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Ibuprofen alters human testicular physiology including testosterone production

pnas.org

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Re: Ibuprofen alters human testicular physiology including testosterone production

#41

Post by stephen_g »

aiCeivi9 wrote: post #13
raverbashing wrote: post #3

While the results do matter, this is probably being blown out of proportion > One group of subjects received ibuprofen, 2 × 600 mg/d, (Ibumetin; Nycomed Denmark Aps) for a period of 6 wk Yeah, that's a lot of Ibuprofen for a long time

Nope, that is literally the dosage mentioned in leaflet inside my box of pills: 2x200mg, up to 3 times a day, do not exceed 6 weeks.

Wow, all the ones I have (and I don't remember seeing any different in Australia) all say do not take for more than three days at a time (except with a doctor's advice).

6 weeks is a long time to be popping 1200mg/d!

Re: Ibuprofen alters human testicular physiology including testosterone production

#42

Post by taneq »

reallymental wrote: post #4

I read the paper, I saw the plots accompanying the paper, and I tried following the rabbit hole in search of some raw data that I can get my hands on, just to see if I can. Perhaps the data is the result of the experiments that have been paid for by a third party, fine, but please mention that! People might be willing to pay for it, for example, me! What's wrong with "Here's the raw data, here's how we measured it, H…

> What's wrong with "Here's the raw data, here's how we measured it, Here's how we've shown the data, and look you can see for yourself that we are right! oh and the data costs $$$ much." ?

Well, what with the current replication crisis, maybe some researchers feel it's safer not to make it too easy... /s

(Not impugning the integrity of the authors in question here, of course, just musing on this widespread phenomenon in general...)

Re: Ibuprofen alters human testicular physiology including testosterone production

#43

Post by vanderZwan »

reallymental wrote: post #36
vanderZwan wrote: post #29

Earlier quoted context omitted.

This is exactly the motivation behind the Loom file format[0] being developed and used in the molecular neurobiology-group I work for[1]. It is an HDF5-based file format for 'omics data, to deal with the ever-growing size of the data sets. I specifically work on the Loom Viewer[1], a SPA that we're trying to design in such a way that it will be really easy and cheap for research groups to host and share these loom fi…

This is a significant amount of effort, and has some very good touches. Especially the Loom-Viewer, I really liked the ease with which one's workflow can integrate into the data analysis.

Thanks! :) It's always good to hear that we're on the right track with usability.

It's one of the things that I'm most worried about: I've been working pretty isolated for the last year and a half, and lack a background in biology or bioinformatics, and did not even have webdev experience when I took on this project (plenty of embarrassing proof of that in the code). Kudos to Sten Linnarsson, the PI of the group and my boss, for taking a gamble and hiring me anyway.

> I really liked the ease with which one's workflow can integrate into the data analysis.

Just to make this clear: the file format is a "dumb" data storage, and the viewer a "dumb" plotter of that data. To do more in-depth analysis requires loading the file in python, R, or anything else that might support the files in the future. The idea is to then store the results of this as attributes in the file. For example, the tSNE plot here[0] is just pre-calculated x/y data stored as two attributes.

Currently there is an issue with fully integrating the viewer into such a work-flow: for performance reasons, it caches accessed data from the file. This cache needs to be refreshed manually.

Sten recently added library support for keeping track of file modifications[1]. That enables me to make the viewer automatically update stale cache whenever a file is modified, making it even easier to integrate. Currently working on that.

There's still a ton of polishing and bug-fixing to do. Feedback, suggestions and help are always welcome!

[0] http://loom.linnarssonlab.org/dataset/cells/Dentate%20gyrus/...

[1] https://github.com/linnarsson-lab/loompy/issues/26

Re: Ibuprofen alters human testicular physiology including testosterone production

#44

Post by sclangdon »

stephen_g wrote: post #41
aiCeivi9 wrote: post #13

Earlier quoted context omitted.

Nope, that is literally the dosage mentioned in leaflet inside my box of pills: 2x200mg, up to 3 times a day, do not exceed 6 weeks.

Wow, all the ones I have (and I don't remember seeing any different in Australia) all say do not take for more than three days at a time (except with a doctor's advice). 6 weeks is a long time to be popping 1200mg/d!

Are you sure it didn't have codine in it? In the UK, the only (AFAIK) non-prescription medication with that sort of warning is anything containing codine.

Re: Ibuprofen alters human testicular physiology including testosterone production

#45

Post by hanklazard »

testplzignore wrote: post #34
aiCeivi9 wrote: post #13

Earlier quoted context omitted.

Nope, that is literally the dosage mentioned in leaflet inside my box of pills: 2x200mg, up to 3 times a day, do not exceed 6 weeks.

And I believe the max dose is even higher - 3200mg per day (800mg 4 times per day).

Correct. Adults can take up to 800mg q6hrs and I routinely prescribe that dosing after ankle sprains, etc for a few days. 6 wks duration would be way out of my comfort zone.

Re: Ibuprofen alters human testicular physiology including testosterone production

#46

Post by pilsetnieks »

fiblye wrote: post #37
pilsetnieks wrote: post #27

Earlier quoted context omitted.

My money would be on increasing levels of education and healthcare instead of fire retardant chemicals and ibuprofen.

How exactly would education affect the testicles?

He started by talking about global fertility rates. He then mentions lower sperm counts but it's not a given that one is solely or mostly because of the other. Fertility rates are expressed in children per woman, not sperm count.

A large drop in global fertility rates is attributable to lower infant mortality, better access to healthcare, contraception, and education about using it. Also, as levels of education in general rise, people tend to have fewer children.

Re: Ibuprofen alters human testicular physiology including testosterone production

#47

Post by bazfoo »

sclangdon wrote: post #44
stephen_g wrote: post #41

Earlier quoted context omitted.

Wow, all the ones I have (and I don't remember seeing any different in Australia) all say do not take for more than three days at a time (except with a doctor's advice). 6 weeks is a long time to be popping 1200mg/d!

Are you sure it didn't have codine in it? In the UK, the only (AFAIK) non-prescription medication with that sort of warning is anything containing codine.

I'm in Australia and looking at a box of plain Ibuprofen. It also recommends limiting to a few days at a time unless told otherwise by a doctor.

Re: Ibuprofen alters human testicular physiology including testosterone production

#48

Post by wowbot »

vanderZwan wrote: post #29
stinos wrote: post #10

Earlier quoted context omitted.

As far as I know this is slowly changing. According to scientists I've met (life science fields) there is an ongoing trend towards demanding raw data and even the code used to analyze it. Not every journal everywhere yet of course, but the consensus seemed to be that in 5 to 10 years it would become the new norm. Which might cause quite the disruption. Having seen quite the amounts of code written by PHD students I'm…

This is exactly the motivation behind the Loom file format[0] being developed and used in the molecular neurobiology-group I work for[1]. It is an HDF5-based file format for 'omics data, to deal with the ever-growing size of the data sets. I specifically work on the Loom Viewer[1], a SPA that we're trying to design in such a way that it will be really easy and cheap for research groups to host and share these loom fi…

What's the difference between this and jupyter? besides the file format itself obviously

Re: Ibuprofen alters human testicular physiology including testosterone production

#49

Post by peg_leg »

raverbashing wrote: post #14
aiCeivi9 wrote: post #13

Earlier quoted context omitted.

Nope, that is literally the dosage mentioned in leaflet inside my box of pills: 2x200mg, up to 3 times a day, do not exceed 6 weeks.

I'm not saying it's an overdose (and their tests of renal and hepatic function corroborate that) But it's not a dose people will commonly take in their "day to day" activities and ideally not something that is done without medical supervision

I disagree. People regularily take 800mg of ibuprophen for regular/tension/miagrane headaches. These can be quite regular and chronic occurances.

Re: Ibuprofen alters human testicular physiology including testosterone production

#50

Post by afandian »

Gatsky wrote: post #7
reallymental wrote: post #4

I read the paper, I saw the plots accompanying the paper, and I tried following the rabbit hole in search of some raw data that I can get my hands on, just to see if I can. Perhaps the data is the result of the experiments that have been paid for by a third party, fine, but please mention that! People might be willing to pay for it, for example, me! What's wrong with "Here's the raw data, here's how we measured it, H…

Blame the journal. Scientists are generally pretty busy. Writing a (life sciences) paper is an incredible amount of work usually done in a short period of time. Preparing raw data and explaining what everything means is quite involved. If they don't have to do something they won't. The journal should mandate data access, then it will get done. This is crucial for human experiments, if only because the authors can los…

If you're interested in how this data gets exchanged you might want to read this:

https://www.crossref.org/blog/how-do-you-deposit-data-citati...

https://www.crossref.org/blog/the-research-nexus---better-re...

(I work for Crossref)

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