Links for 2020-05-20

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Links for 2020-05-19

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Links for 2020-05-18

  • ECDC COVID-19 Contact Tracing Guidelines

    Current guidelines for contact tracing and infection control of COVID-19 in the EU. Good data, with sources!, on what’s recommended here (although of course each country can make their own guidelines).

    (tags: covid-19 pandemics contact-tracing eu medicine)

  • An open letter to software engineers criticizing Neil Ferguson’s epidemics simulation code

    the main message of this letter is something different: it’s about your role in this story. That’s of course a collective you, not you the individual reading this letter. It’s you, the software engineering community, that is responsible for tools like C++ that look as if they were designed for shooting yourself in the foot. It’s also you, the software engineering community, that has made no effort to warn the non-expert public of the dangers of these tools. Sure, you have been discussing these dangers internally, even a lot. But to outsiders, such as computational scientists looking for implementation tools for their models, these discussions are hard to find and hard to understand. There are lots of tutorials teaching C++ to novices, but I have yet to see a single one that starts with a clear warning about the dangers. You know, the kind of warning that every instruction manual for a microwave oven starts with: don’t use this to dry your dog after a bath. A clear message saying “Unless you are willing to train for many years to become a software engineer yourself, this tool is not for you.”

    (tags: software coding engineering science teaching c++)

  • The ‘lockdown sceptics’ want a culture war, with experts as the enemy | Coronavirus outbreak | The Guardian

    in the comment sections of some of the rightwing press, a new, virulent strain of Covid-19 scepticism has emerged that is the precise opposite of journalism. Rather than holding power to account, it distorts and bends reality to serve elite interests – and to warp public debate. In the pages of the Daily Telegraph, the Spectator and other outlets, Britain’s contemporary “lockdown sceptics” have dedicated themselves to a singular cause: proving that the UK response to coronavirus has been a massive, hysterical overreaction. “Lift the lockdown” is their cogito ergo sum; Sweden their promised land.

    (tags: lockdown uk politics brexit experts daily-telegraph spectator right-wing covid-19 sceptics libertarians contrarians culture-war)

  • MyDIY

    Dublin online supplier of DIY equipment and parts, apparently decent enough. Free shipping for orders over 50 Euro

    (tags: diy building construction home dublin ireland)

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Links for 2020-05-14

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Links for 2020-05-13

  • An evidence summary of Paediatric COVID-19 literature

    ‘This post is a rapid literature review of pertinent paediatric literature regarding COVID-19 disease. We are proud to have joined forces with the UK Royal College of Paediatrics and Child Health to provide systematic search, and selected reviews of all the COVID-19 literature relevant to children and young people. Here we present the top 10 papers from each category (Paediatric clinical cases, Epidemiology and transmission, and Neonates). At the top is an Executive summary followed by all New and noteworthy studies.’

    (tags: covid-19 epidemiology diseases transmission school kids children)

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Links for 2020-05-12

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Links for 2020-05-11

  • The Risks – Know Them – Avoid Them

    Informative blog post summarising the dangers of enclosed spaces with a high density of people and poor air circulation in spreading COVID-19:

    Ignoring the terrible outbreaks in nursing homes, we find that the biggest outbreaks are in prisons, religious ceremonies, and workplaces, such a meat packing facilities and call centers. Any environment that is enclosed, with poor air circulation and high density of people, spells trouble. [….] Basically, as the work closures are loosened, and we start to venture out more, possibly even resuming in-office activities, you need to look at your environment and make judgments. How many people are here, how much airflow is there around me, and how long will I be in this environment. If you are in an open floorplan office, you really need critically assess the risk (volume, people, and airflow). If you are in a job that requires face-to-face talking or even worse, yelling, you need to assess the risk. If I am outside, and I walk past someone, remember it is “dose and time” needed for infection. You would have to be in their airstream for 5+ minutes for a chance of infection. While joggers may be releasing more virus due to deep breathing, remember the exposure time is also less due to their speed.

    (tags: covid-19 health viruses infection epidemiology diseases work)

  • ‘Finally, a virus got me.’ Scientist who fought Ebola and HIV reflects on facing death from COVID-19

    Dr. Peter Piot reflects on his bout with COVID-19:

    ‘Many people think COVID-19 kills 1% of patients, and the rest get away with some flulike symptoms. But the story gets more complicated. Many people will be left with chronic kidney and heart problems. Even their neural system is disrupted. There will be hundreds of thousands of people worldwide, possibly more, who will need treatments such as renal dialysis for the rest of their lives.’

    (tags: covid-19 cytokine-storms immunology health diseases peter-piot)

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Links for 2020-05-08

  • Universal basic income seems to improve employment and well-being | New Scientist

    The world’s most robust study of universal basic income has concluded that it boosts recipients’ mental and financial well-being, as well as modestly improving employment. Finland ran a two-year universal basic income study in 2017 and 2018, during which the government gave 2000 unemployed people aged between 25 and 58 monthly payments with no strings attached. The payments of €560 per month weren’t means tested and were unconditional, so they weren’t reduced if an individual got a job or later had a pay rise.

    (tags: finland ubi dole unemployment society money life)

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Links for 2020-05-07

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Links for 2020-05-06

  • COVID-19 immunity passports and vaccination certificates: scientific, equitable, and legal challenges – The Lancet

    Caution is warranted about how population level serology studies and individual tests are used. It is not yet established whether the presence of detectable antibodies to SARS-CoV-2 confers immunity to further infection in humans and, if so, what amount of antibody is needed for protection or how long any such immunity lasts.3 Data from sufficiently representative serological studies will be important for understanding the proportion of a population that has been infected with SARS-CoV-2. These data might inform decisions to ease physical distancing restrictions at the community level, provided that they are used in combination with other public health approaches.5 The use of seroprevalence data to inform policy making will depend on the accuracy and reliability of tests, particularly the number of false-positive and false-negative results, and requires further validation.6 At the individual level, this reliability could have public health ramifications: a false-positive result might lead to an individual changing their behaviour despite still being susceptible to infection, potentially becoming infected, and unknowingly transmitting the virus to others. Individual-targeted policies predicated on antibody testing, such as immunity passports, are not only impractical given these current gaps in knowledge and technical limitations, but also pose considerable equitable and legal concerns, even if such limitations are rectified.

    (tags: immunity covid-19 future society vaccination)

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Links for 2020-05-05

  • Face Masks for the General Public | Royal Society DELVE Initiative

    Face masks could offer an important tool for contributing to the management of community transmission of Covid19 within the general population. Evidence supporting their potential effectiveness comes from analysis of: (1) the incidence of asymptomatic and pre-symptomatic transmission; (2) the role of respiratory droplets in transmission, which can travel as far as 1-2 meters; and (3) studies of the use of homemade and surgical masks to reduce droplet spread. Our analysis suggests that their use could reduce onward transmission by asymptomatic and pre-symptomatic wearers if widely used in situations where physical distancing is not possible or predictable, contrasting to the standard use of masks for the protection of wearers. If correctly used on this basis, face masks, including homemade cloth masks, can contribute to reducing viral transmission.

    (tags: facemasks masks health covid-19 uk infection)

  • Tim Bray: Bye, Amazon

    This takes a lot of guts, I’m impressed:

    May 1st was my last day as a VP and Distinguished Engineer at Amazon Web Services, after five years and five months of rewarding fun. I quit in dismay at Amazon firing whistleblowers who were making noise about warehouse employees frightened of Covid-19.

    (tags: amazon aws ethics tim-bray covid-19 pandemics health workers-rights taking-a-stand)

  • 7 Upper Back Stretches For Pain Relief – YouTube

    recommendation from Damien Mulley — useful with my current shit homeworking setup

    (tags: wfh exercises back health stretches posture ergonomics via:mulley)

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Links for 2020-05-03

  • The Coronavirus and Our Future

    Top notch KSR:

    We know that our accidental alteration of the atmosphere is leading us into a mass-extinction event, and that we need to move fast to dodge it. But we don’t act on what we know. We don’t want to change our habits. This knowing-but-not-acting is part of the old structure of feeling. Now comes this disease that can kill anyone on the planet. It’s invisible; it spreads because of the way we move and congregate. Instantly, we’ve changed. As a society, we’re watching the statistics, following the recommendations, listening to the scientists. Do we believe in science? Go outside and you’ll see the proof that we do everywhere you look. We’re learning to trust our science as a society. That’s another part of the new structure of feeling.

    (tags: covid-19 ksr kim-stanley-robinson future sf feeling society pandemics climate-change)

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Links for 2020-05-01

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Links for 2020-04-29

  • Kim Stanley Robinson proposing “carbon quantitative easing”

    I love this idea. “It would be complicated and messy, sure, but not as complicated and messy as a mass extinction event”

    (tags: finance carbon climate-change kim-stanley-robinson economics quantative-easing future green-recovery)

  • Joint Statement regarding the NHSX contact tracing app

    From over 170 UK infosec and privacy scientists and researchers —

    It has been reported that NHSX is discussing an approach which records centrally the de-anonymised ID of someone who is infected and also the IDs of all those with whom the infected person has been in contact. This facility would enable (via mission creep) a form of surveillance. Echoing the letter signed by 300 international leading researchers, we note that it is vital that, when we come out of the current crisis, we have not created a tool that enables data collection on the population, or on targeted sections of society, for surveillance. Thus, solutions which allow reconstructing invasive information about individuals must be fully justified. Such invasive information can include the “social graph” of who someone has physically met over a period of time. With access to the social graph, a bad actor (state, private sector, or hacker) could spy on citizens’ real-world activities. We are particularly unnerved by a declaration that such a social graph is indeed aimed for by NHSX. We understand that the current proposed design is intended to meet the requirements set out by the public health teams, but we have seen conflicting advice from different groups about how much data the public health teams need. We hold that the usual data protection principles should apply: collect the minimum data necessary to achieve the objective of the application. We hold it is vital that if you are to build the necessary trust in the application the level of data being collected is justified publicly by the public health teams demonstrating why this is truly necessary rather than simply the easiest way, or a “nice to have”, given the dangers involved and invasive nature of the technology.

    (tags: nhs nhsx privacy data-privacy security contact-tracing covid-19 surveillance)

  • Revealed: the inside story of the UK’s Covid-19 crisis

    Wow, the knives are out inside the UK government. Massive leaks from the SAGE and other committees, to the Guardian, as the scientists involve find themselves being blamed for the UK’s COVID-19 disaster

    (tags: uk government covid-19 omnishambles leaks guardian)

  • For future use: “Fancy dataviz” vs “best chart for the data”

    great pic from Rodolfo Almeida on Twitter

    (tags: twitter funny comic dataviz graphs visualisation)

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Links for 2020-04-28

  • Coronavirus and Brexit: the connections and their consequences

    Have to agree with this…

    What both Brexit and coronavirus reveal are some fundamental flaws in the way [the UK] are governed and the political discourse around it. The populist explosion of this decade, of which Brexit was a prime example, has bequeathed a way of governing which is impervious to reason, and incapable of engaging with complexity. It isn’t just chance that we have a woefully incompetent Prime Minister, a dud stand in, and a cabinet of mediocrities, propped up by a cadre of special advisors with few skills beyond contrarian posturing. They are the legacy of Brexit. They were brought into power by Brexit. But all the things which secured the vote for Brexit – the clever-but-dumb messaging, the leadership-by-slogan, the appeal to nostalgic sentiment, the disdain for facts and evidence, the valorisation of anger and divisiveness, the bluff ‘commonsense’ and the ‘bluffers’ book’ knowledge – are without exception precisely the opposite of what is needed for effective governance in general, and crisis management in particular.

    (tags: uk-politics uk politics brexit covid-19 government populism crisis-management)

  • Google’s medical AI was super accurate in a lab. Real life was a different story. | MIT Technology Review

    When it worked well, the AI did speed things up. But it sometimes failed to give a result at all. Like most image recognition systems, the deep-learning model had been trained on high-quality scans; to ensure accuracy, it was designed to reject images that fell below a certain threshold of quality. With nurses scanning dozens of patients an hour and often taking the photos in poor lighting conditions, more than a fifth of the images were rejected. Patients whose images were kicked out of the system were told they would have to visit a specialist at another clinic on another day. If they found it hard to take time off work or did not have a car, this was obviously inconvenient. Nurses felt frustrated, especially when they believed the rejected scans showed no signs of disease and the follow-up appointments were unnecessary. They sometimes wasted time trying to retake or edit an image that the AI had rejected. Because the system had to upload images to the cloud for processing, poor internet connections in several clinics also caused delays. “Patients like the instant results, but the internet is slow and patients then complain,” said one nurse. “They’ve been waiting here since 6 a.m., and for the first two hours we could only screen 10 patients.” The Google Health team is now working with local medical staff to design new workflows. For example, nurses could be trained to use their own judgment in borderline cases. The model itself could also be tweaked to handle imperfect images better. 

    (tags: google health medicine ai automation software internet developing-world real-world images scanning)

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Links for 2020-04-27

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Links for 2020-04-24

  • Cloud Jewels: Estimating kWh in the Cloud – Code as Craft

    Good stuff from Etsy, who are attempting to reduce their non-renewable energy usage:

    Cloud providers generally do not disclose to customers how much energy their services consume. To make up for this lack of data, we created a set of conversion factors called Cloud Jewels to help us roughly convert our cloud usage information (like Google Cloud usage data) into approximate energy used. We are publishing this research to begin a conversation and a collaboration that we hope you’ll join, especially if you share our concerns about climate change.

    (tags: energy green climate-change power etsy kwh measurement estimation)

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Links for 2020-04-22

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Links for 2020-04-21

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Links for 2020-04-20

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Links for 2020-04-17

  • 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).’

    (tags: lockdown covid-19 r0 pandemics nphet ireland)

  • 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:

    (tags: pepp-pt dp3t protocols ios android contact-tracing covid-19 pandemics)

  • Sarah Owens’ Table Loaf Recipe

    recommended by Colette

    (tags: bread baking food recipes sourdough)

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Links for 2020-04-16

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Links for 2020-04-15

  • 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”

    (tags: twitter threads contact-tracing apps tools covid-19)

  • 8051Enthusiast/regex2fat

    Turn your favourite regex into FAT32. ‘Haha OS-driven regex engine go brrrrr’

    (tags: insane stupid funny fat32 drivers filesystems regexps regex)

  • We scientists said lock down. But UK politicians refused to listen | Helen Ward | Opinion | The Guardian

    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.

    (tags: pcr covid-19 testing sars-cov-2 infection diseases)

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Links for 2020-04-14

  • DP^3T

    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)

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Links for 2020-04-13

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Links for 2020-04-10

  • 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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Links for 2020-04-09

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Links for 2020-04-08

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Links for 2020-04-07

  • 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)

  • Special Report: Johnson listened to his scientists about coronavirus – but they were slow to sound the alarm

    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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Links for 2020-04-06

  • The MakerMask

    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.

    (tags: masks facemasks covid-19 sewing)

  • “A recent Nature paper reveal a remarkable trick SARS-Cov-2 learned that makes it nastier than the first SARS”

    an educational twitter thread by virologist @PeterKolchinsky

    (tags: viruses sars covid-19 sars-cov-2 medicine science)

  • 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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Links for 2020-04-05

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Links for 2020-04-03

  • Fangcang shelter hospitals

    … 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)

  • Unified research on privacy-preserving contact tracing and exposure notification for COVID-19 – Google Docs

    ‘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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Links for 2020-04-02

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Links for 2020-04-01

  • 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)

  • ‘Guidance on cocooning to protect people over 70 years and those extremely medically vulnerable from COVID-19’

    Official HSE guidance doc

    (tags: hse cocooning social-distancing lockdown quarantine covid-19)


    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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Links for 2020-03-31

  • ‘They are leading us to catastrophe’: Sweden’s coronavirus stoicism begins to jar | World news | The Guardian

    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.”

    (tags: sweden fear covid-19 europe politics science)

  • ‘Estimating the number of infections and the impact of nonpharmaceutical interventions on COVID-19 in 11 European countries’

    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)

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Links for 2020-03-30

  • 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 ( – 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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Links for 2020-03-28

  • Percy Ludgate

    ‘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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Links for 2020-03-27

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Links for 2020-03-26

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Peer-to-peer COVID-19 contact tracing without the surveillance

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

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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