Justin Mason's Weblog Posts

Venous or arterial thrombosis and deaths among COVID-19 cases: a European network cohort study – The Lancet Infectious Diseases

“For people with a positive PCR test or a diagnosis of COVID-19, 90-day cumulative incidence ranged from 0.2% to 0.8% for venous thromboembolism and 0.1% to 0.8% for arterial thromboembolism”. Those are _very_ high incidences for these rare and very risky conditions.

(tags: thromboembolism risks covid-19 sars-cov-2 papers embolism thrombosis health)

Researchers Pinpoint Reason Infants Die From SIDS

This is a great breakthrough for such a tragic disease, and one which has led to terrible miscarriages of justice.

SIDS refers to the unexplained deaths of infants under a year old, and it usually occurs while the child is sleeping. According to Mayo Clinic, many in the medical community suspected this phenomenon could be caused by a defect in the part of the brain that controls arousal from sleep and breathing. The theory was that if the infant stopped breathing during sleep, the defect would keep the child from startling or waking up.  The Sydney researchers were able to confirm this theory by analyzing dried blood samples taken from newborns who died from SIDS and other unknown causes. Each SIDS sample was then compared with blood taken from healthy babies. They found the activity of the enzyme butyrylcholinesterase (BChE) was significantly lower in babies who died of SIDS compared to living infants and other non-SIDS infant deaths. BChE plays a major role in the brain’s arousal pathway, explaining why SIDS typically occurs during sleep.  Previously, parents were told SIDS could be prevented if they took proper precautions: laying babies on their backs, not letting them overheat and keeping all toys and blankets out of the crib were a few of the most important preventative steps. While safe sleep practices are still important for protecting infants, many children whose parents took every precaution still died from SIDS. These parents were left with immense guilt, wondering if they could have prevented their baby’s death. Dr. Carmel Harrington, the lead researcher for the study, was one of these parents. Her son unexpectedly and suddenly died as an infant 29 years ago. In an interview with the Australian Broadcasting Corporation (ABC), Harrington explained what she was told about the cause of her child’s death.  “Nobody could tell me. They just said it’s a tragedy. But it was a tragedy that didn’t sit well with my scientific brain.”  Since then, she’s worked to find the cause of SIDS, both for herself and for the medical community as a whole. She went on to explain why this discovery is so important for parents whose babies suffered from SIDS.  “These families can now live with the knowledge that this was not their fault,” she said.

(tags: healthcare medicine parenting science via:damienmulley sids diseases neurochemistry)

CeP Heating System | EcoVolt – Innovation in Energy

Interesting green retrofitting product — it’s a large, wall-sized electric heating panel that mounts seamlessly in plasterboard and can be painted — so like a large, invisible radiator which can run off solar PV.

(tags: solar pv retrofitting heating home radiators ecovolt)

Chat Control

“The End of the Privacy of Digital Correspondence”:

The EU wants to oblige providers to search all private chats, messages, and emails automatically for suspicious content – generally and indiscriminately. The stated aim: To prosecute child pornography. The result: Mass surveillance by means of fully automated real-time messaging and chat control and the end of secrecy of digital correspondence. Other consequences of the proposal are ineffective network blocking, screening of person cloud storage including private photos, mandatory age verification leading to the end of anonymous communication, censorship in Appstores and the paternalism and exclusion of minors in the digital world.

(tags: surveillance censorship chat-control eu laws messaging apps privacy data-privacy)

Thought-terminating cliché

A thought-terminating cliché (also known as a semantic stop-sign, a thought-stopper, bumper sticker logic, or cliché thinking) is a form of loaded language, often passing as folk wisdom, intended to end an argument and quell cognitive dissonance. Its function is to stop an argument from proceeding further, ending the debate with a cliché rather than a point.

(tags: cliches semantics logic cognitive-dissonance arguing arguments via:mltshp)

CarTrawler

the un-skinned booking site for car hire

(tags: cars car-hire holidays vacation)

“Hypercoagulation” as a potential long COVID sign

Interesting Twitter thread discussing a potential treatment for long COVID — no interest in providing even the relevant _tests_ in the UK, so a British kid was brought to Germany to receive the treatment, and is now responding well. Here’s details on the specific biosigns:

Her fluorescent microscopy showed very hyperactivated sticky platelets. Mine are on the right for comparison. She also had microclots and evidence of endothelial damage (but latter not severe). I believe she was the first UK child under 12 to have these tests done. The platelets and microclots show that her blood is ‘hypercoaguable’ – too sticky. These may be blocking up the very small blood vessels that allow oxygen into muscles and nerves, which could explain some of her symptoms.

(tags: platelets microclots long-covid treatments hypercoagulation covid-19)

“The first Starlink war”

Very interesting thread from Trent Telenko on how a Ukrainian GIS app, combined with Starlink internet access, has created 21st century artillery warfare and outflanked the Russia military:

Ukraine’s ‘GIS Art for Artillery’ app combined with Starlink actually gives the Ukrainian military measurably better than US Military standard artillery command and control. The Ukraine War is the first Starlink War & the side with Starlink is beating the side without.

(tags: starlink artillery internet gis elon-musk warfare tech gis-art)

Trino | Project Tardigrade delivers ETL at Trino speeds to early users

This looks fantastic — Trino (nee Presto) adds some significant improvements for long-running and heavyweight query support.

When your long-running queries experience a failure, they don’t have to start from scratch. When queries require more memory than currently available in the cluster they are still able to succeed. When multiple queries are submitted concurrently they are able to share resources in a fair way, and make steady progress.

(tags: trino presto sql storage querying etl batch scheduling)

metabolically-led post-exertional symptoms in Long COVID

Interesting thread from a Mount Sinai-based lab discussing the side effects of possible mitochondrial dysfunction and oxidative stress:

Our cells use a very specific fuel source called ATP that is produced in a part of the cell called the mitochondria. Unfortunately, ATP also fuels the cellular activities of viruses. As such, when a virus enters our cells it quickly hijacks our mitochondria to fuel viral replication and other viral activities. In other words when you are infected by a virus like #COVID19, you are infected by a little energy thief: taking your hard-earned ATP and using it for its own purposes. Not only does this mean that the virus is proliferating on stolen energy (rude!) but it also means that your cells must perform their regular functions with far less energy. So this is where things get cyclical: we have hijacked mitochondria resulting in inefficient, “stressed“ cells. Our cells are producing energy “for two” now, but barely managing to function, leading to the overproduction of reactive oxygen species (ROS), which we can think of as the “exhaust fumes” of our mitochondria. ROS are bad characters – systemically, they can trigger inflammation and hypocapnia. Unfortunately, once the body is experiencing oxidative stress, the mere act of producing more energy starts to damage the mitochondria.

(tags: mitochondria oxidative-stress long-covid covid-19 dysautonomia mcas inflammation)

SARS-CoV-2 Omicron Variant is as Deadly as Previous Waves After Adjusting for Vaccinations, Demographics, and Comorbidities

The numbers are in; omicron was as severe as previous variants, it was just that people had been vaccinated. (preprint)

(tags: omicron covid-19 severity vaccination diseases epidemiology)

Data Broker Is Selling Location Data of People Who Visit Abortion Clinics

“It costs just over $160 to get a week’s worth of data on where people who visited Planned Parenthood came from, and where they went afterwards.” …and this is why the GDPR is needed. grim

(tags: abortion capitalism data data-privacy privacy location safegraph)

Noto Emoji

‘an open source font that has you covered for all your emoji needs, including support for the latest Unicode emoji specification (14.0). It has multiple weights and features 3,663 emoji.’

(tags: emoji fonts typography type google noto)

An Post & OSI company “GeoDirectory” uses Census data to profile every Irish home

This is unpleasant stuff:

The Irish Council for Civil Liberties (ICCL) reveals that An Post & OSI use Census data to profile every Irish home and sell ‘location intelligence’ to data brokers and insurance companies. ICCL has lodged a complaint with the Data Protection Commission.

(tags: data-privacy data-protection iccl experian an-post osi census data privacy ireland)

Ireland by land quality

aka. “Classification of Ireland’s land area into four categories in relation to availability for forestry expansion and the area of productive and marginal agricultural land with most potential for forestry expansion” — good way to identify regions with poor agricultural land, ie. a better probability of rewilding

(tags: rewilding rural land ireland maps geodata fishery agriculture farming)

“Living with COVID” has been a lie

This is a fantastic thread from Luca Ferretti:

“Living with COVID” has been a lie. Not because it isn’t possible, or because it isn’t the right goal. But in practice it has clearly morphed into “let’s stop talking about COVID, and the problem will disappear by itself”. A dangerous and irresponsible bet. Most of the political & health authorities have implicitly chosen to rely mainly on vaccination to control COVID. A reasonable choice… if only the vaccination campaign would have aimed at protecting the entire population with sterilising vaccines adapted to the new variants. Instead, despite hundreds of vaccines in the pipeline, there are no next-generation or sterilising vaccines on the horizon… little large-scale clinical trials (apart from Israel)… and few updated vaccines against variants (Moderna’s Omicron-Delta booster and little else). Of course, protection for children has been repeatedly delayed (English kids between 5-11 were vaccinated only last month) and kids under 5 are still unprotected worldwide, with the laudable exception of Cuba. Everybody’s waiting for the US FDA, whose intentions are unclear. It is truly depressing to see so little and slow concrete progress on what is meant to be “the ultimate weapon” against SARSCoV2. It seems to suggest that we don’t really rely so much on it, and that we’re satisfied with postponing the problems until the next not-so-mild variant. Simple precautionary public hygiene measures – face masks and ventilation – are mostly ignored. Testing and surveillance, downsized or limited. And the growing stress on the healthcare system is being swept under the carpet, even as we risk paying the price for it for years. This is not the product of any large conspiracy. It is simply the result of a combination of neglect, inertia, bureaucracy, selfishness, careerism, lack of long-term perspective and so on, among some (though not all!) politicians, doctors, academics, bureaucrats and others…

(tags: covid-19 sars-cov-2 public-health medicine healthcare pandemics vaccination)

COVID Travel Restrictions Map

Decent summary tool from Sherpa, a Canadian travel company

(tags: sherpa travel covid-19 vaccination forms bureaucracy)

CoVariants

Ireland is included:

These graphs show [COVID-19] cases per million for selected countries, coloured by the estimated frequency of variants. Only a small percentage of cases are sequenced in most countries, therefore these graphs show the reported case numbers coloured by the frequency of variants detected by sequences in these countries – which may represent <5% of cases.

(tags: sars-cov-2 covid-19 cases variants charts graphs)

Bringing emulation into the 21st century

Well executed satire:

An 8080 microprocessor utilising a modern, containerised, microservices-based architecture running on Kubernetes with frontends for a CP/M test harness and a full implementation of the original Space Invaders arcade machine. The full project can be found as a github organisation https://github.com/21st-century-emulation which contains ~60 individual repositories each implementing an individual microservice or providing the infrastructure.

(tags: emulation kubernetes satire k8s containers microservices yikes)

GitHub has wiped out open source history by “suspending” Russian users

This sounds like a pretty crappy way to go about things:

It is unclear to me what GitHub’s intended result was with these account suspensions, but it appears to be incredibly destructive for any open source project that has interacted with a now-suspended account. On a service like Twitter, you can visit the placeholder profile of a suspended account and see a message communicating that the account is suspended, and other users’ @mentions of the account still link to the suspended account’s profile. On GitHub, that’s not how it works at all. Apparently, “suspending an account” on GitHub actually means deleting all activity for a user — which results in (1) every pull request from the suspended account being deleted, (2) every issue opened by the suspended account being deleted, (3) every comment or discussion from the suspended account being deleted. In effect, the user’s entire activity and history is evaporated. All of this valuable data is lost. The only thing left intact is the raw Git commit history. It’s as if the user never existed.

(tags: github fail russia sanctions git pull-requests suspensions accounts)

CVE-2022-21449: Psychic Signatures in Java

Argh, this is a bad one:

Recent releases of Java were vulnerable to a similar kind of trick, in the implementation of widely-used ECDSA signatures. If you are running one of the vulnerable versions then an attacker can easily forge some types of SSL certificates and handshakes (allowing interception and modification of communications), signed JWTs, SAML assertions or OIDC id tokens, and even WebAuthn authentication messages. All using the digital equivalent of a blank piece of paper. It’s hard to overstate the severity of this bug. If you are using ECDSA signatures for any of these security mechanisms, then an attacker can trivially and completely bypass them if your server is running any Java 15, 16, 17, or 18 version before the April 2022 Critical Patch Update (CPU). For context, almost all WebAuthn/FIDO devices in the real world (including Yubikeys*) use ECDSA signatures and many OIDC providers use ECDSA-signed JWTs.

(tags: java jvm crypto security ecdsa webauthn saml jwt fail)

Keep Ukraine Connected

A project by the NOG Alliance:

We are creating a platform so that we can collect what our colleagues in Ukraine need to keep the internet up and running. We will be the link between the tech community, manufacturers, whoever else wants to get involved and Ukraine. Where absolutely necessary we can even transport the required hardware from Europe to the Ukraine. The aim of the “Keep Ukraine Connected” task force is not only to mediate, but also to actively help the Ukrainian internet stay up.

(tags: inog nogs networking internet ukraine)

4a doesn’t connect to LTE after leaving WiFi : GooglePixel

I’m having this problem (with GoMo in Ireland). it’s annoying

(tags: lte google pixel pixel-4a hardware phones mobile)

Data from French long COVID cohort

This is a decent step forward in long COVID research. 968 self-selected long covid sufferers reporting their symptom progression over a year: “Proud to present our results on the course of Long Covid symptoms over time, using the @PatientsComPaRe cohort and recently published in @NatureComms. after 1 year 85% of patients still reported some symptoms; there were specific trajectories depending on symptoms (pane A). For example, 40% reported cough 60 days after symptom onset vs. 20% at 12 months after onset; 50% of patients report a considerable impact on their professional lives; Long Covid is a relapsing remitting disease. It seems that, over time, relapses tend to be less frequent; Future research will look at patient trajectories (understanding those who get better vs others) and looking at biomarkers of long COVID”.

(tags: long-covid covid-19 papers france symptoms)

ICGP Migraine Quick Reference Guide

The Irish College of General Practitioners have published their guidance for migraine treatment and it’s an excellent guide to symptoms, diagnosis, and treatment (as of 3 years ago at least). Sadly the new CGRP treatments aren’t available for my level of episodic migraine yet…

(tags: migraine headaches medicine icgp health diagnosis cgrp)

AWS Lambda Function URLs

“Built-in HTTPS Endpoints for Single-Function Microservices”. _Finally_ — this should have been part of Lambda right from the start

(tags: aws http lambda serverless microservices web-services)

“FAANG promo committees are killing Kubernetes”

This makes a lot of sense. Letting “working for a big software company” be the only way to effectively get paid to collaborate on open source wasn’t a great idea.

Promo committees have, for years now, been consistently undervaluing the work of full-time Kubernetes contributors. Or really of open source work more broadly. Attributable revenue has been taking over as one of the most important factors at most companies. And Kubernetes has very little of that. It’s happened gradually, and I don’t think this was ever an intended outcome but it’s a thing and we have to live with it. It’s too indirect, fixing a bug in kube-apiserver might retain a GCP customer or avoid a costly Apple services outage, but can you put a dollar value on that? How much is CI stability worth? Or community happiness? And then add on top of it, the time cost. “FOSS maintainers are overloaded” should not be news to anyone, but now add 20/hours a week of campaigning to other high-level folks to “build buzz” for your work and let me know how that goes.

(tags: k8s open-source google amazon faang work promotions career)

Absolutely mad numbers on Long COVID from the UK

via Dr. Deepti Gurdasani: ‘1.7 million people now living with long COVID (28 day definition) – that’s 1 in 37 people in the community; 780,000 have had this for *more than a year*; at least 334,000 got it during the omicron wave (impact since Feb not felt yet) increases are disproportionately high among young children — which is likely a combination of mass exposure and lack of vaccinations & other protections.’

(tags: long-covid covid-19 society health uk pandemics future)

A battle is raging over long covid in children | MIT Technology Review

We don’t know how many children are affected, and we don’t know which symptoms came from infections and which might have resulted indirectly from the pandemic. Scientists can’t even agree over what it means for children to have long covid.

(tags: long-covid children kids covid-19)

aws aws-sdk containers docker eks ec2 bugs fail imdsv2)

Russia’s plans for Ukraine

This is absolutely horrific — if this is an accurate output of the state (and I don’t doubt it is), then it’s a blueprint for current and future war crimes. ‘Russian state-owned propaganda outlet RIA published the new programmatic article with the title “What Russia must do with Ukraine”. The article reveals a detailed plan for a genocide, starting from full elimination of Ukrainian state.’

(tags: genocide politics russia ukraine war)

Tailscale moving _back_ to SQLite

this is quite an interesting story — the key detail is the addition of litestream, which streams writes from the write-ahead log up to S3 to provide live replication of SQLite dbs, near-real-time backups, and replays. nifty

(tags: databases sqlite sql storage litestream wal s3 state)

A Foolish Consistency: Consul at Fly.io

A good blog post about strong consistency in config data, and how it’s often not all that useful, and can pose a risk:

We mostly like Consul and would use it again in new designs. It’s easy to stand up. It’s incredibly useful to deploy infrastructure configurations. […] But we probably wouldn’t use Consul as the backing store for a global app platform again, in part because a global app platform might not even want a single globally consistent backing store. Our trajectory is away from it.

(tags: consul distcomp distributed raft configuration consistency)

‘Bot holiday’: Covid disinformation down as social media pivot to Ukraine

In case there was any doubt how much of Western COVID disinformation was being driven by Russian bot campaigns, this was a pretty big tell

(tags: internet bots russia propaganda misinformation disinformation covid-19 ukraine-invasion)

The three big myths about Omicron

These bear repeating, despite being known since January. This is quite a failure by our media, IMO. The 3 myths are: “endemic doesn’t mean mild; covid is not evolving to become milder; vaccinations are not ‘finished'”.

(tags: covid-19 uk ireland omicron sars-cov-2 pandemics health)

We can’t rely on boosters to get through each new wave of Covid

This is very worrying, given our government’s current “just boosters” strategy for dealing with COVID-19:

We are living in a precarious truce imposed through frequent mRNA boosters to keep the viral caseload “manageable”. But there are signs this isn’t sustainable, and that a strategy simply consisting of boosters in perpetuity may not be fit for purpose. Recent case surges in Hong Kong, Denmark and Scotland emphasise the fragility of that balance. And new evidence from the past two years suggests that encounters with different variants of Covid or different vaccine types can alter the effectiveness of later jabs in surprising ways – an effect called immune imprinting. This raises the possibility that booster performance could be even less predictable and effective in the future. Sars-CoV-2 began as a single variant, which we term the Wuhan strain. But we now inhabit a world where no two people share precisely the same exposure history: we have never been infected, or were asymptomatically, mildly or severely infected during any or a combination of the Wuhan to Alpha, Delta, Omicron or BA.2 waves, and we’ve all had somewhere from zero to four doses of diverse vaccines. The combination of these exposures gives each of us a unique immune memory repertoire.

(tags: covid-19 boosters vaccines vaccination immunology sars-cov-2 variants immune-imprinting)

Resilience4J

‘a lightweight fault tolerance library inspired by Netflix Hystrix, but designed for Java 8 and functional programming.’

(tags: fp hystrix java fault-tolerance retries timeouts architecture patterns circuit-breakers)

When is it safe to stop isolating after you have an omicron infection?

decent guide from NPR

(tags: omicron covid-19 isolation health sars-cov-2 quarantine)

Aerial Laser and Photogrammetry Survey of Dublin City

Nifty, I didn’t realise there was such high-resolution LIDAR imagery of Dublin available for free…

This record serves as an index to a suite of high density, aerial remote sensing data for a 2km² area of Dublin, Ireland obtained at an average flying altitude of 300m. Collected in March 2015, the data include aerial laser scanning (ALS) from 41 flight paths in the form of a 3D point-cloud (LAZ) and 3D full waveform ALS (LAS and Pulsewave), and imagery data including ortho-rectified 2D rasters (RGBi) and oblique images. The ALS data consist of over 1.4 billion points (inclusive of partially covered areas) and were acquired by a TopEye system S/N 443.

(tags: dublin city lidar scanning modelling 3d open-data surveys mapping)

A detailed shaded relief map of San Francisco California rendered from LIDAR data

Very pleasant rendering of LIDAR data for SF (via Nelson)

(tags: lidar maps relief mapping via:nelson san-francisco)

Komoot

“Find, plan and share your adventures” — good for sharing hiking trails, cycle routes, and walks

(tags: mapping maps cycling hiking walking routes)

Receive SMS Online

Useful to receive SMS verification codes with a specific country code

(tags: sms verification authentication)

“node-ipc” npm package deletes all files on local storage to protest Ukraine war

as one Twitter user put it, “one of the dumbest examples of performative activism in tech that I have ever seen” — side effects of this include allegedly wiping over 30,000 messages and files detailing war crimes committed in Ukraine by Russian army and government officials since the start of the invasion.

(tags: node-ipc fail malware war-crimes ukraine russia activism javascript node npm)

What doctors wish patients knew about long COVID | American Medical Association

At the June 2021 AMA Special Meeting, delegates adopted policy to support “the development of an ICD-10 code or family of codes to recognize Post-Acute Sequelae of SARS-CoV-2 infection (‘PASC’ or ‘long COVID’) and other novel post-viral syndromes as a distinct diagnosis.” Read about the AMA’s support for more resources to help millions living with long COVID. The AMA’s What Doctors Wish Patients Knew series provides physicians with a platform to share what they want patients to understand about today’s health care headlines, especially throughout the COVID-19 pandemic. For this installment, AMA member Devang Sanghavi, MD, took the time to discuss what patients need to know about long-haul COVID. Dr. Sanghavi is an intensivist and medical director of the medical intensive care unit (ICU) at Mayo Clinic in Jacksonville, Florida. Since summer of 2020, he has seen about 100 patients with long COVID, many of whom take weeks to recover.

(tags: health covid-19 long-covid pasc ama)

Incidence, co-occurrence, and evolution of long-COVID features: A 6-month retrospective cohort study of 273,618 survivors of COVID-19

‘Long-COVID clinical features occurred and co-occurred frequently and showed some specificity to COVID-19, though they were also observed after influenza. Different long-COVID clinical profiles were observed based on demographics and illness severity.’

(tags: long-covid flu covid-19 papers plos)

Primary schools & childcare services antigen programme – HSE.ie

Handy, the HSE now offer the free 5 tests for a Irish primary school close contact online, no phone call required

(tags: hse ireland covid-19 testing antigen-tests free)

Human Life International operating in Ireland

This US-based anti-abortion and anti-gender-rights group is now operating in Ireland, receiving an annual income of nearly €1m per year. It “[runs] the anti-abortion pregnancy counselling service Ask Majella, campaigns against the use of contraceptives, and […] a host of other Catholic endeavours […] also been linked to a Russian oligarch closely associated with the Kremlin and Vladimir Putin.”

(tags: human-life-international hli ireland abortion gender-rights ask-majella contraception politics right-wing)

A quick take on three pretty terrifying changes to the Online Safety Bill

If true, this is going to be bananas:

The UK is, indeed, taking the “world-leading” stance – not duplicated by any other western nation – of requiring any business or organisation whose online presence could possibly be accessed in the UK to proactively monitor and scan for legal content. That means you and your business and your project, not just the five or six companies the people who cooked up this law think the Internet is. This hits everyone and everything.

(tags: politics uk online-safety-bill web regulation)

the economics of DIY solar in Ireland

“Find me a single electricity tariff in Ireland that provides electricity for as cheap as 5.3c/kWh for at least one hour during the daytime. *crickets*.”

(tags: solar-power diy electricity power green-living ireland solar-panels)

“We were the last journalists in Mariupol. Now there are none”

Truly, truly horrific —

We are still flooded by messages from people wanting to learn the fate of loved ones we photographed and filmed. They write to us desperately and intimately, as though we are not strangers, as though we can help them. When a Russian airstrike hit a theater where hundreds of people had taken shelter late last week, I could pinpoint exactly where we should go to learn about survivors, to hear firsthand what it was like to be trapped for endless hours beneath piles of rubble. I know that building and the destroyed homes around it. I know people who are trapped underneath it. And on Sunday, Ukrainian authorities said Russia had bombed an art school with about 400 people in it in Mariupol. But we can no longer get there.

(tags: mariupol ukraine war journalism)

Dual use of artificial-intelligence-powered drug discovery | Nature Machine Intelligence

Well, this is terrifying:

In less than 6 hours after starting on our in-house server, our [machine learning] model generated 40,000 molecules that scored within our desired threshold. In the process, the AI designed not only VX, but also many other known chemical warfare agents that we identified through visual confirmation with structures in public chemistry databases. Many new molecules were also designed that looked equally plausible. These new molecules were predicted to be more toxic, based on the predicted LD50 values, than publicly known chemical warfare agents (Fig. 1). This was unexpected because the datasets we used for training the AI did not include these nerve agents. The virtual molecules even occupied a region of molecular property space that was entirely separate from the many thousands of molecules in the organism-specific LD50 model, which comprises mainly pesticides, environmental toxins and drugs (Fig. 1). By inverting the use of our machine learning models, we had transformed our innocuous generative model from a helpful tool of medicine to a generator of likely deadly molecules.

(tags: dual-use grim-meathook-future ai machine-learning drugs vx scary papers)

New-onset IgG autoantibodies in hospitalized patients with COVID-19

This is not great — this article in Nature from Sep 2021 details “autoimmune features and autoantibody production” associated with COVID-19 infection.

COVID-19 is associated with a wide range of clinical manifestations, including autoimmune features and autoantibody production. Here we develop three protein arrays to measure IgG autoantibodies associated with connective tissue diseases, anti-cytokine antibodies, and anti-viral antibody responses in serum from 147 hospitalized COVID-19 patients. Autoantibodies are identified in approximately 50% of patients but in less than 15% of healthy controls. When present, autoantibodies largely target autoantigens associated with rare disorders such as myositis, systemic sclerosis and overlap syndromes. A subset of autoantibodies targeting traditional autoantigens or cytokines develop de novo following SARS-CoV-2 infection. [….] We conclude that SARS-CoV-2 causes development of new-onset IgG autoantibodies in a significant proportion of hospitalized COVID-19 patients and are positively correlated with immune responses to SARS-CoV-2 proteins.

(tags: covid-19 autoimmune autoantibodies immune-system diseases sclerosis igg antibodies via:fitterhappieraj)

Long Covid now major cause of long-term job absence, say quarter of UK employers | Financial Times

A quarter of UK employers say long Covid is now one of the main causes of long-term sickness absence among their staff, according to research that suggests the debilitating condition could be exacerbating labour shortages that are plaguing many parts of the economy. A survey of 804 organisations, representing more than 4.3m employees, found that one in four put it among the top three reasons for long-term absence, the Chartered Institute of Personnel and Development said on Tuesday, while half had staff who had suffered from long Covid in the past 12 months.

(tags: long-covid future uk disabilities covid-19 health economy)

RangeBitmap

‘How range indexes work in Apache Pinot’ — a complex, but fast algorithm to support range indexes efficiently using bitmaps

(tags: bitmaps algorithms coding ranges indexes indexing databases storage pinot richard-startin)

Why America Became Numb to COVID Deaths – The Atlantic

Excellent article by Ed Yong. ‘The U.S. is nearing 1 million recorded COVID-19 deaths without the social reckoning that such a tragedy should provoke. Why?’

(tags: covid-19 ed-yong us-politics death disease medicine public-health pandemics economy capitalism)

Fuck leftist westplaining

Polish leftie giving out about western Tankies supporting Putin:

Antifascism is protecting people from individuals with structural power. Right now that is Putin. If you are protecting his hegemony over his vast and increasing empire, if you are What Abouting into helplessness, you are part of the aggressor. So pick up a weapon, or organise a fundraiser, or welcome a refugee, but even more preferably at this point – shut the fuuuuck up. Log out, touch grass, leave this war with people that actually know what they’re fighting for. You’re fighting for likes – it’s humiliating – to the left in general, and to future generations who will be left demoralised, rather than inspired to fight for a world sans dictators. Yes, your leaders are some of them, so take care of taking them down. Sadly we seldom even trust the leaders you’d put in their place. This is the level of faith that you’re losing. Look in the mirror, destroy the imperialist exceptionalist cop inside your head. Good luck.

(tags: politics ukraine putin whataboutery tankies)

Decent SQL patterns for data science pipelines

If you wind up using complex SQL queries run frequently to generate reports, OLAP-style, this blog post details a few good patterns worth following — particularly the use of clean SQL using common table expressions and WITH … AS

(tags: sql coding clean-code patterns data-science data-pipelines olap)

study of “Long COVID” symptoms in the Danish population

These numbers are frankly massive:

Six to twelve months after the test date, the risks of 18 out of 21 physical symptoms were elevated among test-positives and one third (29.6%) of the test-positives experienced at least one physical post-acute symptom. [jm: “test-positives” are “individuals aged 15-years or older, consisting of RT-PCR confirmed SARS-CoV-2 cases between September 2020 – April 2021”] The largest risk differences were observed for dysosmia (RD = 10.92%, 95%CI 10.68-11.21%), dysgeusia (RD=8.68%, 95%CI 8.43-8.93%), fatigue/exhaustion (RD=8.43%, 95%CI 8.14-8.74%), dyspnea (RD=4.87%, 95%CI 4.65-5.09%) and reduced strength in arms/legs (RD=4.68%, 95%CI 4.45-4.89%). More than half (53.1%) of test-positives reported at least one of the following conditions: concentration difficulties (RD=28.34%, 95%CI 27.34-28.78%), memory issues (RD=27.25%, 95%CI 26.80-27.71%), sleep problems (RD=17.27%, 95%CI 16.81-17.73%), mental (RD=32.58%, 95%CI 32.11-33.09%) or physical exhaustion (RD=40.45%, 95%CI 33.99-40.97%), compared to 11.5% of test-negatives. New diagnoses of anxiety (RD=1.15%, 95%CI 0.95-1.34%) or depression (RD=1.00%, 95%CI 0.81-1.19%) were also more common among test-positives. Interpretation: At the population-level, where the majority of test-positives (96.0%) were not hospitalized during acute infection, a considerable proportion experience post-acute symptoms and sequelae 6-12 months after infection.

(tags: long-covid denmark studies papers covid-19)

Telegram Harm Reduction for Users in Russia and Ukraine

The EFF’s position on “should you use Telegram in Ukraine”.

(tags: apps communication eff encryption ukraine russia war security)

What Exactly are AWS VPC Endpoints

VPC endpoints are AWS magic to allow private, secure access to S3, DynamoDB, and other AWS services without any traversal outside of your private VPC network. This blog post is a good description of how this is accomplished, and very useful if you need to debug AWS networking issues. (via Last Week In AWS)

(tags: aws networking vpc vpc-endpoints architecture ops s3 dynamodb security)

Additional Checksum Algorithms for Amazon S3

This is good stuff:

It is now very easy for you to calculate and store checksums for data stored in Amazon S3 and to use the checksums to check the integrity of your upload and download requests. You can use this new feature to implement the digital preservation best practices and controls that are specific to your industry. In particular, you can specify the use of any one of four widely used checksum algorithms (SHA-1, SHA-256, CRC-32, and CRC-32C).

(tags: checksums integrity uploads s3 sha crc md5)

Fixing retries with token buckets and circuit breakers

Very interesting writeup from Marc Brooker detailing a new (to me) retry strategy, the “retry token bucket”:

Adaptive Retries (aka the retry token bucket). When a client wants to make a call, it makes that call as normal. If it succeeds, it drops part of a token into a limited-size token bucket. If the call fails, retry up to N times as long as there are (whole) tokens in the bucket. For example, each success could deposit 0.1 tokens, and each retry could consume 1 token.

(tags: circuit-breakers distributed-systems distcomp retries retrying token-buckets algorithms reliability marc-brooker)

Crowdworking platforms used as a tool of war

File under “grim dystopian 21st century”: Bogdan Kulynych on Twitter: “New (to me) dimension of crowdwork platforms: Russian military [used] Premise microtasking platform to aim and calibrate fire during their invasion of Ukraine. Example tasks are to locate ports, medical facilities, bridges, explosion craters. Paying ¢0.25 to $3.25 a task.” This may explain why Google Maps coverage of the area wound up with many of those features tagged in the past week.

(tags: ethics security google crowdwork crowdsourcing warfare war ukraine grim-meathook-future)

Why you should develop a correction of error (COE) | AWS Cloud Operations & Migrations Blog

AWS are proselytising their post-outage retrospective analysis process, the COE. Generally good stuff but they are clearly _still_ married to jeffb’s local timezone:

When documenting times, be sure to include a time zone, and make sure that you’re using it correctly (e.g., PDT vs. PST). Better yet, either use UTC or omit the middle letter of the time zone (e.g., “PT”).

(tags: amazon aws timezones coe process postmortems dates pdt pst utc)

New – Customer Carbon Footprint Tool | AWS News Blog

‘Starting today customers can calculate the environmental impact of their AWS workloads with the new customer carbon footprint tool. This new tool uses easy-to-understand data visualizations to provide customers with their historical carbon emissions, evaluate emission trends as their use of AWS evolves, approximate the estimated carbon emissions they have avoided by using AWS instead of an on-premises data center, and review forecasted emissions based on current use. The forecasted emissions are based on current usage, and show how a customer’s carbon footprint will change as Amazon stays on path to powering its operations with 100% renewable energy by 2025, five years ahead of its original target of 2030, and drives toward net-zero carbon by 2040 as part of The Climate Pledge. The customer carbon footprint tool is visible today through the AWS Billing console and helps to support customers on their sustainability journey. When signed into the AWS Billing console, customers can view their carbon emissions data by geographical location and by AWS services, such as Amazon Elastic Compute Cloud (EC2) and Amazon Simple Storage Service (S3). They can also measure changes in their carbon footprint over time, as they deploy new resources in the cloud. The new tool uses data that meets the Greenhouse Gas Protocol, which is the international standard for greenhouse gas reporting.’ Covers Scope 1 and Scope 2 emissions.

(tags: aws carbon emissions climate-change sustainability climate infrastructure ops ec2 s3)

more nails in the coffin of the lab-leak theory

Michael Worobey on Twitter:

We have just released two preprints on the origin of SARS-CoV-2: 1. “The Huanan market was the epicenter of SARS-CoV-2 emergence” ( https://zenodo.org/record/6299116#.YhpLBi9h06w ) & 2. “SARS-CoV-2 emergence very likely resulted from at least two zoonotic events” ( https://zenodo.org/record/6291628 )

(tags: animals china epidemiology sars-cov-2 covid-19 lab-leak michael-worobey papers preprints zoonosis)

Good thread on UK COVID testing and random sampling

The UK has an ongoing, population-wide random-sampling study of COVID prevalence in the UK population, operated by the ONS. This is a solid write-up on how it can be used to estimate two parameters for modelling prevalence from the more up-to-date case numbers: the detectability window, and ascertainment level.

(tags: covid-19 testing sampling random measurement ascertainment detectability epidemiology sars-cov-2 uk ons modelling)

How to create a simple Twitter bot

super-simple guide from b3ta’s Rob Manuel

(tags: python twitter bots rob-manuel)

Excellent Twitter thread on the current COVID-19 situation in Denmark

Courtesy of Kristian Andersen:

So looking at this report – and only focusing on population-based acute effects – I see several trends that concern me. Are these acute consequences acceptable? For me, no, but politicians need to decide. Are we making decisions based on a realistic outlook? I’m not sure.

(tags: covid-19 endemicity pandemics denmark ireland omicron public-health)

GitHub now supports embedded graphs and diagrams using Mermaid

This is very handy!

Mermaid is a JavaScript based diagramming and charting tool that takes Markdown-inspired text definitions and creates diagrams dynamically in the browser. Maintained by Knut Sveidqvist, it supports a bunch of different common diagram types for software projects, including flowcharts, UML, Git graphs, user journey diagrams, and even the dreaded Gantt chart. Working with Knut and also the wider community at CommonMark, we’ve rolled out a change that will allow you to create graphs inline using Mermaid syntax.

(tags: diagrams github markdown mermaid charts graphs)

UKHSA review shows vaccinated less likely to have long COVID than unvaccinated – GOV.UK

Good data from UKHSA:

The data from some of the studies included in the review suggests that: people with COVID-19 who received 2 doses of the Pfizer, AstraZeneca, or Moderna vaccines or one dose of the Janssen vaccine, were about half as likely as people who received one dose or were unvaccinated to develop long COVID symptoms lasting more than 28 days; vaccine effectiveness against most post-COVID symptoms in adults was highest in people aged 60 years and over, and lowest for younger participants (19 to 35 years)

(tags: long-covid uk ukhsa vaccines sars-cov-2)

a short story about pandemic misinformation & biased reporting

Well-illustrated case study from 2021 in how misinformation evolves in the mainstream press. First, an Irish Times journalist concocted a thesis (“Given that only 1 in 1,000 cases of COVID-19 come from an outdoor setting, is the government too prohibitive on people meeting outdoors?”), and got a weakly confirmatory response from the HPSC (who should have known better). Through poor reporting by other newspapers around the world, this quickly became a “fact” reported by an Irish “study” — despite being nothing of the sort — and published in the New York Times and NPR. Eventually it became a research reference in several academic papers and the BMJ. Naturally, warnings from experts, and the Minister for Health, about its inaccuracy, were ignored. What a mess…

(tags: misinformation irish-times fail health covid-19 safety hpsc new-york-times npr bmj)

A decade of major cache incidents at Twitter

a massive list of cache-related outages from Dan Luu — I still have fear of large scale cache reliance, inherited from Amazon, and this terrifying list doesn’t help!

(tags: caching architecture twitter ops outages history)

COVID-19 takes serious toll on heart health—a full year after recovery | Science

In an analysis of more than 11 million U.S. veterans’ health records, researchers found the risk of 20 different heart and vessel maladies was substantially increased in veterans who had COVID-19 1 year earlier, compared with those who didn’t. The risk rose with severity of initial disease and extended to every outcome the team examined, including heart attacks, arrhythmias, strokes, cardiac arrest, and more. Even people who never went to the hospital had more cardiovascular disease than those who were never infected. The results are “stunning … worse than I expected, for sure,” says Eric Topol, a cardiologist at Scripps Research. “All of these are very serious disorders. … If anybody ever thought that COVID was like the flu this should be one of the most powerful data sets to point out it’s not.” He adds that the new study “may be the most impressive Long Covid paper we have seen to date.” […] “In the post-COVID era, COVID might become the highest risk factor for cardiovascular outcomes,” greater than well-documented risks such as smoking and obesity, says Larisa Tereshchenko.

(tags: covid-19 health medicine long-covid sars-cov-2 heart stroke)

Radio station snafu in Seattle bricks some Mazda infotainment systems

Bananas. Crappy code in Mazda Connectivity Master Units (CMUs), a component in the Mazda infotainment system in models built between 2014 and 2017, had a massive bug: they would crash and enter a crash/reboot cycle on receiving unexpected input via radio.

The problem, according to Mazda, was that the radio station sent out image files in its HD radio stream that did not have extensions, and it seems that Mazda’s infotainment system of that generation needs an extension (and not a header) to tell what a file is. No extension, no idea, and the system gets corrupted.

(tags: radio security mazdas infotainment cars embedded-systems fail bugs images)

We won! UK Home Office to stop using racist visa algorithm

Spectacular inbuilt algorithmic discrimination in the UK:

The visa algorithm discriminated on the basis of nationality – by design. Applications made by people holding ‘suspect’ nationalities received a higher risk score. Their applications received intensive scrutiny by Home Office officials, were approached with more scepticism, took longer to determine, and were much more likely to be refused. We argued this was racial discrimination and breached the Equality Act 2010. Entrenched bias and racism in the visa system breaks hearts and tears families apart, like the four siblings from Nigeria unable to travel to the UK for their sister’s wedding, or the countless skilled professionals refused unable to contribute to conferences and events in the UK just because they don’t come from a rich white country – including scores of African academics and artists denied entry for no good reason. The streaming tool was opaque. Aside from admitting the existence of a secret list of suspect nationalities, the Home Office refused to provide meaningful information about the algorithm. It remains unclear what other factors were used to grade applications. The algorithm suffered from a feedback loop — a vicious circle in which biased enforcement and visa statistics reinforce which countries stay on the list of suspect nationalities. In short, applicants from suspect nationalities were more likely to have their visa application rejected. These visa rejections then informed which nationalities appeared on the list of ‘suspect’ nations. This error, combined with the pre-existing bias in Home Office enforcement (in which some nationalities are targeted for enforcement because they are believed to be easier to remove), accelerated bias in the Home Office’s visa process. Such feedback loops are a well-documented problem with automated decision systems.

(tags: algorithms racism uk immigration automation home-office)

Environmental Reporting Dashboards for OpenStack

A neat integration of Scaphandre into an OpenStack cluster by BBC R&D:

While researching tools to monitor VM power usage, we evaluated Scaphandre – an open-source monitoring agent for energy consumption metrics created by Hubblo and Benoit Petit. Scaphandre can measure the CPU power consumption of the whole server and its processes using Intel RAPL alongside CPU utilisation statistics stored in proc/stat. Scaphandre estimates how many CPU watts each process is responsible for by looking at the CPU time spent on it, and the CPU power consumption for the whole server reported by Intel RAPL. Each running VM appears as a process running on the server – therefore, Scaphandre can report the CPU power consumption for each VM. We then used the Carbon Intensity API, created by the UK National Grid ESO, to calculate the carbon dioxide emissions corresponding to each VM’s CPU power consumption. This API provides the number of grams of carbon dioxide (gCO2) emitted to generate a kilowatt-hour (kWh) of electricity consumed at a UK regional level. This figure, referred to as the carbon intensity of electricity generation, varies over time according to the type of generation and electricity demand. Multiplying the carbon intensity figure by the CPU power consumption of a VM at a given point in time results in the carbon dioxide emissions the VM is responsible for.

(tags: scaphandre bbc openstack co2 climate emissions power)

Energy crisis: Is net zero and environmental policy responsible for rising energy bills?

If we’re serious about replacing fossil fuels with renewables we will have to build an awful lot of them, and while the eventual lifetime cost could be lower than fossil fuels, the short-term cost per MWh is way, way higher. So if we’re serious about net zero you’d expect our governments and companies to be spending extraordinary amounts on new primary power projects right now. But glance at the statistics and it turns out we’re not. On the contrary, investment in primary energy — those plans and solar panels and wind turbines we need to give us power — has flatlined since 2015.

(tags: energy future climate-change power fossil-fuels renewables research net-zero)

braided cables

prized by audiophiles, but TBH I think they just look pretty cool

(tags: cables braiding cool)

Missing Manuals – io_uring worker pool

‘Calling io_uring just an asynchronous I/O API doesn’t do it justice, though. Underneath the API calls, io_uring is a full-blown runtime for processing I/O requests. One that spawns threads, sets up work queues, and dispatches requests for processing. All this happens “in the background” so that the user space process doesn’t have to, but can, block while waiting for its I/O requests to complete. A runtime that spawns threads and manages the worker pool for the developer makes life easier, but using it in a project begs the questions: 1. How many threads will be created for my workload by default? 2. How can I monitor and control the thread pool size? […..] 3. What is an unbounded worker? 4. How does it differ from a bounded worker? Things seem a bit under-documented as is, hence this blog post. Hopefully, it will provide the clarity needed to put io_uring to work in your project when the time comes.’

(tags: linux io_uring apis runtime kernel system-calls coding performance)