmission’; ‘ the majority of patients in the present study seemed to be already beyond their shedding peak [first 5 days] in upper respiratory tract samples when first tested, while shedding of infectious virus in sputum continued through the first week of symptoms. Together, these findings suggest a more efficient transmission of SARS-CoV-2 than SARS-CoV through active pharyngeal viral shedding at a time when symptoms are still mild and typical of upper respiratory tract infection.’ However this study did not include any severe cases.
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Marcel Salathe says: ‘Decentralized Privacy-Preserving Proximity Tracing (#DP3T): SDK and calibration app for iOS and Android, and a backend implementation, are now open source. Actual app with nice UI will follow soon’
(tags: open-source dp3t privacy data-privacy covid-19 contact-tracing)
Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period | Science
We used estimates of seasonality, immunity, and cross-immunity for betacoronaviruses OC43 and HKU1 from time series data from the USA to inform a model of SARS-CoV-2 transmission. We projected that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after the initial, most severe pandemic wave. Absent other interventions, a key metric for the success of social distancing is whether critical care capacities are exceeded. To avoid this, prolonged or intermittent social distancing may be necessary into 2022. Additional interventions, including expanded critical care capacity and an effective therapeutic, would improve the success of intermittent distancing and hasten the acquisition of herd immunity. Longitudinal serological studies are urgently needed to determine the extent and duration of immunity to SARS-CoV-2. Even in the event of apparent elimination, SARS-CoV-2 surveillance should be maintained since a resurgence in contagion could be possible as late as 2024.
(tags: covid-19 forecasting papers science medicine pandemics sars-cov-2 herd-immunity epidemiology)
Good thread on what Iceland is doing right wrt. COVID-19
Gummi ???? on Twitter: ““What’s up with Iceland?” – this graph has caught the attention of several of my friends abroad and there are probably things others can learn from the Covid response here in Iceland. Let me elaborate (chart: https://t.co/qMt3a0V7oZ) 1/ https://t.co/ZYtJMcjWKK” / Twitter
(tags: covid-19 iceland contact-tracing testing medicine pandemics)
dúchas.ie Volunteer Transcription Project
Fred Logue says: ‘If you’ve got a bit of time on your hands you could do some crowd-sourced transcription of folklore gathered from schools. It’s a really good way to get an insight into life in the 1930s’
(tags: transcription duchas meitheal folklore history ireland 1930s)
Mutant enzyme could vastly improve recycling of plastic bottles
‘A huge step forward’ for PET recycling:
They isolated a mutant enzyme that’s 10,000 times more efficient at PET bond breaking than the native LLC. It also works without breaking down at 72°C, close to the temperature at which PET becomes molten. In a small reactor designed to test the enzyme, the team found that it could break down 90% of 200 grams of PET in 10 hours. The researchers then used the terephthalate and ethylene glycol building blocks generated by the enzyme to generate new PET and produce plastic bottles that were just as strong as those made from conventional plastics, they report today in Nature.
(via Boing Boing)(tags: pet plastic recycling enzymes via:boingboing)
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On the basis of these results the scientist advises that for walking the distance of people moving in the same direction in 1 line should be at least 4–5 meter, for running and slow biking it should be 10 meters and for hard biking at least 20 meters. Also, when passing someone it is advised to already be in different lane at a considerable distance e.g. 20 meters for biking.
(tags: covid-19 cycling running health aerosols infection gross exercise droplets)
“Pre-existing conditions” vs age as risk factors in COVID-19
Twitter thread with some data from a recent CDC paper: ‘Authors report that among those 19-64 y.o. WITH a pre-existing conditions, ~18-20% were hospitalized. Among those WITHOUT conditions: ~6% were hospitalized. Among those equal to or >65 y.o. WITH pre-existing conditions, ~42-44% were hospitalized. For those WITHOUT conditions: ~17-18% were hospitalized.’
(tags: icu hospitalisations hospitalizations covid-19 cdc papers health age)
Mortality rate of COVID-19 patients on ventilators
Probably the best published information we have so far is from the Intensive Care National Audit and Research Center (ICNARC) in the UK. Of 165 patients admitted to ICUs, 79 (48%) died. Of the 98 patients who received advanced respiratory support—defined as invasive ventilation, BPAP or CPAP via endotracheal tube, or tracheostomy, or extracorporeal respiratory support—66% died. Compare that to the 36% mortality rate of non-COVID patients receiving advanced respiratory support reported to ICNARC from 2017 to 2019.
Amazon may be running Folding@Home on their unused EC2 spot instances
A mysterious team called “AWSFolds” is using a massive amount of AWS spot capacity
(tags: aws amazon ec2 spot-instances foldingathome covid-19)
Where To Get Groceries Delivered From In A Lockdown
Holy cow, loads of good places are delivering now
(tags: lockdown dublin food shopping deliveries)
How long SARS-CoV-2 can live on surfaces, and how to disinfect
Summary of the latest data on best practices for disinfecting, from a Lancet paper: the virus lasts longest — up to seven days — on stainless steel, plastic, and surgical masks.
(tags: covid-19 disinfecting cleaning sars-cov-2 facemasks health)
WHO endorses voluntary patent pool to develop Covid-19 products
The World Health Organization director-general has endorsed the idea of creating a voluntary pool to collect patent rights, regulatory test data, and other information that could be shared for developing drugs, vaccines, and diagnostics. The concept was proposed two weeks ago by Costa Rican government officials amid mounting concerns that some Covid-19 medical products may not be accessible for poorer populations. By establishing a voluntary mechanism under the auspices of the WHO, the goal is to establish a pathway that will attract numerous governments, as well as industry, universities and nonprofit organizations. “I support this proposal, and we are working with Costa Rica to finalize the details,” said WHO Director-General Tedros Adhanom Ghebreyesus in a statement on Monday. “Poorer countries and fragile economies stand to face the biggest shock from this pandemic, and leaving anyone unprotected will only prolong the health crisis and harm economies more. I call on all countries, companies and research institutions to support open data, open science, and open collaboration so that all people can enjoy the benefits of science and research.”
(tags: patents covid-19 who ip medicine pharma science research open-data open-science collaboration)
Private Contact Tracing Protocols Compared: DP-3T and CEN
it’s critically important to prevent the creation of new surveillance infrastructure […] But contact tracing will be a critical part of COVID-19 recovery, particularly in the period after the surge of cases, but before widespread immunity prevents transmission. So it’s been incredibly exciting to see how many people have been working on this problem in a spirit of radical collaboration. Some of these projects are mentioned in our previous post on design tradeoffs in contact tracing systems. At the Zcash Foundation, we’ve been collaborating with existing efforts on the CEN Protocol, originally started as a joint effort between two projects, CoEpi and Covid-Watch. And earlier this week, a group of European academics from eight universities announced a new effort called DP-3T. These protocols are very similar, and it would be great if they could both evolve towards a common standard. To support that goal, this post will compare and contrast the current designs of the DP-3T and CEN protocols.
(tags: contact-tracing protocols crypto covid-19 dp-3t cen security privacy)
The 1700s Plague Cure That Inspired an Uncannily Contemporary Cocktail
Sounds like Green Chartreuse is the closest modern equivalent to Plague Water
(tags: chartreuse cocktails booze plague-waters pandemics epidemics history)
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A behind-the-curtain story on the UK’s disastrous COVID-19 response.
Until March 12, the risk level, set by the government’s top medical advisers on the recommendation of the scientists, remained at “moderate,” suggesting only the possibility of a wider outbreak. “You know, there’s a small little cadre of people in the middle, who absolutely did realise what was going on, and likely to happen,” said John Edmunds, a professor of infectious disease modelling and a key adviser to the government, known for his work on tracking Ebola. Edmunds was among those who did call on the government to elevate the warning level earlier. [….] “I do think there [was] a bit of a worry in terms you don’t want to unnecessarily panic people.” […] Minutes and interviews show Britain was following closely a well-laid plan to fight a flu pandemic – not this deadlier disease.
March 12!! What a staggering screwup.(tags: covid-19 coronavirus fail uk disasters pandemics diseases history)
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a source for science-based mask designs for community makers to combat the spread of COVID-19. It is important that we use the best information possible to help protect ourselves and our communities. The MakerMask designs use latex-free, water-resistant materials that are likely to provide improved protection over cotton and elastic. We need makers/sewists/helpers of all abilities to begin ramping up production to meet community needs.
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an educational twitter thread by virologist @PeterKolchinsky
CCC’s 10 requirements for the evaluation of “Contact Tracing” apps
“Corona apps” are on everyone’s lips as a way to contain the SARS-CoV-2 epidemic. CCC publishes 10 requirements for their evaluation from a technical and societal perspective. Currently, technically supported “contact tracing” is being considered as means to counteract the spread of SARS-CoV-2 in a more targeted manner. The general motivation is to allow greater freedom of movement for the broad spectrum of society by allowing quick tracing and interruption of infection chains. Contacts of infected persons should be alerted more quickly and thus be able to quarantine themselves more quickly. This, in turn, should prevent further infections. A “corona app” could therefore protect neither ourselves nor our contacts: It would be designed to break chains of infection by protecting the contacts of our contacts.
(tags: covid-19 pandemics contact-tracing ccc privacy data-privacy)
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‘The Miura fold (?????, Miura-ori) is a method of folding a flat surface such as a sheet of paper into a smaller area. The fold is named for its inventor, Japanese astrophysicist Koryo Miura.’ (via Robby Kraft)
(tags: via:robby-kraft origami miura-fold miura-ori space folding surfaces paper)
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some important details for iOS/Android interop on BLE COVID-19 contact tracing. bookmarking for possible future reference
(tags: covid-19 ble bluetooth contact-tracing apps ios android interop bugs)
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… a novel public health concept. They were implemented for the first time in China in February, 2020, to tackle the coronavirus disease 2019 (COVID-19) outbreak. The Fangcang shelter hospitals in China were large-scale, temporary hospitals, rapidly built by converting existing public venues, such as stadiums and exhibition centres, into health-care facilities. They served to isolate patients with mild to moderate COVID-19 from their families and communities, while providing medical care, disease monitoring, food, shelter, and social activities.
(tags: fangcangs hospitals covid-19 buildings architecture emergencies china pandemics medicine)
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‘This document has been created to share information across the numerous projects that are working to create mobile apps to help contact tracers fight COVID-19. Many technologists who are designing privacy-preserving apps and tools for this process are new to contact tracing, and want to ensure that their work is solidly grounded in the work that public health professionals are doing around the world. This document aims to collate questions, statistics and experiences to ensure that apps are relevant and well-designed.’
(tags: docs gdocs contact-tracing privacy apps coding tech covid-19 collaboration)
Vitamin D supplementation recommended to help fight COVID-19 in Ireland
‘Epidemiological studies, including several meta-analyses, have shown that people with low vitamin D levels have a higher risk of acute respiratory tract infection and community-acquired pneumonia. While these data do not necessarily infer causality, multiple molecular mechanisms have been identified by which vitamin D deficiency impairs resistance to viral respiratory tract infection. There are also a significant number of studies, including several meta-analyses, which have indicated that vitamin D supplementation may reduce the likelihood of acute respiratory tract infection, and decrease its severity and duration where such infection does occur. These respiratory tract infections may include Covid-19. Proposed Protective Mechanisms against Covid-19: In this regard, vitamin D supplementation has been shown to suppress CD2614, a cell surface receptor which is thought to facilitate entry of the Covid-19 virus into the host cell. There is also good evidence that enhanced vitamin D status may protect against the critical immunological sequelae which are thought to elicit poorer clinical outcome in Covid-19 infection. These include prolonged interferon-gamma response, and persistent interleukin 6 elevation, a negative prognostic indicator in acutely-ill pneumonia patients, including those with Covid-19.’
(tags: covid-19 health medicine vitamins vitamin-d supplements)
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lhl’s giant list of COVID advice. This is exhaustive and well-researched. (via Waxy)
(tags: via:waxy lhl covid-19 health medicine advice self-treatment)
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via Amit Agarwal on Twitter — India’s COVID-19 contact-tracing app, using GPS location and Bluetooth.
(tags: ble bluetooth contact-tracing via:amit-agarwal india apps android ios covid-19)
EC regulations regarding cancelled flights
‘REGULATION (EC) No 261/2004 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 11 February 2004, establishing common rules on compensation and assistance to passengers in the event of denied boarding and of cancellation or long delay of flights, and repealing Regulation (EEC) No 295/91’ This may be handy in the coming months I suspect.
(tags: aviation flights holidays cancellation consumer-rights consumer ec eu)
How they flattened the curve during the 1918 Spanish Flu
How some cities ‘flattened the curve’ during the 1918 flu pandemic Social distancing isn’t a new idea—it saved thousands of American lives during the last great pandemic. Here’s how it worked.
(via Vipul Ved Prakash)(tags: via:vipul covid-19 history coronavirus pandemics flu 1918 social-distancing)
COVID-19 and the NHS—“a national scandal” – The Lancet
Bloody hell, the UK is heading for a disaster. ‘The NHS has been wholly unprepared for this pandemic. It’s impossible to understand why. Based on their modelling of the Wuhan outbreak of COVID-19, Joseph Wu and his colleagues wrote in The Lancet on Jan 31, 2020: “On the present trajectory, 2019-nCoV could be about to become a global epidemic…for health protection within China and internationally…preparedness plans should be readied for deployment at short notice, including securing supply chains of pharmaceuticals, personal protective equipment, hospital supplies, and the necessary human resources to deal with the consequences of a global outbreak of this magnitude.” This warning wasn’t made lightly. It should have been read by the Chief Medical Officer, the Chief Executive Officer of the NHS in England, and the Chief Scientific Adviser. They had a duty to immediately put the NHS and British public on high alert. February should have been used to expand coronavirus testing capacity, ensure the distribution of WHO-approved PPE, and establish training programmes and guidelines to protect NHS staff. They didn’t take any of those actions. The result has been chaos and panic across the NHS. Patients will die unnecessarily. NHS staff will die unnecessarily. It is, indeed, as one health worker wrote last week, “a national scandal”. The gravity of that scandal has yet to be understood.’
(tags: covid-19 government uk disasters nhs the-lancet pandemics ppe scandals)
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Official HSE guidance doc
(tags: hse cocooning social-distancing lockdown quarantine covid-19)
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Yet another privacy-preserving contact tracing app system, this time from a pan-European consortium:
Pan-European Privacy-Preserving Proximity Tracing (PEPP-PT) makes it possible to interrupt new chains of SARS-CoV-2 transmission rapidly and effectively by informing potentially exposed people. We are a large and inclusive European team. We provide standards, technology, and services to countries and developers. We embrace a fully privacy-preserving approach. We build on well-tested, fully implemented proximity measurement and scalable backend service. We enable tracing of infection chains across national borders.
(via Cory)(tags: coronavirus tracing gdpr covid-19 privacy contact-tracing apps europe via:doctorow)
Proprietary reagents are blocking COVID-19 testing worldwide
Workers Solidarity on Twitter: “HSE briefing last night revealed the limit on number of #cornoravirus tests that can be carried out is due to companies keeping the manufacturing process for a key reagent secret” — top twitter thread. Proprietary IP rights over COVID-19 reagents are liable to kill thousands, if not millions. It’s time to put these into the commons for the public good.
(tags: wsm twitter threads hse covid-19 reagents testing chemicals)
Jonas Nart’s COVID19 dashboard
Fantastic dataviz built using Tableau
(tags: tableau dataviz graphs covid-19 dashboards pandemics)
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A petition signed by more than 2,000 doctors, scientists, and professors last week – including the chairman of the Nobel Foundation, Prof Carl-Henrik Heldin – called on the government to introduce more stringent containment measures. “We’re not testing enough, we’re not tracking, we’re not isolating enough – we have let the virus loose,” said Prof Cecilia Söderberg-Nauclér, a virus immunology researcher at the Karolinska Institute. “They are leading us to catastrophe.”
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new paper from the Imperial College COVID-19 epidemiological team: ‘Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe is now experiencing large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, widescale social distancing including local and national lockdowns. In this report, we use a semi-mechanistic Bayesian hierarchical model to attempt to infer the impact of these interventions across 11 European countries. Our methods assume that changes in the reproductive number – a measure of transmission – are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from the deaths observed over time to estimate transmission that occurred several weeks prior, allowing for the time lag between infection and death.’
(tags: covid-19 papers europe uk lockdowns pandemics social-distancing modelling medicine)
Medtronic releases PB560 Ventilator Design and Manufacturing docs
Schematics, manuals, manufacturing docs for the Medtronic PB560 ventilator, released under a permissive license. Awesome stuff. ‘We appreciate your interest in using the design specifications for the Medtronic PB560 ventilator system to help address the shortage of ventilators due to the COVID-19 pandemic. We invite manufacturers, engineers, and other innovators to use these files as inspiration for their own innovations.’
(tags: medtronic ventilators covid-19 specifications hardware manuals medicine)
Notes From the Battlefield March 30, 2020 – SAGES
‘Despite that devastation from the disease still continues, and being too early to draw any definitive conclusions, there are some signs that the slope of COVID-19 new cases in Italy may be starting to slow down. Italian epidemiologists feel it is the result of the strict physical distancing measures. As health care providers, this appears to be the best preventive measure to emphasize and possibly the only intervention currently available to overcome this epidemic.’
(tags: pandemics covid-19 italy medicine social-distancing)
‘Production of 3D printed components for ventilation systems: practical hints’
Notes from the front lines in Italy: ‘The current emergency allows exceptions to the use of not certified medical devices, if it is proved that no certified choices are available and in accordance with the local ethical committee. Furthermore, due to the short time required for the production, it is not possible to run extensive testing campaigns on the components, but each [additive manufacturing] operator must pay attention to the selection of materials and technologies that are suitable for the specific application, considering the risk classification of the components and the operational environment. In the following we summarize the workflow we applied at 3D4Med (http://www.3d4med.eu) – the Clinical 3D Printing Laboratory of San Matteo Hospital in Pavia – and Protolab – its engineering counterpart – to produce some of the requested components, along with some practical examples.’
(tags: 3d-printing emergencies italy covid-19 medicine healthcare 3d4med ventilators cpap)
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‘a Dublin corn merchant clerk who designed the second analytical engine (general-purpose Turing-complete computer) in history. Charles Babbage in 1843 and Ludgate in 1909 designed the only two mechanical analytical engines before the electromechanical analytical engine of Leonardo Torres y Quevedo of 1920 and its few successors, and the six first-generation electronic analytical engines of 1949. Working alone, Ludgate designed an analytical engine while unaware of Babbage’s designs.’
(tags: history ireland analytical-engines dublin computers hardware)
What happened with the UK’s “herd immunity” COVID-19 strategy
“I’ll tell you what happened in the UK. Over the past decade, eminent figures in public health developed complex models that would help inform the UK response to a pandemic. The response plan would allow slow spread through a population and a number of deaths that would be deemed acceptable in relation to low economic impact. Timing of population measures such as social distancing would be taken, not early, but at a times deemed to have maximal psychological impact. Measures would be taken that could protect the most vulnerable, and most of the people who got the virus would hopefully survive. Herd immunity would beneficially emerge at the end of this, and restrictions could relax. This was a ground-breaking approach compared to suppressing epidemics. It was an approach that could revolutionise the way we handled epidemics. Complex modelling is a new science, and this was cutting edge. But a model is only ever as good as the assumptions you build it upon. The UK plan was based on models with an assumption that any new pandemic would be like an old one, like flu. And it also carried a huge flaw – there was no accounting for the highly significant variables of ventilators and critical care beds that are key to maintaining higher survival numbers.” Amazing. The sheer arrogance and hubris of assuming the model was right! Somebody will have to pay for this, it’s shocking.
(tags: herd-immunity hubris arrogance covid-19 uk uk-politics pandemics models data-science epidemiology)
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This is very clever:
New rules for old games! The Board Game Remix Kit is a collection of tips, tweaks, reimaginings and completely new games that you can play with the board and pieces from games you might already own: Monopoly, Cluedo, Scrabble and Trivial Pursuit.
(via Macker)(tags: via:macker games boardgames trivial-pursuit cluedo scrabble monopoly remixing)
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“a personal thread about the experience of working at the intersection of infectious disease modeling and the study of misinformation during the worst pandemic in a century:
the fight against misinformation is not merely a scientific communication issue. It’s a vital public health necessity. […] In all the years of studying infectious disease and planning for this day, I never dreamed that when it came I’d be opposed by my own federal government, a non-trivial fraction of my fellow citizens, and as yet undetermined fraction of hostile foreign actors.
(tags: disinformation misinformation propaganda trump covid-19 scicomm science public-health social-media twitter pandemics)
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From this twitter thread: https://twitter.com/jeremyphoward/status/1242894378441506816
(tags: facemasks covid-19 diseases transmission infection ppe)
Maciej Ceglowski asks for a massive surveillance program to defeat COVID-19.
However, as I mentioned on twitter — there IS an alternative, privacy-preserving approach, which is what is being done in Singapore with their TraceTogether app.
In summary, everyone carries a phone running an app which has an anonymized a random ID, scans local Bluetooth periodically for other people’s apps with their random IDs, and records them locally (not uploading to a server). If you find out you have COVID-19 you then trigger an upload of your contact history to a central server. That server then broadcasts out the list of IDs, and everyone you’ve been in contact with will then get a ping on their app to get tested, self-isolate, etc.
No central surveillance, no creepy big brother watching your location.
My pinboard has a few more write-ups on basically the same idea from various other places, including MIT. This is similar to what China’s app does, but (as far as I can tell) with more privacy.
It looks like the Singaporean government digital services team behind TraceTogether is putting together an open source version, at Bluetrace.io.
IMO we have to do this or we will never get out of COVID-19 lockdown before 2021. I am massively in favour of adopting this approach in Ireland and across the world.
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the official ArcGIS dashboard for Ireland’s COVID-19 response
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‘a style of software distribution similar to Postcardware, distributed by the author on the condition that users buy the author a tree.’
(tags: treeware oss open-source software licensing licenses)
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‘At this point, you’ve probably heard a ton about chloroquine and hydroxychloroquine and how they may be effective in treating COVID-19. I wanted to tell you about a different molecule that’s getting less attention but may have good potential – Remdesivir.’ How Remdesivir works to inhibit viral replication. Fascinating stuff
(tags: remdesivir viruses science chemistry medicine drugs covid-19 treatment)
Professor Sara Sawyer’s Decon Station Instructions
If you are sheltering-in-place and feel that you need to take extra precautions for a high-risk member of your household, you can decontaminate things before they come into your house. Read on if you want to know how. This post addresses common questions that I am getting about mail, fruits, groceries, etc. The following advice is my own, tailored for this specific situation, and is the best advice I can come up with based on the extensive biosafety training that I have received as a research scientist who works with human viruses.
(via Pam)(tags: biosafety viruses covid-19 decontamination sterilising sterilizing health via:pam)
We Need A Massive Surveillance Program (Idle Words)
The most troubling change this project entails is giving access to sensitive location data across the entire population to a government agency. Of course that is scary, especially given the track record of the Trump administration. The data collection would also need to be coercive (that is, no one should be able to opt out of it, short of refusing to carry a cell phone). […] But the public health potential of commandeering surveillance advertising is so great that we can’t dismiss it out of hand. I am a privacy activist, typing this through gritted teeth, but I am also a human being like you, watching a global calamity unfold around us. What is the point of building this surveillance architecture if we can’t use it to save lives in a scary emergency like this one?
+1000.(tags: surveillance advertising contact-tracing contact-tracking tracking location smartphones covid-19 pandemics\)
What’s the Evidence on Face Masks? What You Heard Was Probably Wrong
According to research on the SARS epidemic, face masks were the most consistently effective intervention for reducing the contraction and spread of SARS. In a Cochrane Review on the subject, 6 out of 7 studies showed that face masks (surgical and N95) offered significant protection against SARS. Hand washing was also very effective, supported by 4 out of 7 studies in a multivariate analysis. Although most of the studies in the Cochrane Review were on medical workers in a hospital setting, one study followed community transmission of SARS in Beijing. It found that consistently wearing a mask in public was associated with a 70% reduction in risk of catching SARS. Additionally, the authors of the paper noted that most people in the community wore simple surgical masks, not N95 respirators.
(tags: cochrane-reviews health medicine face-masks covid-19 germs masks transmission sars)
Anosmia could be a symptom of COVID-19
ENT UK on Twitter: “There is the potential to reduce COVID-19 transmission by requesting that individuals with new onset of anosmia self-isolate. A lost sense of smell as marker of COVID-19 infection…”
good twitter thread roundup on smartphone contract-tracing apps
Juliana Couras on Twitter:
Mobile contact tracing for #COVID19 A thread with multiple references about what is being done in the world, what has already been done and what is not being done in the European Union.
(tags: contact-tracing tracking apps smartphone mobile eu)
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The Singapore government’s version of the anonymised-ids-with-BLE local contact tracing app for COVID-19. This has a fancy video! (via Dorothy)
(tags: contact-tracing singapore contacts ble bluetooth covid-19 pandemics)
Rapidly manufactured ventilator system specification – GOV.UK
This is a specification of the minimally (and some preferred options) clinically acceptable ventilator to be used in UK hospitals during the current SARS-CoV2 outbreak. It sets out the clinical requirements based on the consensus of what is ‘minimally acceptable’ performance in the opinion of the anaesthesia and intensive care medicine professionals and medical device regulators. It is for devices, which are most likely to confer therapeutic benefit on a patient suffering with ARDS caused by COVID-19, used in the initial care of patients requiring urgent ventilation. A ventilator with lower specifications than this is likely to provide no clinical benefit and might lead to increased harm, which would be unacceptable for clinicians and would, therefore, not gain regulatory approval.
(tags: disease covid-19 crowdsourcing hospitals medicine 3d-printing ventilators)
Open Source COVID19: Our Intent, Needs, and Your Role – Google Docs
‘PPE (Personal Protection Equipment) is critical to the protection of healthcare workers, acting as a barrier and therefore controlling exposure to COVID-19. Some of the most fundamental items comprising PPE include gloves, goggles, surgical masks, respirators, protective gowns, and disinfectant. Many of these crucial PPE items are now in short supply due to interruptions in the supply chain, and also from the massive demand as the number of patients infected continues to grow exponentially. Numerous medical devices are required to treat the COVID-19 patient and will also fall into short supply (e.g. ventilators). Shortages of necessary PPE and medical devices will continue to pose a significant problem for healthcare workers and patients around the globe.’
(tags: open-source covid-19 ppe medicine 3d-printing makers volunteers)
Coronavirus: Deaconess asks public to sew medical face masks
Shortages of specialized masks moved federal health officials this month to liberalize their recommendations about which face protection front line health-care workers should use to ward off the highly contagious disease stemming from coronavirus. “Prior to modern disposable masks, washable fabric masks were standard use for hospitals,” said Dawn Rogers, MSN, RN, FNP-C, Patient Safety & Infection Prevention Office in a release to media. “We will be able to sterilize these masks and use them repeatedly as needed. While it’s less than ideal, we want to do our best to protect our staff and patients during this pandemic.”
(tags: facemasks covid-19 shortages pandemics medicine emergency)
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Good wrap-up on the Open Source Ventilator project
(tags: ventilators covid-19 medicine open-source 3d-printing emergencies pandemics)
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This is the report from the Imperial College COVID-19 Response Team which, it seems, *finally* got the UK and US to realise that this is going to require a massive social-distancing and lockdown to avoid killing millions. The graph on the last page in particular is a kicker.
(tags: covid-19 health pandemics epidemics medicine social-distancing imperial-college uk)
Specifications for simple open source mechanical ventilator
from Julian Botta, Johns Hopkins Emergency Medicine Resident PGY-3 , Twitter: @julianbotta ‘This is a living document intended to give non-clinicians/non-respiratory therapists an idea of key ventilator features and one proposed simplified design. I encourage other healthcare professionals who are very familiar with ventilators and their use to give me feedback using the comments feature to improve these specifications.’
(tags: specifications ventilators open-source covid-19 medicine hardware)
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This is absolutely appalling behaviour. People are dying — free the blueprints!
A medical device manufacturer has threatened to sue a group of volunteers in Italy that 3D printed a valve used for life-saving coronavirus treatments. The valve typically costs about $11,000 from the medical device manufacturer, but the volunteers were able to print replicas for about $1 (via Techdirt). A hospital in Italy was in need of the valves after running out while treating patients for COVID-19. The hospital’s usual supplier said they could not make the valves in time to treat the patients, according to Metro. That launched a search for a way to 3D print a replica part, and Cristian Fracassi and Alessandro Ramaioli, who work at Italian startup Isinnova, offered their company’s printer for the job, reports Business Insider. However, when the pair asked the manufacturer of the valves for blueprints they could use to print replicas, the company declined and threatened to sue for patent infringement, according to Business Insider Italia. Fracassi and Ramaioli moved ahead anyway by measuring the valves and 3D printing three different versions of them.
(tags: covid-19 ip patents italy 3d-printing hardware ip-rights law)
Open Source COVID19 Medical Supplies | Facebook
A very active group of makers sharing designs and plans for open source face masks, ventilators, etc.
(tags: covid-19 open-source facebook medicine face-masks ppe hardware 3d-printing)
Global MediXchange for Combating COVID-19 – Alibaba Cloud
The Jack Ma Foundation and Alibaba Foundation, together with the First Affiliated Hospital of Zhejiang University, jointly established the Global MediXchange for Combating COVID-19 (GMCC) programme, with the support of Alibaba Cloud Intelligence and Alibaba Health, to help combat the global outbreak of the novel coronavirus, COVID-19. This platform was established to facilitate continued communication and collaboration across borders, as well as to provide the necessary computing capabilities and data intelligence to empower pivotal research efforts. The platform can provide frontline medical teams with the necessary communication channels to share practical experience and information about fighting the pandemic.
They’ve put together a handbook of COVID-19 preventation and treatment, based on the Chinese experience.(tags: treatment medical covid-19 china jack-ma alibaba medicine health)
Neil Jackman’s favourite places in Ireland, county by county
Fantastic list of ancient sites, from the archaeologist, podcaster and author:
It’s my first #StPatricksDay as an Irish citizen. There may be fewer parades & pints, but seeing the solidarity kindness & meitheal has made me love this country even more. I’ve been lucky to see a lot of this island over the last 21 years. Here’s some favourite places by county
(tags: ireland archaeology history paleolithic neolithic neil-jackman)
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Another privacy-preserving COVID-19 contact-tracing app, this one from MIT:
The news: An app that tracks where you have been and who you have crossed paths with—and then shares this personal data with other users in a privacy-preserving way—could help curb the spread of Covid-19, says Ramesh Raskar at the MIT Media Lab, who leads the team behind it. Called Private Kit: Safe Paths, the free and open-source app was developed by people at MIT and Harvard, as well as software engineers at companies such as Facebook and Uber, who worked on it in their free time.
(tags: mit contact-tracing privacy apps smartphones android ios covid-19 epidemics pandemics)
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China have enforced a variety of measures aimed at social distancing including lockdowns, restrictions on movement and cordon-sanitaires, as well as the Alipay Health Code smartphone application (an add on to the WeChat app system) now adopted in over 200 cities and by 90% of individuals in one Chinese province. A separate system has been implemented in South Korea, and both have come under public scrutiny over issues of data protection and privacy. We sought to design a broadly acceptable version of this platform, leveraging commonly used smartphone functionality. This system is currently in development, and based on a very simple algorithm, that we show through mathematical modelling will enable public health agencies to prevent a COVID-19 epidemic while minimizing social and economic disruption.
This also introduced me to a new concept, “herd protection”, which is described as “Ronald Ross’s great discovery: you don’t need to stop all infections to stop an epidemic, you need to get and keep R<1.”(tags: papers toread covid-19 social-distancing movement cordons quarantine epidemics pandemics china smartphones location herd-protection)
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COVID-19 has a relatively long infectious incubation period, averaging five days but potentially up to two weeks, during which there may be asymptomatic transmission. In other words, there may be a period of time in which people who carry COVID-19 don’t necessarily show symptoms and may not even realise they are infected, but are still capable of infecting others. This makes it harder for health professionals and epidemiologists to trace who has come into contact with infected persons (‘contact tracing’), which in turn makes the virus more difficult to effectively contain. Many people, however, now carry GPS-enabled smartphones which already track their location over time – most mapping apps, like Google Maps or MapQuest, already collect this data by default. We believe that this information could be used to rapidly and automatically perform a type of contact tracing, helping limit the spread of COVID-19 and other infectious diseases. These phones are usually also Bluetooth-enabled, allowing them to track and record which other phones they’re in proximity to. We believe that together, these two pieces of information can be used to inform and empower our users in a range of ways. Firstly, we can generate heatmaps of high-risk areas from demographic data, known cases, and epidemiological modelling, allowing users to adjust their behaviour accordingly. Secondly, we can use Bluetooth connections between users to enact cryptographically secure contact tracing and alerting them if we learn that they have been exposed to COVID-19, without revealing the identities or infection status of any other users.
(tags: covid-19 contact-tracing apps android ios smartphones privacy location)
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Chris Hayes on Twitter: “A doctor I spoke to today called this the “paradox of preparation” and it’s the key dynamic in all this. The only way to get ahead of the curve is to take actions that *at the time* seem like overreactions, eg: Japan closing all schools for a month with very few confirmed cases”. See also the Millennium Bug, and what’s currently (failing) to happen with climate change. This is a great concept, and good to have a name for it.
(tags: millennium-bug paradox-of-preparation covid-19 pandemics preparation)
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We are working on medical devices, such as open source ventilators, to have a fast and easy solution that can be reproduced and assembled locally worldwide. If you have any skills that you consider might help, join the Helpful Engineering group.
(tags: health medicine ventilators devices hardware design engineering covid-19)
If You Go Out Now, You Might Feel Guilty Later. I Do.
Others have written eloquently of the importance of social distancing. But the scale and scope of this is something every single one of us is having to grapple with. Things that felt like a dumb overreaction a week ago — “Canceling vacation? Really?” — now feel hilariously quaint. Or if they don’t, they will soon. If you still can’t quite believe that you need to take these measures, or that people’s lives may hang in the balance, or if you still think that it will be okay because the numbers where you live aren’t so bad yet, I am not here to scold you. But if you do go out, and you do risk infecting somebody else, you may feel the guilt — and the fear — that I’m struggling with right now. Trust me, it’s not worth it.
(tags: social-distancing covid-19 isolation quarantine infection pandemics)
COVID-19 may be infectious for 3 days prior to symptoms becoming noticeable
Examination of 124 Wuhan cases with clear contact history showed incubation period of 5 days (range: 1-11 days). It found that 73% of secondary cases were infected *before* onset of symptoms in first case. It estimated the mismatch period to be 3 days.
This is bad news for controlling the spread based on testing only people with symptoms.Cut / Fold Templates for paper mechanisms
Origami wizard Robby Kraft says “this site comes up in conversations 1/mo on average. if you need some suggestions: #1 flexagon; #4 auxetic (awesome, a little complex); #6 bistable (so much untapped potential, i believe); #14 flasher; all the optical illusion ones”
(tags: geometry origami paper templates pdf todo kids papercraft making crafting)
COVID-19 Notes from UCSF Expert panel – March 10
Superb set of points from a star-studded panel:
Joe DeRisi: UCSF’s top infectious disease researcher. Co-president of ChanZuckerberg BioHub (a JV involving UCSF / Berkeley / Stanford). Co-inventor of the chip used in SARS epidemic. Emily Crawford: COVID task force director. Focused on diagnostics. Cristina Tato: Rapid Response Director. Immunologist. Patrick Ayescue: Leading outbreak response and surveillance. Epidemiologist. Chaz Langelier: UCSF Infectious Disease doc.
How to crossplay Minecraft on PS4 with Nintendo Switch, Xbox One and PC
The killer app for kids in COVID-19 lockdown!
However, while the new snapshot is extremely neat, so too is the ability for PlayStation 4 players to crossplay with mates on Nintendo Switch, PC and Xbox One. This feature was introduced to Sony’s version at the tail-end of last year, and in this article you’ll find out how to play with your mates on other devices.
educational/maths resources for your children at home
Another good set of links for the COVID-19 lockdown
Health expert brands UK’s coronavirus response ‘pathetic’
There were no strategies for protecting the vulnerable and there had been a failure to engage the public. “We have a superficial prime minister who has got no grasp of public health,” Ashton said. “Our lot are behaving like 19th-century colonialists playing a five-day game of cricket. “This virus will find the weak points. You can’t just plan this from an office in Whitehall. It’s pathetic. The government doesn’t seem to understand classic public health. You need to be out and about. You need to get your hands dirty – though preferably gloved and using frequent gel,” he said.
(tags: coronavirus covid-19 guardian uk health medicine herd-immunity)
The Dismantled State Takes on a Pandemic | The New Republic
It didn’t occur to the right that a more terrifying series of words than “I’m from the government, and I’m here to help” would turn out to be “I’m from the government, and I guess I anticipated that the private sector would have engaged.”
(tags: cdc coronavirus covid19 politics republicans us-politics pandemics government)
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‘Program to decode radio transmissions from devices on the ISM bands (and other frequencies)’. Turns out a staggering amount of devices these days broadcast their signals on 433Hz and can be picked up with cheap SDR gear…
A New Dublin Group Looks to Deepen What We Know About Plastic | Dublin Inquirer
Precious Plastic Dublin is up and running!
(tags: precious-plastic recycling plastic making dublin ireland)
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good tip from Nelson on a decent TV – “excellent picture quality for the price. It’s quite cheap even for an LCD TV, and definitely way way cheaper than an OLED.” I need to upgrade one here so this is useful
(tags: toget tvs television hardware home)
Online Resources For Isolation
Now that Ireland’s schools are to be closed, I’m going to need this :(
Here we have it. My free ‘what the heck do I do with my kids while they are at home in isolation’ guide to online resources. Bookmark this; in all likelihood we are all going to need it. Just to mention; don’t unleash your kids at all of this in the first day or even days. There is loads for them to work their way through. If you let them do everything all at once they will become overwhelmed and disinterested.
(tags: education kids ireland self-isolation)
How to Utilise Twinkl during the Coronavirus Shutdown: A Guide for Schools
Another “what to do with the kids during self-isolation” resource, used by our kids’ school apparently
(tags: kids education self-isolation covid-19)
Don’t Panic: The comprehensive Ars Technica guide to the coronavirus
Ars Technica are doing a good job maintaining a FAQ list here
Coronavirus: Why You Must Act Now – Tomas Pueyo – Medium
some good estimates of current COVID-19 epidemiology
(tags: coronavirus covid19 healthcare epidemiology diseases statistics)
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Good to know. This is testing against a H1N1 flu virus, but hopefully applies for COVID-19 too.
… Rapid treatment of the virus with hot water had little effect on the virus, reducing the titre by around two-fold, but prolonged incubation at 55°C abolished detectable infectivity. However, the addition of any of 1% bleach, 50% and 10% malt vinegar and 1%, 0.1% and 0.01% washing up liquid were all effective at rapidly reducing viable virus below the limit of detection, while a low concentration of vinegar (1%) was no more effective than hot water alone (Figure 1A). In contrast to the plaque assay results, most agents were ineffective at reducing the number of detectable genome copies as determined by RT-PCR, with only bleach having a significant effect (Figure 2A). The data for the plaque assays and RT-PCR assays are compiled in Tables S1 and S2. Thus, while a strong oxidizing agent such as bleach is effective at reducing both genome detection and virus infectivity, low pH and detergent are equally efficacious virucidal agents. These results also indicate that whilst vinegar and detergent disrupt the viral envelope proteins reducing infectivity, only bleach disrupts the viral genome.
(Via Damien)(tags: via:damien health cleaning covid-19 washing)
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supposedly this is about “tuning in the era of containers”, but really it’s more about which metrics are usable for GC tuning with the newish java G1 garbage collector.
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Unpleasant stuff:
A week ago, Italy had so few cases of corona that it could give each stricken patient high-quality care. Today, some hospitals are so overwhelmed that they simply cannot treat every patient. They are starting to do wartime triage. Here’s the guidance for that.
(tags: italy healthcare safety medicine covid-19 emergencies triage hospitals)
Trees on commercial UK plantations ‘not helping climate crisis’
“There is no point growing a lot of fast-growing conifers with the logic that they sequester carbon quickly if they then go into a paper mill because all that carbon will be lost to the atmosphere within a few years,” said Thomas Lancaster, head of UK land policy at the Royal Society for the Protection of Birds (RSPB), which commissioned the report. “We should not be justifying non-native forestry on carbon grounds if it’s not being used as a long-term carbon store.”
Absolutely. Commercial forestry is not going to help address the climate change problem.(tags: business economics environment climate-change forestry trees coillte)
low-cost mechanical ventilator prototype
a team of students from MIT has devised a better way to keep patients breathing in places that lack standard mechanical ventilators, or during times of emergency such as pandemics or natural disasters, when normal hospital resources may be overextended. They have designed a system that uses the same widely available manual pump — the same type used for the farmer in India. The new system encases the pump in a plastic box with a battery, motor and controls to take the place of the manual compression process.
This article from 2010 notes ‘a U.S. government study in 2005 found that in a worst-case pandemic scenario, this country alone might need more than 700,000 mechanical ventilators, while only 100,000 are now in use.’(tags: ventilators covid-19 breathing healthcare hardware mit ambu-bag)
Testimony of a surgeon working in Bergamo, in the heart of Italy’s coronavirus outbreak : medicine
Terrifying:
After thinking for a long time if and what to write about what’s happening here, I felt that silence was not responsible. I will therefore try to convey to lay-people, those who are more distant from our reality, what we are experiencing in Bergamo during these Covid-19 pandemic days. I understand the need not to panic, but when the message of the danger of what is happening is not out, and I still see people ignoring the recommendations and people who gather together complaining that they cannot go to the gym or play soccer tournaments, I shiver. I also understand the economic damage and I am also worried about that. After this epidemic, it will be hard to start over.
(tags: viral reddit bergamo healthcare covid-19 epidemics medicine)
Nextstrain / narratives / ncov / sit-rep / 2020-03-05
This is an amazing piece of data — phylogenetic analysis of the COVID-19 epidemic as it spreads across the globe. ‘The following pages contain analysis performed using Nextstrain. Scrolling through the left-hand sidebar will reveal paragraphs of text with a corresponding visualization of the genomic data on the right-hand side. To have full genomes of a novel and large RNA virus this quickly is a remarkable achievement. These analyses have been made possible by the rapid and open sharing of genomic data and interpretations by scientists all around the world (see the final slide for a visualization of sequencing authorship).’
(tags: genetics phylogenetics nextstrain covid-19 diseases epidemics viruses)
We’re learning a lot about the coronavirus. It will help us assess risk
Early studies on Covid-19 suggest people who have contracted the coronavirus are emitting, or “shedding,” infectious viruses very early on — in fact sometimes even before they develop symptoms. “We do know from shedding studies that people can shed in the pre-symptomatic phase,” Van Kerkhove said, adding that while the data are still preliminary “it seems that people shed more in the early phases rather than the late phases of disease.”
…also: ‘This week the WHO said the case fatality ratio currently looks like 3.4% — which is not a reassuring number.’(tags: diseases coronavirus covid-19 health pandemics)
Internet Book of Critical Care (IBCC) on COVID-19
Detailed info on COVID-19 diagnosis and treatment for healthcare professionals
(tags: medicine covid-19 coronavirus diseases pandemics)
The Bulletin of the Atomic Scientists on nuclear power plant risks
The Japan Center for Economic Research, a source sympathetic to nuclear power, recently put the long-term costs of the 2011 Fukushima accident as about $750 billion. […] The main public risk of nuclear power plants comes from rare but devastating nuclear accidents. Because data on such accidents is sparse, the probability of their occurrence has to be calculated on the basis of a model, rather than obtained from experience. Moreover, the extent of an accident and its monetary consequences are postulated on the basis of models that are limited by analysts’ imagination. Who would have imagined, for example, that the Fukushima accident would involve several reactors? Or that Japan would subsequently shut down all its other nuclear power plants?
(tags: fukushima nuclear nukes power risks danger probability insurance nuclear-power reactors)
k-Nearest Neighbor (k-NN) similarity search engine with Amazon Elasticsearch
Well, that’s handy:
Amazon Elasticsearch Service now offers k-Nearest Neighbor (k-NN) search which can enhance search by similarity use cases like product recommendations, fraud detection, and image, video and semantic document retrieval. Built using the lightweight and efficient Non-Metric Space Library (NMSLIB), k-NN enables high scale, low latency nearest neighbor search on billions of documents across thousands of dimensions with the same ease as running any regular Elasticsearch query.
(tags: elasticsearch aws knn algorithms similarity searching search nmslib)
The history of leaded gasoline is nuts
It is frankly shocking that this was ignored for so long! “The history of leaded gasoline is nuts. Scientists warned it was poison, the factory where it was made was making workers loopy, but GM/Standard Oil enlisted the surgeon general to convince everyone it was safe and rejected alternatives. Massive public harm resulted.” “A Yale physiologist named Yandell Henderson had tested tetraethyl lead as a potential nerve agent during WWI, and when asked his thoughts on putting it into gasoline, he reacted with alarm. ‘Widespread lead poisoning was almost certain to result.’ Later he deemed it the ‘single greatest question in the field of public health that has ever faced the American public.'”
(tags: gasoline petrol lead health poisoning healthcare yandell-henderson)
Numbers Every Programmer Should Know, By Year
interactively explore how Jeff Dean’s “Numbers Every Programmer Should Know” have changed over time (via Kishore Gopalakrishna)
(tags: memory latency hardware history jeff-dean latencies speed performance)
When Bloom filters don’t bloom
A good exploration into modern CPU/memory performance behaviour, and profiling same on Linux using “perf stat -d” and “google-perftools”:
Modern CPUs are really good at sequential memory access when it’s possible to predict memory fetch patterns (see Cache prefetching). Random memory access on the other hand is very costly. Advanced data structures are very interesting, but beware. Modern computers require cache-optimized algorithms. When working with large datasets, not fitting L3, prefer optimizing for reduced number loads, over optimizing the amount of memory used. I guess it’s fair to say that Bloom filters are great, as long as they fit into the L3 cache. The moment this assumption is broken, they are terrible. This is not news, Bloom filters optimize for memory usage, not for memory access. For example, see the Cuckoo Filters paper.
(tags: cloudflare bloom-filters performance data-structures cpu cache l3 hashing perf perftools)
Connectivity at the origins of domain specificity in the cortical face and place networks | PNAS
Wow, this is cool — babies are born with some “pre-wired” visual connectivity networks, specifically for faces and scenes:
Where does knowledge come from? We addressed this classic question using the test cases of the cortical face and scene networks: two well-studied examples of specialized “knowledge” systems in the adult brain. We found that neonates already show domain-specific patterns of functional connectivity between regions that will later develop full-blown face and scene selectivity. Furthermore, the proto face network showed stronger functional connectivity with foveal than with peripheral primary visual cortex, while the proto scene network showed the opposite pattern, revealing that these networks already receive differential visual inputs. Our findings support the hypothesis that innate connectivity precedes the emergence of domain-specific function in cortex, shedding new light on the age-old question of the origins of human knowledge.
(tags: brains vision babies knowledge learning science biology)
Ciarán Murray on Twitter – another Coronavirus thread – estimating the COVID-19 case fatality rate
‘on the basis of what we can learn from the very unfortunate experiment that was the Diamond Princess, the coronavirus is probably at most 13x more lethal than the flu and likely a lot less lethal – probably closer to 5x more lethal (.3% CFR).’
(tags: cfr diseases covid-19 coronavirus medicine)
Coronavirus in China: The most important lessons from China’s Covid-19 response – Vox
Here, again, is where I’ve seen things starting to break down. What I’ve been told is if you think you’ve been exposed and have a fever, call your [general practitioner]. We’ve got to be better than that. If we are going to use our GPs — do they have an emergency line where you can get through? Do they know what to do? In China, they have set up a giant network of fever hospitals. In some areas, a team can go to you and swab you and have an answer for you in four to seven hours. But you’ve got to be set up — speed is everything.
(tags: covid19 coronavirus china hospitals healthcare medicine pandemics)