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2-hydroxybutyrate and cysteine were both elevated in Jason et al 2022's pre-illness data study in ME/CFS: I don't recall seeing it in other metabolomics studies, but on the other hand the design of this one is quite unique.

That's fair enough! I'll make an account in that case

This looks really interesting - no individual TAG passes adjusted p<0.05, but (like with Germain 2020) they all seem to be biased higher in ME. I'd quite like to repeat the analysis I did on that data (ie volcano plot and testing global TAG differences): @forestglip how would you feel about...

That's great thank you :) Mann whitney is a safe bet since it doesn't make any assumptions about distribution and simply asks the question of whether one group is higher or lower than another, so their p values are probably fine. Biserial correlation I think is ok too but assumes that the data...

For sure, there's evidence that in general serum contains higher levels of many amino acids and differing levels of pyruvate:lactate than plasma - possibly due to platelet activation in serum. I don't know about lipids. This would be great, and of course it's difficult to get a mechanistic...

This is the CSF data if I recall right? I believe from when I looked at this earlier in the year that the ones in that heatmap are the top results from a simple mann whitney u test between groups. They also analysed it using a more complicated (but probably more appropriate) glm model. If it's...

Thanks that's interesting. They don't report on triglycerides or phosphatidylcholine in Germain et al 2020 but they do mention they are detectable in their lipid panel so it follows they would probably be insignificant. I wanted to check anyway so went into the supplementary and calculated the...

Good point. My hypothetical plot is simply based on the cohen's d effect size value from the raw data, the sample size they report for males and imagining that the mean is zero and SD is 1. The Z score values they report comes after accounting for age and an activity mediator so it would be a...

High leptin levels seen in this thread's paper in men, was also seen in Hoel et al 2021

To compare some of the lipid findings to previous studies that have done lipidomics: This thread's paper describes low levels of phosphatidylcholine, sphingolipids (types of membrane lipid) and high levels of triglycerides. Low levels of phospholipids and sphingolipids are also seen in Che &...

It looks like the protein with the greatest significance for men only is BCHE (adjusted p=0.0003) which is a cholinesterase - Butyrylcholinesterase. Its function appears to be as a non specific cholinesterase that is structurally similar to acetylcholinesterase, but that in addition to just...

Fantastic, thank you, that makes sense. : ) In that case I wonder as a suggestion if it might be good to report the units alongside each blood trait/molecule, or to do away with it completely and use z scores as the numbers currently don't mean anything to the reader without units. If not maybe...

I'm not sure I agree with that. I would expect that inactivity and ME/CFS status are particularly confounded more so than the other factors you mention. Also given Wuest's recent study where he argued an insulin resistance phenotype in healthy individuals assigned to bed rest, I think it's...

@Chris Ponting Thank you for your answer! In this extreme example for Chylomicron concentration from fig4A, is it therefore correct that the ME group has a Z score ~ 5e-5 higher than the control group? How does this result end up as significant which such an extremely small z score...

I'm not totally sure how you're supposed to interpret the results from these direct effect plots: These are reported as 'effect sizes' but I don't think they are comparable to an effect size like Cohen's D which indicates the magnitude of the difference after taking into account the variance...

This looks like a really exciting paper I'm looking forward to properly reading through it. Here is the same table you showed but for the NMR results rather than blood traits (only showing some of the top ones, there's many more with Cohen's D > 0.2). What's really nice is that is...

As for a preference for amino/fatty acids as substrates for aerobic respiration, this was also argued in Fluge et al 2016: Lower levels of certain serum amino acids which may be used to replenish TCA cycle intermediates were observed, as well as higher transcript levels of genes involved in...

Reductions in oxygen consumption have been reported in isolated PBMCs. This is what Thomas et al 2020 reported and was the trend reported by Fisher, Missailidis et al 2020 in lymphocytes (not significant, and also no plate technical replicates from what I can tell). In long covid reduced oxygen...

@butter. sent you a DM :thumbup:

Echoing this thank you everybody for your kind words :) Not for this project. We recruited/collected from Sheffield with our collaborator Caroline Dalton and prioritized getting as large a sample size as we could over selecting for whether they were currently in PEM or not. We anticipate that...