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Justin Mason's Weblog Posts

Links for 2022-03-21

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Links for 2022-03-15

  • 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.
    (via Theophite)

    (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)

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Links for 2022-03-11

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Links for 2022-03-09

  • 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)

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Links for 2022-03-07

  • 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).
    (via Last Week in AWS)

    (tags: checksums integrity uploads s3 sha crc md5)

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Links for 2022-03-04

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Links for 2022-03-02

  • 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”).
    As Brian Scanlan sez: “A good 1/4 of the neurons in my brain were wired to quickly add and subtract 8 hours from timestamps by the time I left there” Just. Use. UTC.

    (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)

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Links for 2022-03-01

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Links for 2022-02-22

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Links for 2022-02-18

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Links for 2022-02-16

  • 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.
    Nearly graphviz but not quite :)

    (tags: diagrams github markdown mermaid charts graphs)

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Links for 2022-02-15

  • 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)
    They also estimate prevalence of long COVID as affecting 2% of the UK population.

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

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Links for 2022-02-14

  • 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)

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Links for 2022-02-10

  • 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.
    Just to add insult to injury, there’s no way to field-repair this embedded system — no “factory reset” switch was provided — so the only way to fix it is to install a new CMU at the cost of $1,500, and none are available due to “supply chain issues”. Goes to show you that image decoding libraries remain a fine source of vulnerability surfaces…

    (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)

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Links for 2022-02-09

  • 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)

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DynamoDB-local on Apple Silicon

DynamoDB Local is one of the best features of AWS DynamoDB. It allows you to run a local instance of the data store, and is perfect for use in unit tests to validate correctness of your DynamoDB client code without calling out to the real service “in the cloud” and involving all sorts of authentication trickiness.

Unfortunately, if you’re using one of the new MacBooks with M1 Apple silicon, you may run into trouble:

11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB > Feb 04, 2022 11:08:56 AM com.almworks.sqlite4java.Internal log
11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB > SEVERE: [sqlite] SQLiteQueue[]: error running job queue
11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB > com.almworks.sqlite4java.SQLiteException: [-91] cannot load library: java.lang.UnsatisfiedLinkError: /.../DynamoDBLocal_lib/libsqlite4java-osx.dylib: dlopen(/.../DynamoDBLocal_lib/libsqlite4java-osx.dylib, 0x0001): tried: '/.../DynamoDBLocal_lib/libsqlite4java-osx.dylib' (fat file, but missing compatible architecture (have 'i386,x86_64', need 'arm64e')), '/usr/lib/libsqlite4java-osx.dylib' (no such file)
11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB >      at com.almworks.sqlite4java.SQLite.loadLibrary(SQLite.java:97)
11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB >      at com.almworks.sqlite4java.SQLiteConnection.open0(SQLiteConnection.java:1441)
11:08:56.893 [DEBUG] [TestEventLogger]          DynamoDB >      at com.almworks.sqlite4java.SQLiteConnection.open(SQLiteConnection.java:282)
11:08:56.894 [DEBUG] [TestEventLogger]          DynamoDB >      at com.almworks.sqlite4java.SQLiteConnection.open(SQLiteConnection.java:293)

It’s possible to invoke it via Rosetta, Apple’s qemu-based x86 emulation layer, like so:

arch -x86_64 /path/to/openjdk/bin/java dynamodb-local.jar

But if you don’t have control over the invocation of the Java command, or just don’t want to involve emulation, this is a bit hacky. Here’s a better way to make it work.

First, download dynamodb_local_latest.tar.gz from the DynamoDB downloads page, and extract it.

The DynamoDBLocal_lib/libsqlite4java-osx.dylib file in this tarball is the problem. It’s OSX x86 only, and will not run with an ARM64 JVM. However, the same lib is available for ARM64 in the libsqlite4java artifacts list, so this will work:

wget -O libsqlite4java-osx.dylib.arm64 'https://search.maven.org/remotecontent?filepath=io/github/ganadist/sqlite4java/libsqlite4java-osx-arm64/1.0.392/libsqlite4java-osx-arm64-1.0.392.dylib'
mv DynamoDBLocal_lib/libsqlite4java-osx.dylib libsqlite4java-osx.dylib.x86_64
lipo -create -output libsqlite4java-osx.dylib.fat libsqlite4java-osx.dylib.x86_64 libsqlite4java-osx.dylib.arm64
mv libsqlite4java-osx.dylib.fat DynamoDBLocal_lib/libsqlite4java-osx.dylib

This is now a “fat” lib which supports both ARM64 and x86 hardware. Hey presto, you can now invoke DynamoDBLocal in the normal Rosetta-free manner, and it’ll all work — on both hardware platforms.

(This post is correct as of version 2022-1-10 (1.18.0) of DynamoDB-Local — let me know by mail, or at @jmason on Twitter, if things break in future, and I’ll update it.)

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Links for 2022-02-08

  • Long-term cardiovascular outcomes of COVID-19 | Nature Medicine

    Yikes:

    beyond the first 30 days after infection, individuals with COVID-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease. These risks and burdens were evident even among individuals who were not hospitalized during the acute phase of the infection and increased in a graded fashion according to the care setting during the acute phase (non-hospitalized, hospitalized and admitted to intensive care). Our results provide evidence that the risk and 1-year burden of cardiovascular disease in survivors of acute COVID-19 are substantial. Care pathways of those surviving the acute episode of COVID-19 should include attention to cardiovascular health and disease.

    (tags: covid-19 papers nature disease health long-covid sars-cov-2)

  • Crypto, NFTs, and sports betting: Money is now a hobby – Vox

    “The internet turned “money” into a hobby — Why (mostly) 20- and 30-something dudes made crypto and sports betting their personality”:

    Jeff, like most skeptics for whom the system has actually worked pretty well, is eager to cash out once the price of ethereum goes back up. But talking to him, and to the rest of the (almost entirely) men who’ve turned money into a hobby, made me more than anything feel like I was too late to something that hadn’t even really happened yet. Because of course it isn’t “too late” to become an overnight crypto millionaire or to cash out on an incredibly lucky bet; it’s just highly unlikely that that person will be you. Nobody wants to be a cynical spoilsport, stewing in resentment of these men who have won and will probably keep winning, who look a lot like the ones who have always won: the men who have the time, the knowledge, the energy, and, most importantly, the money to turn “having money” into its own hobby.

    (tags: crypto finance gambling internet nfts ethereum scams hobbies betting)

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Links for 2022-02-07

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Links for 2022-02-03

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Links for 2022-02-02

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Links for 2022-01-26

  • Resurrecting Nikolai Fedorov

    The original “rapture of the nerds”:

    [Fedorov’s] thought was powerfully shaped by both Orthodox Christianity and Hegelian philosophy. […] Rather than passively waiting for God to bring on the Millennium, being a good Christian meant participating in the building of heaven on Earth. It was the way in which he expected this to come about that really separated Fedorov from the others. In his thinking there is only one evil in the world that really counts, death. Moreover, rather than being accepted as a part of “the human condition,” part of the human mission is the technological conquest of death. This means not only achieving immortality, but restoring all the people who have ever walked the Earth to life so that they may share the gift as well, making the heaven of the afterlife a physical reality. […] To help bring the dead back to life, Fedorov believed that humanity would eventually launch expeditions across the cosmos to recover particles that once belonged to their ancestors in order to reconstitute their bodies. Additionally, since Earth would not be big enough to accommodate all of the people who had ever lived at once, room would be found for them on other planets.
    (via Charlie Stross)

    (tags: via:cstross rapture nerds singularity futurism posthumanism space biotechnology death immortality life-extension future nikolai-fedorov philosophy religion)

  • Long Covid risk reduced by double vaccination

    _Self-reported long COVID after two doses of a coronavirus (COVID-19) vaccine in the UK_ – report from the UK Office for National Statistics. Tl;dr: ‘reduced odds of Long Covid if SARS-CoV-2 infection occurs after double vaccination in adults. Almost half less likely (OR 41%) compared to unvaccinated when infected.’ See also this preprint https://www.medrxiv.org/content/10.1101/2022.01.05.22268800v2

    (tags: long-covid covid-19 ons uk vaccines vaccination)

  • rMA 15 – 15 passages resulted in a very pathogenic variant of SARS-CoV

    “A Mouse-Adapted SARS-Coronavirus Causes Disease and Mortality in BALB/c Mice”: “We adapted the SARS-CoV (Urbani strain) by serial passage in the respiratory tract of young BALB/c mice. Fifteen passages resulted in a virus (MA15) that is lethal for mice following intranasal inoculation.” This is the scary paper which Anthony J Leonardi refers to regularly — 15 passages through mice resulted in SARS-CoV (the first one) becoming much more pathogenic.

    (tags: viruses rma-15 sars-cov)

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Links for 2022-01-25

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Links for 2022-01-24

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Links for 2022-01-21

  • My custom solar monitoring system (PVS6)

    Nelson’s telegraf/grafana setup for monitoring his domestic solar power setup. Very nice indeed, I’ll be taking some inspiration from this when I (finally) get around to getting panels on my roof

    (tags: solar-power solar home graphs grafana dashboards monitoring telegraf via:nelson)

  • DeliverMe.ie

    another UK / Northern Ireland delivery address parcel-forwarding service. Extremely expensive compared to the now-obsolete Parcel Motel, at 25 euros per parcel, but if there’s no other option for ordering from Brexitland, at least it’s there.

    (tags: delivery brexit uk parcels shipping ireland)

  • zzh Multiprotocol RF Stick

    Apparently the bees knees for Zigbee usage with an open platform like Home Assistant:

    zzh is the original “USB stick” form-factor development board for TI’s new generation CC2652R chips. It features: TI CC2652R1 2.4 GHz multi-protocol wireless microcontroller targeting Thread, Zigbee, Bluetooth 5 Low Energy, IEEE 802.15.4g, IPv6-enabled smart objects (6LoWPAN) and proprietary systems; Communicates with the host computer via the common CH340 USB-UART bridge, no manual driver installation needed in most cases (Windows and Linux); Self-programming via the TI CC-series serial bootloader. As long as it is not explicitly disabled in code, no external programmer needed! Pushbutton on the default pin to trigger this mode; cJTAG debug header, in case you disable BSL by accident or want a proper debug interface; SMA antenna port for an external antenna of your choice

    (tags: ha hardware toget gadgets zha home home-assistant zigbee bluetooth ble usb)

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Links for 2022-01-20

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Links for 2022-01-19

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Links for 2022-01-17

  • Prof. Akiko Iwasaki Twitter thread on a significant long COVID paper

    ‘Significant long-term neurologic damage can occur after a mild respiratory-only SARS-CoV-2 infection.’ […] ‘In a nutshell, this study illustrates that respiratory-only mild SARS-CoV-2 infection can lead to detrimental changes in the brain, likely mediated by inflammatory factors. Similar neuropathobiology may be shared in chemo-brain, post-ICU syndrome and ME/CFS.’

    (tags: neurology long-covid papers medicine health me cfs inflammation cytokines)

  • Reverse Engineering Nike Run Club Android App Using Frida

    walkthrough of using Frida to decompile, hook into and reverse an Android app

    (tags: android scripting frida reverse-engineering security mobile)

  • Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection | Nature Immunology

    Nature Immunology paper on Long COVID, suggesting a clear physiological syndrome, and a set of reliable biomarkers that may be usable to diagnose it:

    In summary, our data indicate an ongoing, sustained inflammatory response following even mild-to-moderate acute COVID-19, which is not found following prevalent coronavirus infection. The drivers of this activation require further investigation, but possibilities include persistence of antigen, autoimmunity driven by antigenic cross-reactivity or a reflection of damage repair. These observations describe an abnormal immune profile in patients with COVID-19 at extended time points after infection and provide clear support for the existence of a syndrome of LC. Our observations provide an important foundation for understanding the pathophysiology of this syndrome and potential therapeutic avenues for intervention.

    (tags: nature papers covid-19 sars-cov-2 long-covid t-cells immunology)

  • Fever is good for you

    Fever — the feeling of having a high temperature, sweats, shivering etc. — is actually a *good* thing:

    Fever is preserved evolutionarily, suggesting benefit; There is a metabolic cost to fever which may partly explain why we’re not just evolving to be hotter; The benefit relates to its direct anti-pathogen effects and its ability to augment innate and adaptive immunity; Antipyretics are overused.
    In particular, a randomised controlled trial of fever treatment in trauma ICU patients was halted early, due to a significant difference in deaths during the trial!

    (tags: fever temperature body health medicine rcts metabolism trials)

  • The State of Web Scraping 2022

    Blog post from ScrapeOps.io (whoever they are). Interesting to see where web scraping has gone over the years — looks like an arms race has taken place:

    Websites and anti-bot providers have continued to develop more sophisticated anti-bot measures. They are increasingly moving away from simple header and IP fingerprinting, to more complicated browser and TCP fingerprinting with webRTC, canvas fingerprinting and analysing mouse movements so that they can differentiate automated scrapers from real-users. But as of yet no anti-bot has found the magic bullet to completely prevent web scrapers. With the right combination of proxies, user agents and browsers, you can scrape every website. Even those that seem unscrapable. However, whilst scraping a website might be still possible, anti-bots can make it not worth the effort and cost if you have to resort to ever more expensive web scraping setups (using headless browsers with residential/mobile IP networks, etc).

    (tags: scraping web bots arms-races web-scraping)

  • Tek Fog in Action

    “Investigating claims behind the use of ‘Tek Fog’, a sophisticated app used by political operatives affiliated with the Bharatiya Janata Party to drive propaganda at scale in India.” This is grim stuff — a custom app to bulk-post harassment en masse on various social media platforms, targeting women and driving right-wing pro-BJP spam. Can’t imagine this methodology will stay in India in future, either.

    (tags: india tek-fog grim-meathook-future spam abuse harassment bjp politics social-media)

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Links for 2022-01-11

  • Long COVID in a very large Norwegian cohort study

    New preprint, “Excess risk and clusters of symptoms after COVID-19 in a large Norwegian cohort”: ‘Physical, psychological and cognitive symptoms have been reported as post-acute sequelae for COVID-19 patients but are also common in the general, uninfected population. We aimed to calculate the excess risk and identify patterns of 22 symptoms up to 12 months after COVID-19 infection. We followed more than 70,000 participants in an ongoing cohort study, the Norwegian Mother, Father and Child Cohort Study (MoBa) during the COVID-19 pandemic. Infected and noninfected cohort participants registered presence of 22 different symptoms in March 2021. One year after the initial infection, 13 of 22 symptoms were associated with SARS-CoV-2 infection, based on relative risks between infected and uninfected subjects. For instance, 17.4% of SARS-CoV-2 infected cohort participants reported fatigue that persist 12 months after infection, compared to new occurrence of fatigue that had lasted less than 12 months in 3.8% of non-infected subjects (excess risk 13.6%). The adjusted relative risk for fatigue was 4.8 (95 % CI 3.5 to 6.7). Two main underlying factors explained 50% of the variance in the 13 symptoms. Brain fog, poor memory, dizziness, heart palpitations, and fatigue had high loadings on the first factor, while shortness of breath and cough had high loadings on the second factor. Lack of taste and smell showed low to moderate correlation to other symptoms. Anxiety, depression and mood swings were not strongly related to COVID-19. Our results suggest that there are clusters of symptoms after COVID-19 due to different mechanisms and question whether it is meaningful to describe long COVID as one syndrome.’ The participants were all unvaccinated, so hopefully vaccination has a decent protective effect…

    (tags: covid-19 long-covid papers medicine norway preprints)

  • sibbl/hass-lovelace-kindle-screensaver

    ‘generates a PNG from a Home Assistant Lovelace view, which can be displayed on a Kindle device which has the Online Screensaver plugin installed.’ There’s a lovely demo at https://www.reddit.com/r/homeassistant/comments/s0m4b9/kindle_eink_home_info_display/ — although I’d be pretty worried about Kindle updates bricking the jailbreak. In my experience Amazon devices are not very jailbreak-friendly.

    (tags: jailbreaking kindle homeassistant devices gadgets home)

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Links for 2021-12-21

  • _SARS-CoV-2 on surfaces and HVAC filters in dormitory rooms_

    Interesting new preprint on fomite transmission of SARS-CoV-2 from Linsey Marr et al. tl;dr: “SARS-CoV-2 RNA was found on more than half of surface samples and HVAC filters in dormitory rooms [housing students who were in quarantine or isolation]; the virus was not infectious.”

    (tags: fomites transmission covid-19 sars-cov-2 surfaces university students dormitories linsey-marr)

  • Mass rapid tests in Liverpool cut hospital stays by a third

    Rapid antigen tests, deployed carefully to include serial testing of presymptomatic and asymptomatic people, saved lives:

    An analysis has shown that it was more successful than Liverpool’s scientists and public health teams had anticipated, after they compared Covid cases and outcomes in the region with other parts of England. Professor Iain Buchan, dean of the Institute of Population Health, who led the evaluation, said: “This time last year, as the Alpha variant was surging, we found that Liverpool city region’s early rollout of community rapid testing was associated with a 32% fall in Covid-19 hospital admissions after careful matching to other parts of the country in a similar position to Liverpool but without rapid testing. “We also found that daily lateral flow testing as an alternative to quarantine for people who had been in close contact with a known infected person enabled emergency services to keep key teams such as fire crews in work, underpinning public safety.”

    (tags: rapid-tests antigen-tests testing covid-19 sars-cov-2 liverpool public-health lfts serial-testing)

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Links for 2021-12-20

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Links for 2021-12-19

  • The CFS quota container throttling problem

    Well, this is quite a messy one:

    Almost all services at Twitter run on Linux with the CFS scheduler, using CFS bandwidth control quota for isolation, with default parameters. The intention is to allow different services to be colocated on the same boxes without having one service’s runaway CPU usage impact other services and to prevent services on empty boxes from taking all of the CPU on the box, resulting in unpredictable performance, which service owners found difficult to reason about before we enabled quotas. The quota mechanism limits the amortized CPU usage of each container, but it doesn’t limit how many cores the job can use at any given moment. Instead, if a job “wants to” use more than that many cores over a quota timeslice, it will use more cores than its quota for a short period of time and then get throttled, i.e., basically get put to sleep, in order to keep its amortized core usage below the quota, which is disastrous for tail latency1. Since the vast majority of services at Twitter use thread pools that are much larger than their mesos core reservation, when jobs have heavy load, they end up requesting and then using more cores than their reservation and then throttling. This causes services that are provisioned based on load test numbers or observed latency under load to over provision CPU to avoid violating their SLOs. They either have to ask for more CPUs per shard than they actually need or they have to increase the number of shards they use.
    Note that Kubernetes uses CFS to implement CPU quotas by default, too. In the twitter thread about this post, a commenter noted: “‘By shrinking the CFS period, the worst case time between quota exhaustion causing throttling and the process group being able to run again is reduced proportionately’. Our P99s at previous gig reduced in line after I petitioned cloud provider to adjust setting.” — this at least seems like a relatively easy setting to tune.

    (tags: cgroups kubernetes linux k8s cfs scheduling containers quotas)

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Links for 2021-12-17

  • The Web3 Fraud | USENIX

    By now effectively all ;login:’s readers have heard the term “web3” and “dapps” bandied about as if they are some great revolution.  They are not.  The technical underpinnings are so terrible that it is clear they exist only to hype the underlying cryptocurrencies.  The actual utility of these “decentralized” systems is already available in modern distributed systems in ways that are several orders of magnitude more efficient and more capable.

    (tags: bitcoin criticism cryptocurrency web3 crypto ethereum hype scams dapps)

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Links for 2021-12-16

  • Consumer warranties and statutory rights

    wow, I didn’t realise we had statutory right to redress for faulty goods for 6 years:

    Statutory rights are provided for by legislation (Irish law and EU law as transposed in Ireland). These act as a kind of “legal guarantee”, entitling consumers to seek redress where an item is faulty. Consumers may rely on their statutory rights regardless of whether an item has a warranty or not. Under Irish law, consumers have up to six years to seek redress for faulty or defective items (both new and second-hand). If the product is defective, the seller is generally responsible for providing redress. If a fault arises within six months of purchase, it is presumed to have existed at the time of purchase. For this reason, the consumer should not have to provide proof of the defect. If the fault arises more than six months after purchase, the seller may request that the consumer prove the fault did not arise as a result of misuse – for instance, by obtaining a report from an independent expert. Where an item is faulty, the seller may first offer a repair or replacement item. If this is not possible or fails to correct the problem, a refund may then be provided. Remedies for faulty goods must be provided free of charge.

    (tags: rights repair support defective-goods guarantee warranty defects ireland eu)

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Links for 2021-12-15

  • Web3 is going just great

    the ongoing shitfest that is crypto/NFTs

    (tags: blockchain crypto cryptocurrency nfts shitfest web3)

  • rTMS RCT produces excellent results

    This is pretty amazing:

    A recent randomized control trial, published in The American Journal of Psychiatry, shows astounding results are possible in five days or less. Almost 80% of patients crossed into remission — meaning they were symptom-free within days. This is compared to about 13% of people who received the placebo treatment. Patients did not report any serious side effects. The most common complaint was a light headache. […] “This study not only showed some of the best remission rates we’ve ever seen in depression,” said Shan Siddiqi, a Harvard psychiatrist not connected to the study, “but also managed to do that in people who had already failed multiple other treatments.” Siddiqi also said the study’s small sample size, which is only 29 patients, is not cause for concern. “Often, a clinical trial will be terminated early [according to pre-specified criteria] because the treatment is so effective that it would be unethical to continue giving people placebo,” said Siddiqi. “That’s what happened here. They’d originally planned to recruit a much larger sample, but the interim analysis was definitive.”

    (tags: depression fmri health neuroscience medicine rtms brain rcts)

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