Florian Krammer on Twitter: “1) This morning, I shared an enthusiastic tweet about Pfizer’s interim results with their COVID-19 vaccine. Let me explain here why am I am so enthusiastic, how the road to get this to people might look like and why we still need to control the pandemic NOW.”
good writeup from Keith Dawson on the Pfizer vaccine news, it’s all very promising :)
Justin Mason's Weblog Posts
Florian Krammer on Twitter: “Our NYC serosurvey paper is now out in Nature: if extrapolated to the NYC population we found [more than] 1.7 million infected and IFR at 0.97” That’s high! Nearly 1 in 100.
Somebody, somewhere, will have died needlessly due to this bug.
The root of the error, the Guardian has learned, was a decision to incorporate a measure of “infectiousness” into the app’s code. While the app was undergoing testing in the Isle of Wight, it used a simple metric that recommended isolation for anyone who had been in contact – closer than 2 metres – with a potentially infectious person for 15 minutes or more in a single day. But shortly before the app was launched nationally, it was updated to account for the fact that people are most infectious shortly after their symptoms show. The maths was changed so that people outside that period of peak infectiousness counted for just two-fifths of the risk. Since that meant the overall score was likely to be lower, the intention was to reduce the risk threshold correspondingly to ensure that someone of maximum infectiousness would need just three minutes of contact before they triggered an alert. But that change never happened, and as a result, users were only told to isolate if they had spent 15 minutes close to a very infectious person, or nearly 40 minutes near someone who was pre-symptomatic but still thought to be shedding the virus. The error was only discovered when a new version of the contact-tracing app, which can better account for exposures at mid-range (over a metre away) was created. The unfeasibly high risk score also explained another problem plaguing the app: “ghost notifications” warning users that they may have been exposed to someone with Covid, but which never resulted in advice to isolate. The app’s initial advice to users was that these notifications could be safely ignored, since they reflected a contact below the risk threshold; now that the NHS risk threshold is known to have been artificially low, one insider said, it is likely that the vast majority of those ghost notifications should in fact have been advice to self-isolate.
In the last three months America has lost more people than Sri Lanka lost in 30 years of civil war. If this isn’t collapse, then the word has no meaning. You probably still think of Sri Lanka as a shithole, though the war ended over a decade ago and we’re (relatively) fine. Then what does that make you? America has fallen. You need to look up, at the people you’re used to looking down on. We’re trying to tell you something. I have lived through collapse and you’re already there. Until you understand this, you only have further to fall.
The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries – The Lancet Infectious Diseases
‘Study of effect of imposing and lifting COVID-19 measures in 131 countries. Reopening schools was associated with a 24% increase in the reproduction number (R) after 28 days. This was the second-largest increase, after lifting bans of gatherings (25%).’
Pub/Sub messaging with strong ordering and deduping. Great stuff from AWS
Given the prevalence in your location, and various attributes about your risk level and who will be in the area with you and for how long, this computes a comparative risk level for any given activity.
Overall, the team found that while most people with COVID-19 reported being back to normal in 11 days or less, around one in seven (13.3%, 558 users) had symptoms lasting for at least 4 weeks, with around one in 20 (4.5%, 189 users) staying ill for 8 weeks and one in fifty (2.3%, 95 users) suffering for longer than 12 weeks. Extrapolating out to the general UK population, which has a different age and gender makeup compared with the COVID Symptom Study app users, the team estimated that around one in seven (14.5%) of people with symptomatic COVID-19 would be ill for at least 4 weeks, one in 20 (5.1%) for 8 weeks and one in 45 (2.2%) for 12 weeks or more.(via Valen)
‘Lease is a general DynamoDB-based lease implementation, ideal for long-lived work items, with coarse-grained leases’, in Go, by the inimitable ex-Swrver Rob Clancy
‘a command line tool that allows direct execution of SQL-like queries on CSVs/TSVs (and any other tabular text files). q treats ordinary files as database tables, and supports all SQL constructs, such as WHERE, GROUP BY, JOINs etc. It supports automatic column name and column type detection, and provides full support for multiple encodings.’ Awesome!
The denizens of r/Ireland pipe up with their favoured sources of online gifts for Xmas
Now _this_ is a good point.
Maria Van Kerkhove, the WHO’s technical lead for COVID-19 said during the meeting Monday that she’s had lots of friends and family asking her in recent days what, exactly, quarantine is. Essentially, it’s complete isolation from other people, including those you’d normally live with and breathe around, to the fullest extent possible. “That means not going to work,” Van Kerkhove said. “It means not going to the grocery store. It means not socializing with friends. It means not having people over at your home.” Ideally, quarantining is a disease-fighting measure that is supported by local health programs and government support that can allow people to continue making a living and feeding their families while in quarantine, she said.
Muxsan are a Dutch company selling range extension kits for Nissan Leaf EVs, increasing their range from a Gen 1 Leaf’s 110km to a typical 238km; 440km is the max. ‘The extension pack consists of many Lithium-ion cells [NMC], which are of the highest quality, bound by aluminum casing into modules and each module comes with a German built Battery Management System [BMS].’
Looks like a decent place to buy refurbished electronics with a warranty — reviews seem good online
decent list of Irish online shops, to avoid Amazon
these are _amazing_. Huge respect to all the contributors who wrote these great little demos-in-a-tweet
“It scares me to think I’m working,” Ms. Mizelle, 53, said. “I feel like I have dementia.” It’s becoming known as Covid brain fog: troubling cognitive symptoms that can include memory loss, confusion, difficulty focusing, dizziness and grasping for everyday words. Increasingly, Covid survivors say brain fog is impairing their ability to work and function normally. “There are thousands of people who have that,” said Dr. Igor Koralnik, chief of neuro-infectious disease at Northwestern Medicine in Chicago, who has already seen hundreds of survivors at a post-Covid clinic he leads. “The impact on the work force that’s affected is going to be significant. Scientists aren’t sure what causes brain fog, which varies widely and affects even people who became only mildly physically ill from Covid-19 and had no previous medical conditions. Leading theories are that it arises when the body’s immune response to the virus doesn’t shut down or from inflammation in blood vessels leading to the brain. Confusion, delirium and other types of altered mental function, called encephalopathy, have occurred during hospitalization for Covid-19 respiratory problems, and a study found such patients needed longer hospitalizations, had higher mortality rates and often couldn’t manage daily activities right after hospitalization. But research on long-lasting brain fog is just beginning. A French report in August on 120 patients who had been hospitalized found that 34 percent had memory loss and 27 percent had concentration problems months later.
from Adam Kucharski: ‘Data from Scotland on reported activities and venues people visited prior to developing symptoms/testing positive. (Note this necessarily doesn’t imply they were infected in these places, just where infected people have recently been).’ “Hospitality” – ie pubs and restaurants – feature in around 22% of infections.
THE SWEDISH EXPERIMENT is coming to an end, as its policies fall in line with those of its neighbors. FoHM [the country’s public health authority, the Folkhälsomyndigheten] officials are “quietly changing their approach,” Einhorn says. [….] FoHM “should have listened more carefully to the scientific community both inside and outside the country,” Hansson says. Still, he predicts the rifts will eventually heal. “I am sure we will continue to argue, but I don’t see permanent damage,” he says. “We’ll move on. We’ll go back to complaining about grants.” But Ewing worries the fight has left permanent scars. He says at least three more members of the Vetenskapsforum are considering leaving Sweden, as Brusselaers did. And even if it turns out that the country has built up enough immunity to evade a new wave of disease, he says, the price has been too high. “I worry that countries around the world are going to say, ‘We can try what Sweden did.’ But we have killed too many people already.”
‘Preprint on masks and neck gaiters for source control on manikin [sic] by experienced group @NIOSH : https://www.medrxiv.org/content/10.1101/2020.10.05.20207241v1 N95 blocked 99% of aerosols, surgical mask 59%, 3-ply cloth mask 51%, neck gaiter 47% (1 layer) and 60% (2 layer), face shield 2%’ 2% is just shite.
Nicky Ryan is a saint.
Very solid slide deck from a group of aerosols scientists, regarding airborne transmission of SARS-CoV-2, including the evidence for aerosols, beyond droplets
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.”
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
“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
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.
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.’
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.
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
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.’
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.”
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)
Interesting — a new, high-performance, high-concurrency HTTP/1.1 client library in the AWS SDK, outperforming other Java HTTP client libs
+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. [….]
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.
tl;dr: ‘I totally get why people want to believe Sweden figured out a way to do it without suffering, but we didn’t.’
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.”
‘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.
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).
4 cases were more serious the second time around
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).
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.
Brian dug up an old nuclear-war survival pamphlet from the Irish Government, published circa 1965
Cumulative deaths per 100k, Finland/Sweden/Denmark/Norway. Bookmarking for the inevitable discussions with COVID deniers (thanks Soren!)
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’
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
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.’
this is incredible — the word roughly translates as “improvised fixes”, “hacks” or “McGyverism”, that kind of thing. fantastic Image Search
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
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
report from Benchspace on their open source PPE project during March and April. it’s great stuff. 50,000 face shields printed!
‘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.’
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
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.
via Vincent Glad, on Twitter: the positivity rate stratified by age, in the Marseilles region
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.
the latest hot new image format — pretty impressive compression numbers vs quality thresholds here
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…
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)
The current guidance doc for outbreak management in Ireland
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.
A complete guide via the Native Woodland Trust for planting trees in your garden, hedge, etc.
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.”
large number of people in a theatre, applauding
a paean to my favourite podcast
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.
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.’
‘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.’
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.
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.’