Author Archives: Eoin Malins

OPunting 2024

This week (2024-08-07) instead of our usual group meeting, OPIG took to the high seas. The OPIGlets pooled our resources and procured punts from many different berths. Organised by Admiral Nele, we departed from the Cherwell boathouse and shipped out the 0.5 nautical miles (3.28801867e-6 light seconds for those playing along in metric) upriver to the Vicky Arms.

Despite visiting the odd bush on the way, scurvy scallywags one and all were herded in a generally upstream direction with Matt and Eoin leading the way. With the first two punts having safely reached dry land and refuelled their ethanol fuel cells, the question remained where on earth everyone had got to. Sagely concluding they’d probably all sunk another pint was had in their honour.

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Converting or renaming files, whilst still maintaining the directory structure

For various reasons we might need to convert files from one format to another, for instance from lossless FLAC to MP3. For example:

ffmpeg -i lossless-audio.flac -acodec libmp3lame -ab 128k compressed-audio.mp3

This could be any conversion, but it implies that the input file and the output file are in the same directory. What if we have a carefully curated directory structure and we want to convert (or rename) every file within that structure?

find . -name “*.whateveryouneed” -exec somecommand {} \; is the tool for you.

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Deliberately misfolding prions to find the golden thread.

Prion are both fascinating and terrifying. They occur naturally and have a purpose, but what that purpose is we’re still not entirely sure. Gene-knockout mice which no longer code for the prion protein do live, but they ain’t born typical.

The endogenous form of the prion protein (PrPC) can, through currently unknown mechanisms, take a different conformation, the pathogenic PrPSc. PrPSc is responsible for fatal, rapidly progressing neurodegenerative disorders which in many cases can jump species.

At OPIG, we recently discussed a remarkably rigorous series of experiments outlined in the paper “A Protein Misfolding Shaking Amplification-based method for the spontaneous generation of hundreds of bona fide prions” Whilst deliberately creating new pathogenic prions may seem and odd thing to wish to achieve, the authors aimed to determine if there was a golden thread linking “infectivity determinants, interspecies transmission barriers or the structural influence of specific amino acids”.

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Inverse Vaccines

One of the nice things about OPIG, is that you can talk about something which is outside of your wheelhouse without feeling that the specialists in the group are going to eat your lunch. Last week, I gave an overview of the Hubbell group‘s Nature paper Synthetically glycosylated antigens for the antigen-specific suppression of established immune responses. I am not an immunologist by any stretch of the imagination, but sometimes you come across a piece of really interesting science and just want to say to people: Have you seen this, look at this, it’s really clever!

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Out of Band Management

We’ve all had things go wrong with computers, however when they go catastrophically wrong, there’s often little you can do other than to be physically on site to reinstall. This doesn’t have to be the case though. Most PCs have a tiny secondary processor which can allow full remote control of a computer that’s crashed, unresponsive or even switched off.

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Lucubration or Gaslighting?​

Or: The best lies have a nugget of truth in them.​

Lucubration – The action or occupation of intensive study originally by candle or lamplight.

Gaslighting – Psychological abuse in which a person or group causes someone to question their own sanity, memories, or perception.

I was recently having a play with Google Bard. Bard, unlike ChatGPT has access to live data. It also undergoes live feedback and quality control. I was hoping to see if it would find me any journals with articles on prion research which I’d previously overlooked.

Me: Please show me some recent articles about prion research.
(Because always be polite to our AI overlords, they’ll remember!)

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Monoclonal antibody PRNP100 therapy for Creutzfeldt–Jakob disease

Recently, University College London Hospitals (UCLH) received a “Specials License” to allow the treatment of six patients suffering from Creutzfeldt–Jakob Disease (CJD), by way of a novel antibody known as PRN100. The results of this treatment have now been published in The Lancet.

There is currently no cure for CJD, yet over 100 people per year develop it either spontaneously or through external means including (but not limited to) growth hormones, cataract surgery or infected neurosurgical implements [1]. “There is no UK legislation which implements a compassionate use programme as set out in Article 83 of the relevant EU regulation. But the UK has implemented an exemption process known as the “Specials” in light of the requirement to be able to deal with special needs.” [2]

As there is no known cure, the request for use of PRN100 was put before the court as in Law “Some treatment decisions are so serious that the court has to make them.”

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Le Tour de Farce v9.0

With many tours (Farcical and otherwise) restricted due to Covid, 2022 celebrated the resurrection of OPIG’s glorious Tour de Farce. This year’s route was nine miles and an unusually conservative four pubs.

After listening to Lewis’ conference prep talk, we left the Statistics Department around 5pm for a leisurely trundle through Mesopotamia, The Oxford Psychopath, Old Marston and out to our first rest stop, The Victoria.

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Solving WORDLE with grep

People seem to have become obsessed with wordle, just like they became obsessed with sudoku. After my initial burst of “oh a new game!” had waned, I was left thinking “my time is precious and this is exactly what we have computers for”. With this in mind, below is my quick and dirty way of solving these. I’m sure the regexp gurus amongst you will have a more elegant solution.

Step 1: Make sure you’ve got /usr/share/dict/words installed. This is just a huge list of words in a specific language and for me, this required installing the British words list.

sudo apt-get install wbritish

Step 2: Go to wordle

Step 3: Pick a random 5-letter word as your starting point. This is where grep and /usr/share/dict/words comes in:

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