Good thread on the COVID-19 situation in Israel
Eran Segal on Twitter: “Israel: What went wrong? How did we come to lead the COVID-19 cases chart? What caused the 2nd wave, why was it so bad, and is the lockdown working? A thread on Israel, the first country to impose a second lockdown, with lots of (don’t do) lessons to teach the world.”
How contact tracing is being managed in Ireland for COVID-19
Dr Marie Casey on Twitter: “There is a fatal lack of understanding in how contact tracing is being managed in this pandemic. So I will explain.” – Solid, educational thread
(tags: twitter contact-tracing public-health pandemics covid-19)
Justin's Linklog Posts
Marc Bevand’s cases-vs-deaths graph for Florida
“deaths can lag up to 1 month after cases” — clear dataviz. Going to be sadly very relevant in Ireland in about a month’s time
(tags: ireland covid-19 pandemic via:firefoxx66)
Timeline of COVID -19 and Vietnam policy actions at a glance
Vietnam’s policy actions regarding COVID -19 are recapped in a timeline together with the outbreak’s movement and in context with other Asian countries from the start of 2020 to early of August 2020. Quick and decisive actions including touch control on travelling, intensive quarantine for overseas arrivals and suspected cases, massive testing and aggressive contract tracing, sealing off virus hot-spots and timely communication from very early on are considered to have contributed to Vietnam’s performance given its vulnerable position to China, a population of 100 million people and a comparatively under-developed healthcare system.
(tags: vietnam lockdown pandemics covid-19 public-health)
Dr Zoë Hyde’s latest Twitter thread on kids and COVID-19
With an Aussie perspective — Dr. Hyde works in Perth. ‘Summary: further evidence children & adults are equally susceptible & equally likely to transmit; school clusters are increasing; precautions needed in schools.’
(tags: schools education covid-19 transmission)
Selling Our Genes: Government inaction allowing private sector to take control of our DNA
Genuity Science, the main company involved in DNA sequencing in Ireland, has at least 25 links to facilities around Ireland. These include funding and collaborations with major hospitals, universities, research facilities and charities. A collaboration agreement signed between Genuity Science and UCD is “restrictive”, according to an academic expert, though Genuity Science Ireland disagree with this assessment. We have the full details in this breakout article. Hospital clinicians have become “agents of a company” due to the nature of agreements in place, according to experts. Researchers are making “the best of the situation” in Ireland by working with the private sector but most would prefer a public system due to data access concerns. Lack of Government policy and adequate regulation means that private companies have no limit on how long they have exclusive access to the data they collect from Irish patients. Researchers and patient representatives are concerned about a potential erosion of trust in genetics research in Ireland.
(tags: genomics genuity genetics ucd gmi ireland data-privacy data-protection research)
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Extract data from plots, images, and maps:
It is often necessary to reverse engineer images of data visualizations to extract the underlying numerical data. WebPlotDigitizer is a semi-automated tool that makes this process extremely easy: Works with a wide variety of charts (XY, bar, polar, ternary, maps etc.) Automatic extraction algorithms make it easy to extract a large number of data points Free to use, opensource and cross-platform (web and desktop) Used in hundreds of published works by thousands of users Also useful for measuring distances or angles between various features
(tags: data-extraction scraping tools data charts)
‘Only aerosol transmission can explain’ the Skagit Choir transmission incident
Jose-Luis Jimenez on Twitter: The “Skagit Choir” incident of mass spreading of COVID-19 indicates aerosol transmission: ‘Only aerosol transmission can explain how 1 person infected 52, including people who were 13 meters behind the index case.’
(tags: aerosols covid-19 sars-cov-2 transmission infection air)
inside the LAPD/LASD usage of Palantir
Much of the LAPD data consists of the names of people arrested for, convicted of, or even suspected of committing crimes, but that’s just where it starts. Palantir also ingests the bycatch of daily law enforcement activity. Maybe a police officer was told a person knew a suspected gang member. Maybe an officer spoke to a person who lived near a crime “hot spot,” or was in the area when a crime happened. Maybe a police officer simply had a hunch. The context is immaterial. Once the LAPD adds a name to Palantir’s database, that person becomes a data point in a massive police surveillance system. […] At great taxpayer expense, and without public oversight or regulation, Palantir helped the LAPD construct a vast database that indiscriminately lists the names, addresses, phone numbers, license plates, friendships, romances, jobs of Angelenos — the guilty, innocent, and those in between.
This is absolute garbage — total bias built-in. No evidence required to get a person in the firing line: “The focus of a data-driven surveillance system is to put a lot of innocent people in the system,” Ferguson said. “And that means that many folks who end up in the Palantir system are predominantly poor people of color, and who have already been identified by the gaze of police.”(tags: palantir databases privacy law lapd lasd los-angeles surveillance big-brother police crime gangs)
Everything you wanted to know about the Hydrogen economy but were too busy to research
Informative Twitter thread: ‘International hydrogen markets could be a thing, but don’t bet on hydrogen shipping’; ‘H2 future looks good regardless’; and ‘distributed plants could satisfy local industry and power markets while relieving electrical grid bottlenecks. The benefits are more likely to remain local rather than exported. So important for a just transition.’ (via Forge The Future)
(tags: h2 hydrogen green climate-change future eu europe twitter via:ftf)
AWS CRT HTTP Client in the AWS SDK for Java 2.x
Interesting — a new, high-performance, high-concurrency HTTP/1.1 client library in the AWS SDK, outperforming other Java HTTP client libs
Covid: The libertarian population immunity strategy is wrong-headed & dangerous
+1 to this —
As cases of covid in the UK surge once again, the debate has restarted about whether to suppress covid until a vaccine becomes available, or whether to pursue a deliberate strategy of achieving population immunity without a vaccine. The assumption is that vulnerable populations can be protected while the rest of the population, who are at low risk of hospitalisation and death, can be safely encouraged to live life normally and be exposed to the virus without a vaccine. Some even advocate that younger people, because they are at lower risk, should be the first to actively seek infection. “Not only is it a good thing for young people to go out there and become immune,” one commentator said, “but that is almost their duty”. It is this deliberate strategy which I find so troubling, for six reasons. [….]
(tags: uk politics covid-19 herd-immunity immunity risk pandemics)
Florian Krammer on the current SARS-CoV-2 vaccine candidates
amazing writeup of the current state of the vaccine candidates
(tags: florian-krammer vaccines sars-cov-2 covid-19 viruses)
The fake bridges on Euro banknotes are no longer fake
This is glorious:
When the euro bank notes were designed, they used European-style bridges which were *non-existing*, not to have to choose between countries. The Dutch town of Spijkenisse claimed them all for the Netherlands by building them on a waterway.
(tags: banknotes euros currency bridges netherlands holland spijkenisse)
Jane Ruffino on Sweden’s COVID-19 strategy
tl;dr: ‘I totally get why people want to believe Sweden figured out a way to do it without suffering, but we didn’t.’
(tags: sweden covid-19 threads twitter jane-ruffino lockdown)
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Susie Dent @susie_dent: “I feel it’s the day for a reminder of the 18th-century verb ‘quiddle’: to attend to trivial matters as a way of avoiding the important ones.”
(tags: quiddle quiddling prevarication delay words 18th-century language funny)
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‘Prio allows a set of servers to compute aggregate statistics over client-provided data while maintaining client privacy, defending against client misbehavior, and performing nearly as well as data-collection platforms that exhibit neither of these security properties.’ Aggregation operations include: integer sum and mean; variance and std dev; boolean OR/AND; min/max; sets; frequency count and percentiles/quantiles.
(tags: nizk zero-knowledge snark prio crypto privacy data-privacy statistics quantiles percentiles aggregation)
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minimize filesystem caching effects:
The nocache tool tries to minimize the effect an application has on the Linux file system cache. This is done by intercepting the open and close system calls and calling posix_fadvise() with the POSIX_FADV_DONTNEED parameter. Because the library remembers which pages (ie., 4K-blocks of the file) were already in file system cache when the file was opened, these will not be marked as “don’t need”, because other applications might need that, although they are not actively used (think: hot standby).
(tags: cache linux memory performance filesystems backup k8s unix fadvise)
Now 11 reported SARS-CoV-2 reinfections
4 cases were more serious the second time around
(tags: reinfections sars-cov-2 covid-19)
Sweden has the smallest average household size in Europe
This is an interesting factor regarding COVID-19 transmission — the majority of Swedish households have a single occupant, unlike everywhere else in Europe (twice the rate of Ireland, for instance).
(tags: covid-19 sweden households europe statistics eu housing)
Raspberry Pi USB Boot – UASP, TRIM, and performance
In the past few weeks, I reviewed USB drive performance on the Raspberry Pi 4, and the importance of UASP support for USB drive performance. Both posts generated great discussion, and there were three things I wanted to cover in this follow-up, namely: Which drives support UASP; Real-world performance benchmarks; TRIM support.
(tags: raspberry-pi optimization linux trim ssd filesystems usb)
Brand New Retro: Survival in a Nuclear War
Brian dug up an old nuclear-war survival pamphlet from the Irish Government, published circa 1965
(tags: 1960s nuclear-war history ireland ephemera civil-defence)
Coronavirus Pandemic Data Explorer – Our World in Data
Cumulative deaths per 100k, Finland/Sweden/Denmark/Norway. Bookmarking for the inevitable discussions with COVID deniers (thanks Soren!)
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Informative thread from Michael Mina – ‘Monoclonal antibodies (mAbs) have been quietly built and tested for months now. IMO mAbs have some of the best chances of offering powerful treatments for COVID-19’
(tags: twitter threads mabs monoclonal-antibodies immunity covid-19)
Andrew Flood on Michael Levitt
Levitt’s output is being quoted by COVID contrarians in Ireland — this thread is a good collection of examples of him being thoroughly wrong in his previous predictions
(tags: michael-levitt covid-19 covidiots twitter andrew-flood science)
Political Compass of Rural Ireland : ireland
lols
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‘Anti-Soros material is a globalized, freely available, and adaptable open-source weapon. Birnbaum said it was the common denominator of the nationalist movement.’
(tags: politics hungary george-soros lies antisemitism propaganda misinformation)
Rolling the COVID Dice in Ireland
On the Probability of SARS-CoV2 Infection in Ireland & the Benefits of Mitigation: ‘In Ireland today, we have a certain chance of becoming infected with the coronavirus over the course of the next week, unless we take precautions. We can roll this many sided dice once a week for 100 weeks, and hope that our number doesn’t ever come up, or we can take a few simple precautions and only roll the dice one time. That’s the difference wearing a mask, keeping our distance, and behaving sensibly makes. That’s the choice most of us can make to keep everyone safe. I think it’s a simple choice.’
(tags: covid-19 barry-smyth probability safety infection)
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this is incredible — the word roughly translates as “improvised fixes”, “hacks” or “McGyverism”, that kind of thing. fantastic Image Search
(tags: images gambiarra fixes thereifixedit mcgyver hacks kludges funny brazil)
Cillian De Gascun on Twitter: “A short thread on PCR #SARSCoV2”
Decent thread on Irish RT-PCR COVID-19 testing. tl;dr: Ct levels are not reliable in our system, and cannot be used to quantify viral load reliably
(tags: ireland covid-19 testing ct-levels viral-load viruses cillian-de-gascun twitter)
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Keith Dawson summarises a recent discussion on TWiV regarding COVID-19, the current batch of vaccines under development, and sterilising vs. protective immunity. it’s not great news
(tags: immunity immune-system twiv covid-19 alan-dove vaccines)
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report from Benchspace on their open source PPE project during March and April. it’s great stuff. 50,000 face shields printed!
(tags: face-shields covid-19 volunteers open-source 3d-printing ppe benchspace)
America Is Trapped in a Pandemic Spiral – The Atlantic
‘Many Americans trusted intuition to help guide them through this disaster. They grabbed onto whatever solution was most prominent in the moment, and bounced from one (often false) hope to the next. They saw the actions that individual people were taking, and blamed and shamed their neighbors. They lapsed into magical thinking, and believed that the world would return to normal within months. Following these impulses was simpler than navigating a web of solutions, staring down broken systems, and accepting that the pandemic would rage for at least a year. These conceptual errors were not egregious lies or conspiracy theories, but they were still dangerous. They manifested again and again, distorting the debate around whether to stay at home, wear masks, or open colleges. They prevented citizens from grasping the scope of the crisis and pushed leaders toward bad policies. And instead of overriding misleading intuitions with calm and considered communication, those leaders intensified them. The country is now trapped in an intuition nightmare: Like the spiraling ants, Americans are walled in by their own unhelpful instincts, which lead them round and round in self-destructive circles.’
FactFind: No, it’s not correct to say just 100 people have died from Covid-19 in Ireland
The Journal’s fact checking team are knocking it out of the park once again — great debunking of Ben Gilroy’s latest viral claims regarding “pre-existing conditions” and COVID-19
(tags: covid-19 medicine ben-gilroy conspiracies qanon the-journal fact-checking debunking)
QAnon is a Nazi Cult, Rebranded
A secret cabal is taking over the world. They kidnap children, slaughter, and eat them to gain power from their blood. They control high positions in government, banks, international finance, the news media, and the church. They want to disarm the police. They promote homosexuality and pedophilia. They plan to mongrelize the white race so it will lose its essential power. Does this conspiracy theory sound familiar? It is. The same narrative has been repackaged by QAnon. […] The plot, described above, was the conspiracy “revealed” in the most influential anti-Jewish pamphlet of all time. It was called The Protocols of the Elders of Zion. It was written by Russian anti-Jewish propagandists around 1902.
(tags: qanon politics conspiracy-theories history nazism nazis antisemitism)
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via Vincent Glad, on Twitter: the positivity rate stratified by age, in the Marseilles region
(tags: testing covid-19 age epidemiology dataviz statistics marseilles france)
The timing of COVID-19 transmission
new preprint on medRxiv:
We examined the distribution of transmission events with respect to exposure and onset of symptoms. We show that for symptomatic individuals, the timing of transmission of SARS-CoV-2 is more strongly linked to the onset of clinical symptoms of COVID-19 than to the time since infection. We found that it was approximately centered and symmetric around the onset of symptoms, with three quarters of events occurring in the window from 2-3 days before to 2-3 days after. However, we caution against overinterpretation of the right tail of the distribution, due to its dependence on behavioural factors and interventions. We also found that the pre-symptomatic infectious period extended further back in time for individuals with longer incubation periods. This strongly suggests that information about when a case was infected should be collected where possible, in order to assess how far into the past their contacts should be traced. Overall, the fraction of transmission from strictly pre-symptomatic infections was high (41%; 95%CI 31-50%), which limits the efficacy of symptom-based interventions, and the large fraction of transmissions (35%; 95%CI 26-45%) that occur on the same day or the day after onset of symptoms underlines the critical importance of individuals distancing themselves from others as soon as they notice any symptoms, even if they are mild. Rapid or at-home testing and contextual risk information would greatly facilitate efficient early isolation.
(tags: covid-19 transmission infection epidemiology)
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the latest hot new image format — pretty impressive compression numbers vs quality thresholds here
[MA] Post-it notes left in apartment. : legaladvice
Classic Reddit thread. Guy finds mysterious post-it notes around his apartment, suspects his landlord is breaking in and leaving them. I won’t spoil it, but it’s quite a twist ending…
(tags: reddit stories legaladvice apartments landlords post-its)
Starbucks Cafe’s Covid Outbreak Spared Employees Who Wore Masks – Bloomberg
This was pretty striking: ‘A person sitting under an air conditioner infected 27 others with coronavirus at a Starbucks cafe in South Korea, but none of the employees, who were wearing masks, got the virus.’ Another great case writeup from South Korea (Via Andrew Flood)
(tags: via:andrewflood covid-19 korea ventilation air-conditioning aircon masks transmission)
_COVID-19: Interim Public Health guidance for the management of COVID-19 outbreaks_ [pdf]
The current guidance doc for outbreak management in Ireland
Proactive screening for COVID-19 is individually costly
Thread from Professor Carl T. Bergstrom:
[…] proactive testing carries individual costs: those associated with purchasing the tests, time costs of taking them, and serious social and economic costs if one tests positive and has to self-isolate for upward of a week. So, we have an intervention that is costly to you but beneficial to others. We need to think about what the incentives are for people to (1) decide to take a daily test before the results are known and (2) follow through appropriately if a test comes up positive.
(tags: testing covid-19 screening costs economics incentives)
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A complete guide via the Native Woodland Trust for planting trees in your garden, hedge, etc.
Good thread on the current state of play re COVID-19 in Ireland and the rest of Europe
Ewan Birney on Twitter: “Like I suspect a number of scientists I’ve been quizzed by a variety of friends and family on COVID, and its gone up recently because (a) school is back and so people can feel change around them and (b) there is a change in stats in across countries in Europe.”
Darmok and Jalad at Tanagra, in memes
large number of people in a theatre, applauding
(tags: memes gifs reaction-gifs funny darmok-and-jalad sttng star-trek)
Keith Dawson on This Week in Virology
a paean to my favourite podcast
Death, sex, superstition and fear: the hawthorn tree in Ireland
These trees that grew of their own accord, unplanted by human hands, are those most regarded with fear and superstition. These are thought of as faery trees, associated with those unseen beings from the other world. They are believed to mark the places where the faeries, after dark, would assemble and play sweet ethereal music, ready to abduct any beautiful human who took their fancy. Faeries could potentially destroy the crops, livestock, health, fortune or luck of anyone they took a dislike to, or anyone who had somehow wronged them. Thus, anything associated with faery activity in Ireland was traditionally avoided by the people who used many rituals to appease them.
(tags: hawthorn trees superstition fairies sidhe history ireland folklore)
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via DrZoeHyde: ‘Important pre-print study (interpret cautiously) of 992 UK children showing 6.9% had #SARSCoV2 antibodies, suggesting they are at similar risk of infection as adults, & that young and older children are similarly susceptible. 50% were asymptomatic.’ ‘Half of the children (50%) who had antibodies against #SARSCoV2 were asymptomatic (although this may be subject to recall bias). The most common symptoms were fever (31%), gastrointestinal symptoms such as diarrhoea and vomiting (19%), and headache (18%). Only 38% of children who tested positive had fever, cough, or changes in smell or taste. Therefore, the majority of children did not meet criteria for #COVID19 testing in the UK. Current testing strategies [in the UK] will fail to diagnose most cases in children.’
(tags: covid-19 symptoms kids schools sars-cov-2 studies preprints papers uk testing)
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‘This is one of the most horrifying stories I’ve ever read about policing: Because of a flawed algorithm, cops showed up 21 TIMES in 5 months to a 15 year-olds house. He was not accused of any crime.’
(tags: civil-rights police algorithms policing automation florida us-politics)
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One person on a bus infected 23 others, probably through the air during a 100-minute trip. A/C was on with recirculation. Infected people were randomly scattered throughout the bus, not just near the index case.
(tags: covid-19 aerosols airborne transmission diseases buses public-transport travel sars-cov-2)
Gerät 32620: the machine that powered numerous number stations
Fascinating details of the hardware behind “number stations”, the mysterious radio stations broadcasting streams of numbers in a monotone. One example of their use is the story of Gabriele Gast: ‘After agreeing to help [the Stasi], Gast very soon found herself sent on an intensive spycraft course, including hands-on training with the latest in covert communications equipment. She was given a Stasi code name, “Gisela”, which came with a false passport and a new handbag, incorporating a well concealed secret compartment. Back home in Aachen, every Tuesday evening at the same time she tuned into a shortwave radio station from East Germany and carefully wrote down a long line of numbers, read out in a monotone, without further elaboration, by a “radio presenter”. When she decrypted the messages from Schmidt she found some were instructions while others were simply encouraging love messages.’
(tags: spies number-stations 1980s history ussr hardware encryption gabriele-gast germany)
FAQs on Protecting Yourself from Aerosol Transmission of COVID-19
This is pretty extensive
(tags: faqs covid-19 aerosols transmission)
Keeping CALM: When Distributed Consistency Is Easy | September 2020 | Communications of the ACM
‘Consistency As Logical Monotonicity (CALM): A problem has a consistent, coordination-free distributed implementation if and only if it is monotonic.’
(tags: calm computer-science consistency distributed-systems bloom distcomp)
Two metres or one: what is the evidence for physical distancing in covid-19? | The BMJ
Key messages: Current rules on safe physical distancing are based on outdated science Distribution of viral particles is affected by numerous factors, including air flow Evidence suggests SARS-CoV-2 may travel more than 2 m through activities such as coughing and shouting Rules on distancing should reflect the multiple factors that affect risk, including ventilation, occupancy, and exposure time
(tags: epidemiology coronavirus covid-19 papers bmj social-distancing physical-distancing 2-metres aerosols)
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TIL about credit card “interchange fees” — an additional fee levied by credit card companies and banks, roughly 3%, mainly in the US (the EU regulations cap it at 0.3%). ‘Imagine a consumer making a $100 purchase with a credit card. For that $100 item, the retailer would get approximately $98. The remaining $2, known as the merchant discount[13] and fees, gets divided up.’
(tags: fees credit-cards interchange-fees us money)
How I helped fix Canada?s COVID Alert app
Nice writeup of using mitmproxy to detect unwanted accesses to a Google endpoint in an iOS app
interesting results on children and COVID-19 — high asymptomatic infection rate
‘METHODS: We conducted a prospective cohort study of children and adolescents (<21 years of age) with a SARS-CoV-2-infected close contact. We collected nasopharyngeal or nasal swabs at enrollment and tested for SARS-CoV-2 using a real-time PCR assay. RESULTS: Of 382 children, 293 (77%) were SARS-CoV-2-infected. SARS-CoV-2-infected children were more likely to be Hispanic (p<0.0001), less likely to have asthma (p=0.005), and more likely to have an infected sibling contact (p=0.001) than uninfected children. Children ages 6-13 years were frequently asymptomatic (39%) and had respiratory symptoms less often than younger children (29% vs. 48%; p=0.01) or adolescents (29% vs. 60%; p<0.0001). Compared to children ages 6-13 years, adolescents more frequently reported influenza-like (61% vs. 39%; p<0.0001), gastrointestinal (27% vs. 9%; p=0.002), and sensory symptoms (42% vs. 9%; p<0.0001), and had more prolonged illnesses [median (IQR) duration: 7 (4, 12) vs. 4 (3, 8) days; p=0.01]. Despite the age-related variability in symptoms, we found no differences in nasopharyngeal viral load by age or between symptomatic and asymptomatic children.'
Children in close contact with a confirmed case of Covid-19 were not contacted for nine days
‘Children who came into close contact with a confirmed case of the coronavirus at a summer camp run by Ireland’s lead sporting authority were not contacted by the HSE regarding the issue for nine days, it has emerged. Sport Ireland, the State authority charged with the development of sport in Ireland, has been running childrens’ summer camps at the National Aquatic Centre campus in Blanchardstown, Dublin, where SI itself is headquartered, since June 29th. At one such camp on Friday, 14 August, a nine-year-old boy participating apparently came into close contact with a case of the virus. However, he heard nothing about the contact until nine days later on August 23 when his mother received an automated text message stating that the contact had occurred and that he had been referred for a Covid-19 test.’
(tags: sport-ireland ireland contact-tracing covid-19 kids hse children)
Irish coins designed by Percy Metcalfe
the coins used in Ireland between 1928 and 2000 (when the Euro became standard here). Beautiful, classic designs
Asymptomatic SARS-CoV-2 infections: a living systematic review and meta-analysis | medRxiv
‘The overall estimate of the proportion of people who become infected with SARS-CoV-2 and remain asymptomatic throughout infection was 20% (95% CI 17-25) with a prediction interval of 3-67% in 79 studies that addressed this review question.’ — note, asymptomatic throughout infection, not including presymptomatic then symptomatic. (via Andrew Flood)
(tags: via:andrewflood covid-19 asymptomatic papers preprints medicine)
Explanation of the “cases rising but deaths staying static” COVID-19 phenomenon
Featuring lots of graphs and data. This is great
Long-Haulers Are Redefining COVID-19 – The Atlantic
god, this disease is awful
(tags: long-haulers covid-19 health medicine ed-yong)
Richard Neher on Twitter: “What happens to #COVID19 when winter returns”
tl;dr: ‘this suggests controlling #SARSCoV2 in the Northern Hemisphere will become a lot harder over the next six months and things might spiral out of control quickly.’
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The incubation period distribution may be modelled with a lognormal distribution with pooled mu and sigma parameters (95% CIs) of 1.63 (95% CI 1.51 to 1.75) and 0.50 (95% CI 0.46 to 0.55), respectively. The corresponding mean (95% CIs) was 5.8 (95% CI 5.0 to 6.7) days. It should be noted that uncertainty increases towards the tail of the distribution: the pooled parameter estimates (95% CIs) resulted in a median incubation period of 5.1 (95% CI 4.5 to 5.8) days, whereas the 95th percentile was 11.7 (95% CI 9.7 to 14.2) days.
(tags: covid-19 incubation diseases sars-cov-2 papers bmj)
How to Test Every American for COVID-19, Every Day – The Atlantic
Good write-up on Dr. Michael Mina’s testing plan, using quick, cheap testing strips for daily COVID-19 testing
(tags: testing covid-19 coronavirus michael-mina reopening)
A-Levels: The Model is not the Student
Solid description of the many errors in the UK’s attempt to estimate correct grades for their A-level students this year. They really made a massive mess of it. ‘Ultimately, the government can only receive, at best, a D for their efforts; they tried but failed. We can only hope they will now pull themselves up, bring in the experts, and construct an algorithm worthy of an A.’
(tags: ofqual schools marks exams a-levels uk estimation statistics maths fail)
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“The story behind one of the most infamous myths of the Irish pandemic.” Great analysis by The Journal here.
(tags: covid-19 paddy-cosgrave twitter misinformation tweets)
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“Over the next 50 years, keeping to the 2°C pathway would prevent roughly 4.5 million premature deaths, about 3.5 million hospitalizations and emergency room visits, and approximately 300 million lost workdays in the US.” All that prevented death, illness, and lost productivity adds up to a lot of savings: The avoided deaths are valued at more than $37 trillion. The avoided health care spending due to reduced hospitalizations and emergency room visits exceeds $37 billion, and the increased labor productivity is valued at more than $75 billion. On average, this amounts to over $700 billion per year in benefits to the US from improved health and labor alone, far more than the cost of the energy transition. Importantly, many of the benefits can be accessed in the near term. Right now, air pollution leads to almost 250,000 premature deaths a year in the US. Within a decade, aggressive decarbonization could reduce that toll by 40 percent; over 20 years, it could save around 1.4 million American lives that would otherwise be lost to air quality. Of the potential yearly deaths prevented, Rep. Robin Kelly of Illinois remarked at the hearing, “That’s a huge number. That’s nearly three times the number of lives we lose in car accidents every year. It’s twice the number of deaths caused by opioids in the past few years. And it’s even more than the number of Americans we lose to diabetes each year.”
(tags: pollution air energy environment climate-change air-quality health decarbonization)
ESB PVC Ducting Pipe Red 50mm x 6M
decent weatherproof ducting for running cables to garden sheds etc.
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Some prime quotes: ‘You can’t infer the correct grades at an individual level from the prior year’s distribution of grades, no matter how hard you clonk away at the abacus.’ ‘The data *doesn’t* allow that. ThIs puts idea that grade inflation, school level results and maintaining the distribution shape is more important than the fairness of individual results.’ ‘I don’t blame Ofqual, but they’re being asked to correctly estimate the size of each egg that went into an omelette, based on a different omelette.’
(tags: ofqual uk education covid-19 estimation a-levels grades schools)
Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19: Cell
Good news for ongoing immunity:
SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19. We here systematically mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in unexposed individuals, exposed family members, and individuals with acute or convalescent COVID-19. Acute phase SARS-CoV-2-specific T cells displayed a highly activated cytotoxic phenotype that correlated with various clinical markers of disease severity, whereas convalescent phase SARS-CoV-2-specific T cells were polyfunctional and displayed a stem-like memory phenotype. Importantly, SARS-CoV-2-specific T cells were detectable in antibody-seronegative exposed family members and convalescent individuals with a history of asymptomatic and mild COVID-19. Our collective dataset shows that SARS-CoV-2 elicits robust, broad and highly functional memory T cell responses, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19.
(tags: immunity covid-19 sars-cov-2 diseases immune-system t-cells)
How to use ventilation and air filtration to prevent the spread of coronavirus indoors
Given that COVID-19 spreads via aerosols in closed rooms like classrooms, use a CO2 monitor to check levels of ventilation; open windows; or use an air purifier.
(tags: covid-19 aerosols air air-quality co2 air-purifiers schools)
Covid 19 coronavirus: Freight investigated as possible source of community transmission – NZ Herald
Interesting theory in NZ — their current outbreak may have been caused by surface transmission on food shipped from China:
Surfaces in a coolstore workplace are being tested to see whether international freight may have been the origin of the new cases. One of the people who has tested positive for Covid-19 is an employee at an Americold coolstore in Mt Wellington, one of four people who tested positive on Tuesday.
(tags: shipping fomites surfaces transmission covid-19 new-zealand)
Objectives for COVID-19 testing in school settings
‘New ECDC guidance on testing for COVID-19 in schools says anyone who is in a “closed environment, such as a classroom, for more than 15 minutes” with a confirmed case is considered a close contact and should be tested’
(tags: ecdc covid-19 infection transmission airborne aerosols schools kids)
Yes, kids can get COVID-19 – 3 pediatricians explain what’s known about coronavirus and children
So: kids catch the virus at the same rate, and transmit at the same rate as adults. They just don’t tend to become symptomatic as much as adults do.
(tags: covid-19 disease kids schools transmission)
the German meat-factory COVID-19 outbreak was airborne
This is a great article:
The outbreak has been studied comprehensively by scientists using genetic sequencing techniques. The index case, who was masked, spread the disease to co-workers in a radius of more than eight metres over three days of work shifts, they found. Transmission was aided by the confined area of the plant, where air was constantly recirculated and cooled to 10 degrees. Shared apartments, bedrooms or carpools did not play a major role in the initial outbreak.
(Via Dee Gilhawley)(tags: covid-19 airborne aerosols transmission meat)
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New preprint, modelling COVID-19 transmission in Bay Area schools.
Large-scale school closures have been implemented worldwide to curb the spread of COVID-19. However, the impact of school closures and re-opening on epidemic dynamics remains unclear. Methods: We simulated COVID-19 transmission dynamics using an individual-based stochastic model, incorporating social-contact data of school-aged children during shelter-in-place orders derived from Bay Area (California) household surveys. We simulated transmission under observed conditions and counterfactual intervention scenarios between March 17-June 1, and evaluated various fall 2020 K-12 reopening strategies. Findings: Between March 17-June 1, assuming children <10 were half as susceptible to infection as older children and adults, we estimated school closures averted a similar number of infections (13,842 cases; 95% CI: 6,290, 23,040) as workplace closures (15,813; 95% CI: 9,963, 22,617) and social distancing measures (7,030; 95% CI: 3,118, 11,676). School closure effects were driven by high school and middle school closures. Under assumptions of moderate community transmission, we estimate that fall 2020 school reopenings will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1), and elementary school teachers (4.1%, 95% CI: -1.7, 12.0). Results are highly dependent on uncertain parameters, notably the relative susceptibility and infectiousness of children, and extent of community transmission amid re-opening. The school-based interventions needed to reduce the risk to fewer than an additional 1% of teachers infected varies by grade level. A hybrid-learning approach with halved class sizes of 10 students may be needed in high schools, while maintaining small cohorts of 20 students may be needed for elementary schools. Interpretation: Multiple in-school intervention strategies and community transmission reductions, beyond the extent achieved to date, will be necessary to avoid undue excess risk associated with school reopening. Policymakers must urgently enact policies that curb community transmission and implement within-school control measures to simultaneously address the tandem health crises posed by COVID-19 and adverse child health and development consequences of long-term school closures.
Building dashboards for operational visibility | Amazon Builders’ Library
Fantastic set of tips for metric dashboard construction, from John O’Shea
(tags: dashboards aws monitoring metrics alerts amazon)
Nisreen A Alwan: What exactly is mild covid-19?
What is now becoming clear is that mortality is not the only adverse outcome of this infection and our surveillance systems must keep up and reflect that. I am advocating for precise case definitions for covid-19 morbidity that reflect the degree of severity of infection and allow us to measure moderate and long term health and wellbeing outcomes. At this stage of the pandemic, it is vital that we accurately measure and count all degrees of infection, not only in research cohorts, but as part of population-based routine surveillance systems. This includes people like me who were not tested at the time of their initial infection. Death is not the only thing to count in this pandemic, we must count lives changed. We still know very little about covid-19, but we do know that we cannot fight what we do not measure.
Georgia camp outbreak shows rapid virus spread among children
Between 44% and 75% of the people at this summer camp were infected. ‘258 staff gathered for three days before the camp started with no precautions. Then on day 1 of camp someone [felt] chills. By day 6, the camp was closed.’ 597 attendees, 344 tested, 260 positive.
(tags: covid-19 symptoms summer-camps pandemic disease georgia kids schools children)
“Three new important studies came out in the past week about kids & COVID-19”
Good twitter thread from Megan Ranney MD: * ‘South Korea study — Older kids most likely transmit #COVID19 to their household at rates similar to adults. And younger kids transmit the virus, too. But: no masks or distancing, since this took place at home.’ * ‘Chicago — the level of the virus in kids is AT LEAST as high as the level of virus in adults. (Caveat: we don’t know whether this virus is infectious. But this data matches what we know about other respiratory viruses. The next step will be studying test swabs to see if kids’ virus can reproduce. I suspect it can. […] We can’t let kids ignore #SocialDistancing & #MaskUp just bc they’re kids.)’ * ‘States with early closure of schools had reduced levels of #COVID19 compared with states with late closure, *even after* adjusting for policies like “stay-at-home”. […] Once #COVID19 infection rates start to rise, it would be foolhardy to keep schools open IRL. And we should be planning NOW for how to keep kids healthy, safe, & fed, because that moment will likely come for every state.’ ‘Realistically, we MUST control levels of community transmission of #COVID19 if we want kids & teachers in schools. We may be able to send kids back, but we need PPE & regular, random testing of kids & teachers, whether in elementary, middle, high school, or college.’
(tags: parenting kids schools covid-19 transmission pandemics viruses sars-cov-2)
The UX of LEGO Interface Panels – George Cave
love it
RCP8.5 tracks cumulative CO2 emissions | PNAS
Today in “we are still fucked” news:
RCP8.5, the most aggressive scenario in assumed fossil fuel use for global climate models, will continue to serve as a useful tool for quantifying physical climate risk, especially over near- to midterm policy-relevant time horizons. Not only are the emissions consistent with RCP8.5 in close agreement with historical total cumulative CO2 emissions (within 1%), but RCP8.5 is also the best match out to midcentury under current and stated policies with still highly plausible levels of CO2 emissions in 2100.
RCP8.5 is the model associated with a planet where a good chunk of the globe is rendered uninhabitable.(tags: rcp8.5 grim-meathook-future future climate-change co2 pnas papers models climate)
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While the antibody response to SARS-CoV-2 has been extensively studied in blood, relatively little is known about the mucosal immune response and its relationship to systemic antibody levels. Since SARS-CoV-2 initially replicates in the upper airway, the antibody response in the oral cavity is likely an important parameter that influences the course of infection. We developed enzyme linked immunosorbent assays to detect IgA and IgG antibodies to the SARS-CoV-2 spike protein (full length trimer) and its receptor binding domain (RBD) in serum (n=496) and saliva (n=90) of acute and convalescent patients with laboratory-diagnosed COVID-19 ranging from 3-115 days post-symptom onset (PSO), compared to negative controls. Anti-CoV-2 antibody responses were readily detected in serum and saliva, with peak IgG levels attained by 16-30 days PSO. Whereas anti-CoV-2 IgA antibodies rapidly decayed, IgG antibodies remained relatively stable up to 115 days PSO in both biofluids. Importantly, IgG responses in saliva and serum were correlated, suggesting that antibodies in the saliva may serve as a surrogate measure of systemic immunity.
That last line, in particular, is good news.(tags: covid-19 immunity disease assays antibodies sars-cov-2 papers preprints)
Harvard-UC Boulder Portable Air Cleaner Calculator for Schools
A handy calculator spreadsheet to estimate how big of a portable air cleaner would be required to protect kids/teachers/admin staff at a typical US school, based on room size, ceiling height, etc. More info: https://twitter.com/cedenolaurent/status/1290447833959747584 (Catherine Lalanne notes: “Airflows in this sheet are about half the Irish regulations, American regulations are pretty weak.”)
(tags: air-cleaners filtration spreadsheets covid-19 schools kids air-quality air)
Why Aren’t We Talking More About Ventilation? – The Atlantic
Zeynep wins again:
It seems baffling that despite mounting evidence of its importance, we are stuck practicing hygiene theater — constantly deep cleaning everything — while not noticing the air we breathe. How is it that six months into a respiratory pandemic, we still have so little guidance about this all-important variable, the very air we breathe?
(tags: hygiene-theatre deep-cleaning covid-19 aerosols infection air viruses transmission zeynep-tufekci)
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‘also called Detroit agate, it’s created when layers of automotive paint build up and harden. then it’s cut and polished like other rocks.’
(tags: fordite rock agate history paint recycling cars detroit)
Apple tells app devs to use IPv6 as it’s 1.4 times faster than IPv4
“when IPv6 is in use, the median connection setup is 1.4 times faster than IPv4. This is primarily due to reduced NAT usage and improved routing.”
This is counterintuitive?(tags: ipv6 ipv4 networking apple internet performance)
Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care
A paper in Nature, no less. SARS-CoV-2 is airborne and spreads via aerosols. My pal Cassie’s colleague, Travis Longcore, writes: ‘A team at the University of Nebraska collected surface and air samples from the hospital where 13 Covid-19 cases were isolated. They found evidence of virus everywhere — high-volume air samples, low-volume personal samples worn by study personnel, room surfaces, personal items, and toilets. The results are in gene copes (from SARS-CoV-2) per microL for surfaces and per L of air for airborne. Others can do the calculations, but the personal air samples had the highest numbers, and exposure would depend on mask wearing (N95 in a hospital) and the amount of throughput (liters of air in and out of the body). What you really don’t want to be doing is exercising (=high volume of air in and out) without a mask indoors with someone who is infected. Or touching anything around them. Or being inside with recirculated, unfiltered air with anyone who is infected (even if they don’t know it).’
(tags: aerosols nature papers covid-19 sars-cov-2 fomites contamination transmission infection air airborne)
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In aggregate, the distributions of Cts for viral probes used in the qRT-PCR assay were very similar, with a statistically but not meaningfully different mean (?Ct 0.71 cycles, p = 0.006) and a similar range (12-38 cycles), between populations with and without symptoms over the entire time period, across all sub-categories examined (age, race, ethnicity, sex, resident/staff).
Viral load is comparable between COVID-19 victims who are asymptomatic and symptomatic.(tags: covid-19 preprints papers medicine viral-load rt-pcr testing)
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Although SARS-CoV-2 RNA shedding in respiratory and stool can be prolonged, duration of viable virus is relatively short-lived. Thus, detection of viral RNA cannot be used to infer infectiousness. High SARS-CoV-2 titres are detectable in the first week of illness with an early peak observed at symptom onset to day 5 of illness.
…also backs up that infectiousness starts around 2 days prior to symptom onset. -
Arrow combines the benefits of columnar data structures with in-memory computing. It provides the performance benefits of these modern techniques while also providing the flexibility of complex data and dynamic schemas. And it does all of this in an open source and standardized way.
(via Tony Finch)(tags: via:fanf arrow data formats compression columnar-storage storage libraries)
Solving the expiring Root CA certificate-mageddon; partly at least | APNIC Blog
Ugh — PKI expiry lifetimes were such an awful idea.
As of writing, a large number of Samsung Blu-Ray players around the world are stuck in a reboot loop. Although customers are still waiting for the official word on the issue, the suspicion is that the problem is caused by an expired certificate that stops the device firmware from booting properly, possibly because of strict digital rights management requirements that require verification and signing before full start-up of the players. As Scott points out, there are hundreds of ageing Root CAs out there, many more when you include the intermediates. Over the next few years, more will expire.
(via Tony Finch)(tags: security fail pki ssl tls samsung firmware certificates expiration cas)
US Spring school closures tied to drastic decrease in Covid-19 cases, deaths in model
Their projection found that, if schools had stayed open, there could have been roughly 424 more coronavirus infections and 13 more deaths per 100,000 residents over the course of 26 days. Extrapolate that to the American population, and the country might have seen as many as 1.37 million more cases and 40,600 more deaths, explained Samir Shah, the director of hospital medicine at Cincinnati Children’s Hospital Medical Center and one of the authors of the paper. “These numbers seem ridiculously high and it’s mind-boggling to think that these numbers are only … in the first several weeks,” said Shah. “That’s bonkers.” He warned, though, that those numbers should be taken with a grain of salt. While their statistical model attempts to pinpoint the impact of schools staying open or being closed, the method can’t actually establish any sort of causal relationship.
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When Science looked at reopening strategies from South Africa to Finland to Israel, some encouraging patterns emerged. Together, they suggest a combination of keeping student groups small and requiring masks and some social distancing helps keep schools and communities safe, and that younger children rarely spread the virus to one another or bring it home. But opening safely, experts agree, isn’t just about the adjustments a school makes. It’s also about how much virus is circulating in the community, which affects the likelihood that students and staff will bring COVID-19 into their classrooms.