hirenj

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61.
by hirenj 4y ago
I make use of a library in R to render SVG that uses Cairo to render to an intermediate (simplified) format, which looks a lot like what Resvg is doing with usvg. The advantage here seems to be that this is a much more compact library (fewe
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by hirenj 5y ago
What a grim coincidence if this type of saturation error pops up again in relation to Chernobyl.
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by hirenj 5y ago
One of the contributions being solicited on the page is to get DOIs for the given webpage. Right now, it has a few methods to grab DOIs for specific sites. I've had a lot of success running Zotero's translation server for my own b
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by hirenj 5y ago
Thanks for the info! That ability to retune sounds excellent. I wonder if you could spin this out to have an EWS for influenzas too (although hopefully it’ll never get as severe!) I guess for the glycosylation when you say it’s implicitly h
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by hirenj 5y ago
Dear Marcin - congratulations on the manuscript! Do you think the immune escape parameters would need to be retuned in a post Omicron world? Do you need the actual epitopes recognised by antibodies, or can you guess this from structure. Do
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by hirenj 5y ago
I find it’s a lot less interesting to consider the mapping of DNA to code or blueprints, instead considering the process of evolution as a way of dealing with a legacy code base. This code is functional (just barely) but it’s fragile. Lots
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by hirenj 5y ago
It's an odd protein they're hitting - GPMNB is expressed pretty widely, so I wonder what the proteoform is that they're targeting/recognising here. Can't get to the paper using all the usual tricks, so it's har
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by hirenj 5y ago
Here's the paper: https://www.nature.com/articles/s43587-021-00151-2
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by hirenj 5y ago
Here’s the actual article, since the people that write these press releases somehow think that the actual paper is unimportant: https://www.nature.com/articles/s41586-021-04072-3
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by hirenj 5y ago
Coincidentally, I read this amusing story about Ocean Vuong responding to students who were perplexed by his writing this very morning: https://www.theguardian.com/australia-news/2021/nov/11/what-...
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by hirenj 5y ago
Back when I had to choose names for our kids, I needed to find names that were pronounceable in both Danish and Gujarati. Solving this involved taking names lists from both languages, and getting the phonemes for each name (based upon the l
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by hirenj 5y ago
Thinking about this a bit more, I could also imagine that cell state could not only be encoded in the cell proteome, phosphoproteome etc, but also in the set of already activated (primed) receptors on the cell, so that the final signal only
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by hirenj 5y ago
The most remarkable thing about this article is that there are still people surprised that the lock and key analogy has limited utility. I’d even argue that the new model they highlight doesn’t even go far enough, and that a better model ma
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by hirenj 5y ago
There's also a less charitable description of the high trust society as less of a hard-earned trait/moral attribute, and more of an artefact of the monoculture in Denmark (which would also go a long way to explain the prevalent at
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by hirenj 5y ago
There’s an excellent (research-based) thread outlining some possible explanations for the Danish success story over on Twitter: https://threadreaderapp.com/thread/1436193837744107523.html It really boils down to Denmar
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by hirenj 5y ago
Short answer is we probably don’t know what will happen. Long answer: We probably lost the enzyme activity during a fight with some pathogen. The truncated protein is still produced, and there are effects in the body if that is removed. So,
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by hirenj 5y ago
Guess what? It's glycotime again! Gal(ɑ1,3)Gal (Galili epitope) is a common epitope in most animals, but in primates we lost the activity of the gene (GGTA1) to synthesise it. Since we don't produce it any more, it's recognis
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by hirenj 5y ago
My theory is that there is a strong pressure towards uniformity in these countries (Extreme Janteloven in Denmark). This is often marked out as a reason for their success, however I suspect that the strong affinity biases (to use a loaded t
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by hirenj 5y ago
Could someone please point me to the relevant chapter of reference 4 here, where the reference to chimeric proteins is meant to be? (i.e. the right chapter of this handbook: Maier, H. J., Bickerton, E.; Britton, P. Coronaviruses – Methods a
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by hirenj 5y ago
I'd add that you need to do the homework first: If you can adequately formulate and articulate the problem that the lab is solving, and that one cool trick you have that can solve it, that's already a great signal that you would w
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by hirenj 5y ago
I do molecular biology full time, but I truly believe that I learnt the skills I need to do this in my first project where I took over a several thousand line perl web app. The developer had been extremely clever with his use of tricks, whi
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by hirenj 5y ago
I was thinking about this very subject this morning, and I realised the mRNA stuff actually isn’t the exciting part. It’s the packaging in lipid particles that is much more interesting. We can get away with this approach for vaccines becaus
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by hirenj 6y ago
Just to give a bit more detail, those cerebrosides are Glycosphingolipids. They're galactose or glucose attached to a ceramide. So the major components of myelin are lipids/carbohydrate! (Don't know exact proportion of carboh
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by hirenj 6y ago
This makes me wonder about the role of film as a “machine for empathy” as described by Ebert. If movies could prime people for relationship chats by seeding empathetic ideas. This led me to wonder if there’s any relationship between the med
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by hirenj 6y ago
Given Humans arrived in Europe about 40k years ago (on current estimates?), I look forward to referring to ethnic Europeans as young’uns.
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by hirenj 6y ago
Yes, and no. The principle is there, but it is important to understand that each cell type is essentially a specialist factory to produce proteins, and the drug may be produced best when you get exactly the right factory to produce the pr
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by hirenj 6y ago
Do we need one person to understand everything? I don’t believe so, but there could be limits to the efficiency of collaborative understanding and action on complex systems, such that we have to have one person understanding multiple syst
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by hirenj 6y ago
Ha, yes okay maybe just from their secretions may be a tad optimistic. However, there are some papers out there about the associated microbiota, although I have no idea if they just mushed the whole tick up to get enough material.
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by hirenj 6y ago
This is, like so many other stories, another glycobiology story in disguise! I had a great discussion with one of our collaborators about where we thought the alpha-Gal came from that is so antigenic. Our rough hypothesis was that this is a
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by hirenj 6y ago
Apart from the financial system complexity, I actually struggle to see how the systems mentioned are too complex to understand. They’re big, yes, and full of detail - but incomprehensible doesn’t sound right. However, I’m sure that this is

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