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A couple of things. 1) (related) Since I could not see author contributions listed in this paper and I am in the author list, FYI I was asked to write a mitochondrial section for this paper while I was going through a severe period of physical disability last year and early this year - so my...

Hello people, a few answers, comments and a general statement I've wanted to make which is probably best placed in this thread. Hi there, thanks so much for your input. I am the author of the thesis posted in this thread. I very much strive to phrase or interpret things cautiously and to...

Sure, just didn't want the text itself of Sarah's mobile number being immortalised in google.

Hello everybody. I hope I haven't breached any formatting requirements for this forum category! I also hope that it's okay for me to post this directly. In an effort to find more recruits (Melbourne, VIC, Australia) I'm sharing the pwME recruitment flyer for some current and future work here...

Probably not my place to direct manuscripts towards specific journals but might be a good idea to check if a journal is online-only. Space would be less important when that's the case, is my guess.

Did you try submitting to any journals ? Did they say it was were too large during review? You should try if you haven't. I've published ME/CFS papers much longer than that without any length-related problems. I didn't think that would be a concern, especially given how many journals are online...

This thread is a bit heated in spots so I just want to say that I'm not intending any hostility or unpoliteness whatsoever. :) In this paper it says the following: "increased use of Branched-Chain Amino Acids (BCAAs)[10], as observed in CFS/ME by Missailidis et al., 2020" 1) This is jumping...

The analysis here looks very nice! With regard to gene products the study here is looking at mRNA levels. In my opinion it's hard to infer downstream or functional consequences with mRNA levels without protein data alongside it (the authors are responsible about this in my opinion and focus on...

@Ravn I appreciate the warm words and "gentle" encouragement ;). Back on a serious note I gave a short talk about this last year at the IACFS conference but it is now a bit out of date - I was learning how to best approach transcriptome data from home at the time, so the overall interpretation...

I was actually just pretty busy with some other stuff and hadn't come to s4me yet. The paper seemed to be getting some attention on twitter, so I figured there'd be some discussion here, today. I was also now considering not commenting so as not to bias the discussion, but since Hutan said it is...

Q value is 0.42 which excludes it when correcting for multiple comparisons by BH method, would explain its absence from a global-level analysis using tighter Q thresholds.

Dominic spent a lot of time working on and seeking feedback for his hypothesis here, so it's cool to see that he has gotten this published alongside the Uppsala group. Really impressive work for an independent researcher. Happy for him.

Not sure, but if somebody does visually inspect ME/CFS mitochondria specifically in muscle one would hope for a comparison against sedentary controls. Muscle mitochondria from people who can't undertake exercise, or can only undertake reduced exercise (due to disease burden) would probably look...

Possibly but not necessarily. You can have gene products upregulated at the protein level with reduced or unchanged mRNA levels. There may also be nothing wrong with the gene itself. Depends on how exactly the upregulation might be occurring.

Hmm, yes you are of course right with a lot of this - I think it goes back to what I initially suspected: there is variation from journal to journal. Perhaps just moreso than I had thought. I had read the open letter by Dan Brockington too, I remembered it saying something along the lines of...

This is not necessarily the case. Many of the biomedical MDPI journals have high impact factors and are considered reputable, and some of them are *not* easy to publish in. Publishing in an impact factor 4.5 paper is not really settling for less, that's actually pretty good. Especially in ME/CFS...

Hey Ravn, thanks for the tag. I hadn't seen this yet. I've only had a quick read but the statistical approach seems to be commendable as others have already flagged. Good to see a new technical approach too. So obviously, to discuss function/expression of specific gene products based on...

The PPP is generally considered to support aspects of anabolic metabolism - that is it largely assists with the building of molecules such as adenine nucleotides and fatty acids. But it can also produce pyruvate, which can then be utilised to make energy. It also produces reducing equivalents...

Correct, and this is a clever analogy :). In general (not just necessarily in the context of ME/CFS) I think this is possible if something is wrong with the Complex V machinery itself (we don't know if this is the case or not in ME/CFS). But I think this would be pretty apparent and...

Oligomycin is a Complex V inhibitor. When it is injected during a seahorse assay, the OCR is expected to drop. This drop (oligomycin-sensitive component) reflects the OCR by Complex V and thus is a measure of ATP synthesis rates. The value plotted is typically the result of the following: "ATP...