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I see a few reasons: - Different reference panel (1000G vs UK BioBank). - Liftover to another assembly only loses 0.3% of variants, while our mapping to SNP method lost 6% (though it's unclear how many more are lost later in both methods when MAGMA refers to the LD reference panels) - I don't...

Just a guess, but I think the UK BioBank data might not be open access like 1000 Genomes is. Maybe worth checking though.

I get a print subscription to Science. I've been excitedly waiting for this issue, and it finally came:

Yeah, I don't know where to start to find the right files. It's all so interesting. It feels like there's so much hidden treasure in this data file of DNA, and all these free tools across the internet to analyze it. I'm just very lacking in the experience and energy departments, so most of it...

Looks interesting. I tried to see if I could do anything, but it's too much stuff I don't know how to do, like the part about creating credible set files. In other news, based on a suggestion by @hotblack, I tried to use the UK BioBank reference panel for FUMA instead of the 1000 Genomes...

Hmm, the veterans affairs website says: The file it links to is a 2011 document, but the above study (which appears to be commissioned by the VA) is from 2015. Edit: See appendix A for the literature review from the VA in 2009 that found the evidence was not sufficiently strong to connect PB...

Note that the script hotblack posted includes a lot of extras for convenience, like remembering settings for future runs. These are the only required steps we used: FUMA does make MAGMA much easier (though requires converting to GRCh37). I've been looking for other online tools for analyzing...

Information from Veterans Affairs: Bateman Horne Center says this for dosages for orthostatic intolerance: Interestingly, potentially lower dosage for military than for OI patients.

I think ketamine has been regarded as one of the most promising psychiatric drugs, but this seems to show the effect may not be so impressive, at least for suicidality.

Effects of ketamine and esketamine on death, suicidal behaviour, and suicidal ideation in psychiatric disorders: A systematic review and meta-analysis Martin Plöderl, Ruth Cooper, Tom Walker, Vibha Shah, Mark Horowitz, Constantin Volkmann, Joanna Moncrieff [Line breaks added] Background...

Note this is not a new study. This is a very wide-ranging review of gulf war illness research published up to 2015. I'm particularly interested in how sure they appear to be that pyridostigmine bromide (PB) (AKA Mestinon) and pesticides are causally linked to GWI. Table 4 summarizes all the...

Recent research on Gulf War illness and other health problems in veterans of the 1991 Gulf War: Effects of toxicant exposures during deployment Roberta F White, Lea Steele, James P O’Callaghan, Kimberly Sullivan, James H Binns, Beatrice A Golomb, Floyd E Bloom, James A Bunker, Fiona Crawford...

NLRP3 Inflammasome and Caspase-1 Promote Fibronectin Dysregulation in Long COVID Syndrome Hawraa Kadhum Musa, Hussein Kadhem Al-Hakeim [Line breaks added] Abstract Long COVID (LC) syndrome which persist after of acute COVID-19 Neuropsychiatric disorders, fatigue and respiratory symptoms are...

EBV specifically seems to increase the risk of the neurological damage of MS, so maybe there's some common pathway, even if totally different neurological effects.

Just want to post the following because it slightly goes against the postsynapse specifically part. @hotblack and I managed to get standalone MAGMA working. The results were similar to doing it on FUMA, but not exactly the same (probably because of mapping to rs ids instead of liftover to...

Merged thread ------------------- Exploration of Intersections and Divergences of Long COVID and Chronic Fatigue Syndrome Joao A. Kouyoumdjian, Leticia A. Yamamoto, Carla R. Graca [Line breaks added] Background Fatigue is the most common symptom of Long COVID (LC), defined by persistent or...

Hopefully the full paper describes a placebo control. Otherwise, it seems possible the hand grip strength change is placebo effect.

Oh good point. If I'm understanding correctly, the furthest right, uppermost dot is 20:48914387:T:TA (the lead hit in the whole study), but its MAF is around .34.

They reported the raw p-values. In GWAS, they don't exactly use Bonferroni. It's a convention in GWAS to limit to SNPs with a p-value less than 5x10-8. Revisiting the genome-wide significance threshold for common variant GWAS, 2021

We have this other related thread: Lack of fever during acute infections