Vitamin D?

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sTeamTraen
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Re: Vitamin D?

Post by sTeamTraen » Tue Sep 29, 2020 7:10 pm

bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- Why do they take the unusual step of reporting mean 25(OH)D as a natural logarithm? i.e. as ln 25(OH)D? I don't think they used the natural log in any tests?
They say that the log-transformed this (and two other) variables. Whether that was necessary or not is another question. Having done that, it would be normal for them only to report the log values, and coefficients based on them. If they added "ln" to the labels inconsistently, that's a bit sloppy but not a huge problem, I'd have thought.
bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- Why don't they treat 25(OH)D as a continuous variable and test whether it predicts a binary outcome (e.g. survival vs death)? They have dichotomized vitamin D status. What's the betting they tried dichotomizing it in various ways before settling on this particular threshold.
They should have presented the results with continuous predictors as well, but if their aim was really to show that deficient levels of Vitamin D are a problem then the dichotomy doesn't seem to me to be totally worthless.
bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- In any case, they state (for Figure 1) that "the number of red dots (inpatient mortality) above the solid line is significantly less compared to the dots below the line", the solid line being the 30 ng/mL 25(OH)D line. Well, counting the dots I can't get this result with a chi-square.
I count 68 white and 7 red dots above the line, versus 125 and 28 below. Accordingly:

Code: Select all

> chisq.test(matrix(c(68,7,125,28), nrow=2))

	Pearson's Chi-squared test with Yates' continuity correction

data:  matrix(c(68, 7, 125, 28), nrow = 2)
X-squared = 2.4626, df = 1, p-value = 0.1166
Nope, not significant, even if they cheat (as Raoult, doubtless "accidentally", also did in the first HCQ paper) by not using Yates' correction:

Code: Select all

> chisq.test(matrix(c(68,7,125,28), nrow=2), correct=FALSE)

	Pearson's Chi-squared test

data:  matrix(c(68, 7, 125, 28), nrow = 2)
X-squared = 3.1145, df = 1, p-value = 0.0776
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sTeamTraen
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Re: Vitamin D?

Post by sTeamTraen » Tue Sep 29, 2020 10:34 pm

More on this (thanks to Bob for making a much better job than I did of the data): https://twitter.com/sTeamTraen/status/1 ... 18017?s=20
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Re: Vitamin D?

Post by sTeamTraen » Wed Sep 30, 2020 12:18 am

Oh dear. Here is a story about the senior (and only non-Iranian; presumably added for a bit of Western credibility) author on the paper; he seems to be a shill for Big D (not the popular brand of peanuts sold in pubs on ingenious displays that revealed more of a scantily-clad woman with every purchase).

The article states that "The authors have declared that no competing interests exist." I have alerted the Editor in Chief of the journal.
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Re: Vitamin D?

Post by jimbob » Wed Sep 30, 2020 7:45 am

sTeamTraen wrote:
Tue Sep 29, 2020 10:34 pm
More on this (thanks to Bob for making a much better job than I did of the data): https://twitter.com/sTeamTraen/status/1 ... 18017?s=20
I have used https://apps.automeris.io/wpd/ (Webplotdigitizer - web based version before now to look at a badly drawn excel curve: it's pretty straightforward

https://twitter.com/ParkinJim/status/12 ... 5290027009
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Re: Vitamin D?

Post by geejaytee » Wed Sep 30, 2020 12:18 pm

sTeamTraen wrote:
Tue Sep 29, 2020 7:10 pm
bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- Why do they take the unusual step of reporting mean 25(OH)D as a natural logarithm? i.e. as ln 25(OH)D? I don't think they used the natural log in any tests?
They say that the log-transformed this (and two other) variables. Whether that was necessary or not is another question. Having done that, it would be normal for them only to report the log values, and coefficients based on them. If they added "ln" to the labels inconsistently, that's a bit sloppy but not a huge problem, I'd have thought.
bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- Why don't they treat 25(OH)D as a continuous variable and test whether it predicts a binary outcome (e.g. survival vs death)? They have dichotomized vitamin D status. What's the betting they tried dichotomizing it in various ways before settling on this particular threshold.
They should have presented the results with continuous predictors as well, but if their aim was really to show that deficient levels of Vitamin D are a problem then the dichotomy doesn't seem to me to be totally worthless.
bob sterman wrote:
Sun Sep 27, 2020 5:58 pm
- In any case, they state (for Figure 1) that "the number of red dots (inpatient mortality) above the solid line is significantly less compared to the dots below the line", the solid line being the 30 ng/mL 25(OH)D line. Well, counting the dots I can't get this result with a chi-square.
I count 68 white and 7 red dots above the line, versus 125 and 28 below. Accordingly:

Code: Select all

> chisq.test(matrix(c(68,7,125,28), nrow=2))

	Pearson's Chi-squared test with Yates' continuity correction

data:  matrix(c(68, 7, 125, 28), nrow = 2)
X-squared = 2.4626, df = 1, p-value = 0.1166
Nope, not significant, even if they cheat (as Raoult, doubtless "accidentally", also did in the first HCQ paper) by not using Yates' correction:

Code: Select all

> chisq.test(matrix(c(68,7,125,28), nrow=2), correct=FALSE)

	Pearson's Chi-squared test

data:  matrix(c(68, 7, 125, 28), nrow = 2)
X-squared = 3.1145, df = 1, p-value = 0.0776
As it's 2x2, there's an exact test you could run, rather than the chisq appoximation, and that gives:

Code: Select all

>  fisher.test(matrix(c(68,7,125,28), nrow=2))

        Fisher's Exact Test for Count Data

data:  matrix(c(68, 7, 125, 28), nrow = 2)
p-value = 0.08239
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8668037 6.1984502
sample estimates:
odds ratio 
  2.169318 
and the p-value is still not significant.

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Re: Vitamin D?

Post by bob sterman » Thu Oct 01, 2020 7:47 pm

It pains me to have to suggest that Matt Hancock might be taking some unnecessary flak - but the Daily Mail is trying to beat him with the unconvincing scatterplot....

https://www.dailymail.co.uk/news/articl ... id-19.html

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Re: Vitamin D?

Post by raven » Fri Oct 02, 2020 11:34 am

It occurs to me that even if there was some correlation, it's probably not causation. Low vitamin D could be a proxy for either underlying serious health issues, or working long shifts & thus poverty, as both can keep people indoors. And we know the first is already a risk factor independent of Vitamin D status.

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Re: Vitamin D?

Post by jdc » Sat Oct 03, 2020 1:28 am

raven wrote:
Fri Oct 02, 2020 11:34 am
It occurs to me that even if there was some correlation, it's probably not causation. Low vitamin D could be a proxy for either underlying serious health issues, or working long shifts & thus poverty, as both can keep people indoors. And we know the first is already a risk factor independent of Vitamin D status.
And looking at it the other way... maybe people who are health conscious dutifully meet their vitamin D requirements as advised but at the same time are also dutifully following all the other health advice they're given. A bit like that old 'bias of compliance' thing? https://www.nytimes.com/2007/09/16/maga ... ogy-t.html

Spoiler:

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Re: Vitamin D?

Post by raven » Sat Oct 03, 2020 12:49 pm

That research actually makes a lot of sense. Thanks, jdc.

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Re: Vitamin D?

Post by Woodchopper » Tue Oct 27, 2020 4:28 pm

PLOS ONE has issued an expression of concern for a paper it published last month suggesting that vitamin D might protect against severe COVID-19.

Central to the concerns is that the authors seem to have been too far out over their skis in asserting a link between the vitamin and the response to the infection. But as the EoC reveals, many of the potential problems can fairly be attributed to porous peer review as much as over-ambitious authors.
https://retractionwatch.com/2020/10/26/ ... f-concern/

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Re: Vitamin D?

Post by sTeamTraen » Tue Oct 27, 2020 5:36 pm

Woodchopper wrote:
Tue Oct 27, 2020 4:28 pm
PLOS ONE has issued an expression of concern for a paper it published last month suggesting that vitamin D might protect against severe COVID-19.

Central to the concerns is that the authors seem to have been too far out over their skis in asserting a link between the vitamin and the response to the infection. But as the EoC reveals, many of the potential problems can fairly be attributed to porous peer review as much as over-ambitious authors.
https://retractionwatch.com/2020/10/26/ ... f-concern/
I'm pleased to think that I may have been a modest part of the solution here. https://twitter.com/sTeamTraen/status/1 ... 51010?s=20
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Re: Vitamin D?

Post by shpalman » Sun Nov 01, 2020 8:50 am

Scientists are calling for ministers to add vitamin D to common foods such as bread and milk to help the fight against Covid-19.
Up to half the UK population has a vitamin D deficiency, and government guidance that people should take supplements is not working, according to a group convened by Dr Gareth Davies, a medical physics researcher.

Low levels of vitamin D, which our bodies produce in response to strong sunlight, may lead to a greater risk of catching the coronavirus or suffering more severe effects of infection, according to some studies. Last week, researchers in Spain found that 82% of coronavirus patients out of 216 admitted to hospital had low vitamin D levels. The picture is mixed, however – some research shows that vitamin D levels have little or no effect on Covid-19, flu and other respiratory diseases.
See also the CORONAVIT study.
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Re: Vitamin D?

Post by sTeamTraen » Sun Nov 01, 2020 8:33 pm

Doesn't the US already put Vitamin D in milk and flour/bakery products? Would their already appalling death rate be even higher if they didn't?
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Re: Vitamin D?

Post by jdc » Sun Nov 01, 2020 11:17 pm

sTeamTraen wrote:
Sun Nov 01, 2020 8:33 pm
Doesn't the US already put Vitamin D in milk and flour/bakery products? Would their already appalling death rate be even higher if they didn't?
I can answer your first question. OK, part of it. I dunno about flour.

Most cow’s milk sold in stores in the U.S. is fortified with vitamin D. I checked with the CDC. (They were a bit annoyed about me phoning. I think they were having dinner.)

Nutrition data website seems to reckon around 100iu (25% RDA) for a cup of milk (244g in English money). https://nutritiondata.self.com/facts/da ... ducts/69/2 and https://nutritiondata.self.com/facts/da ... ducts/71/2

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Re: Vitamin D?

Post by monkey » Mon Nov 02, 2020 3:49 pm

jdc wrote:
Sun Nov 01, 2020 11:17 pm
sTeamTraen wrote:
Sun Nov 01, 2020 8:33 pm
Doesn't the US already put Vitamin D in milk and flour/bakery products? Would their already appalling death rate be even higher if they didn't?
I can answer your first question. OK, part of it. I dunno about flour.

Most cow’s milk sold in stores in the U.S. is fortified with vitamin D. I checked with the CDC. (They were a bit annoyed about me phoning. I think they were having dinner.)

Nutrition data website seems to reckon around 100iu (25% RDA) for a cup of milk (244g in English money). https://nutritiondata.self.com/facts/da ... ducts/69/2 and https://nutritiondata.self.com/facts/da ... ducts/71/2
Flour in the US is enriched, as far as I can tell. Not sure if it *has* to be, but it may as well be, because you don't get to choose.

It doesn't have vitamin D in it, here's the FDA's definition: clicky

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Re: Vitamin D?

Post by Stephanie » Mon Nov 02, 2020 4:17 pm

discovolante wrote:
Sat Sep 26, 2020 9:02 pm
sTeamTraen wrote:
Sat Sep 26, 2020 7:47 pm
My mother worked as a paediatrician in public health clinics in Birmingham in the 1960s and 1970s. She told me that she saw quite a few cases of rickets in Asian households where the fathers refused to let the mothers leave the house during the day. These were first-generation immigrants from the subcontinent for whom this was standard behaviour. You can make all the vitamin D you need hanging the washing out in the sun every day in Dhaka, not so much stringing it over radiators in Sparkbrook. But 50 years on I would not expect this to be a huge problem for BAME communities.

That said, I'm waiting to see COVID research that unconfounds vitamin D deficiency from all of the other general health variables that go to make someone a well person or not. As far as I know, vitamin D only has one function (calcium uptake) and is unlikely to fight viruses; nor would stronger bones normally be associated with that, other than (again) in a general overall health factor. Maybe people with more vitamin D have that because they spend more time out of doors.

In any case, for otherwise healthy people to rush out and start taking massive doses will cause problems. The body can't store vitamin D for a rainy day --- it's like oil in your car's engine, once you've got enough there's no point in adding more.
On the other hand, it is getting to the time of year where it's sort of woolily recommended that people take a vit D supplement anyway. And I am not sure if covid is going to encourage people to brave the cold of each other's gardens or just stay indoors a lot more anyway e.g. less waiting outside a the bus stop on the daily commute, online shopping etc. So if people are only taking a smallish dose then it probably might be a situation where it doesn't actually do any harm? As long as people don't go round thinking it makes them immune or some.
Yes, the NHS recommends supplements in general:
Advice for adults and children over 4 years old

During the autumn and winter, you need to get vitamin D from your diet because the sun is not strong enough for the body to make vitamin D.

But since it's difficult for people to get enough vitamin D from food alone, everyone (including pregnant and breastfeeding women) should consider taking a daily supplement containing 10 micrograms of vitamin D during the autumn and winter.

Between late March/early April to the end of September, most people can get all the vitamin D they need through sunlight on their skin and from a balanced diet.

You may choose not to take a vitamin D supplement during these months.

People at risk of vitamin D deficiency

Some people will not get enough vitamin D from sunlight because they have very little or no sunshine exposure.

The Department of Health and Social Care recommends that you take a daily supplement containing 10 micrograms of vitamin D throughout the year if you:
  • are not often outdoors – for example, if you're frail or housebound
  • are in an institution like a care home
  • usually wear clothes that cover up most of your skin when outdoors
If you have dark skin – for example you have an African, African-Caribbean or south Asian background – you may also not get enough vitamin D from sunlight.

You should consider taking a daily supplement containing 10 micrograms of vitamin D throughout the year.
As I've fallen into the second category before, I started taking them this year.
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Re: Vitamin D?

Post by nezumi » Mon Nov 02, 2020 6:21 pm

Unsurprisingly, given my medical history outlined elsewhere, I have had vitamin D deficiency and it isn't nice. It all ended up in being unable to walk. It's hard to describe, it comes on so slowly you don't really notice then one day you find yourself dragging yourself up the stairs by your arms because your legs are too weak to carry your own weight. You get lower back pain and muscles refuse to stretch out anymore. For me the first symptom I noticed was just general fatigue, followed by back pain that came on after walking which eased off immediately after sitting down. As it gets worse the distance you can walk without pain gets lower, and sitting down eases it for less and less time. You find yourself unable to walk 20 metres without resting, and resting times go from 30 seconds to 10 minutes or more. Eventually the day comes when it's so bad you have to drag yourself (literally) to a doctor, who them proceeds to not test for Vitamin D because deficiency is just not on the radar.

I actually found out I was deficient by curing myself. It was suggested as an offhand comment by an acquaintance so I did some reading, concluded I was unlikely to be abundant in it so I went ahead and bought myself some 3000IU tablets and tada. Near total cure within 6 weeks. Went and insisted on the test and was still clinically deficient. I take 20000IU once a week because I'm a shut-in and barely get outdoors now, seems about right so far.

I certainly wouldn't dismiss Vitamin D as a promotor for general health, I'd even argue that the RDA is too low, I certainly wouldn't say it would protect against Covid though. Given how low the RDA is I'd be doubtful that any amount of fortifying food would do any good because it's likely to be such a tiny amount. A quick google about found some guidelines that say 20IU per 100 calories, so you'd have to drink an awful lot of fortified milk to get anywhere near the already low RDA. I have no doubt it protects against ricketts in children, but it is nowhere near enough for optimum health, as my experience* shows, you need to be a very long way under the clinically deficient marker to actually have troubling symptoms.

In essence with the whole general-healthy-lifestyle confounding factor along with the likelihood of the majority of Britain walking round deficient for half the year anyway, I think it's unlikely vitamin D intake plays any role other than a cameo. I'd still strongly recommend supplementation in the winter months, and the RDA should be more like 1000IU a day in my opinion.

* And some other anecdotal stuff I read at the time.

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Re: Vitamin D?

Post by jimbob » Mon Nov 02, 2020 9:06 pm

https://blogs.sciencemag.org/pipeline/a ... n-pandemic

The Scientific Literature’s Own Pandemic
You can find many examples of this at literature watchdog sites such as Retraction Watch and For Better Science. For example, here’s a paper on the mental health effect of the pandemic that’s so useful that the authors published it three times in nearly identical form. And there’s been a flood of deeply unimpressive work on Vitamin D, which will make it even harder to figure out if there’s anything worthwhile in the idea to start with. And Retraction Watch has been keeping a list of Covid-19-related retractions and expressions of concern, which will surely grow ever longer. Of course, there are plenty of papers out there (in this field and others) that haven’t been retracted but sure look as if they should be.For example, this thing, which just recently appeared in Science of the Total Environment, an Elsevier journal that I’d never heard of. That’s no particular distinction – Elsevier has a lot of journals that no one has ever heard of, and quite a few that people wish that they never had heard of, either. The title of the paper really says it all: “Can Traditional Chinese Medicine provide insights into controlling the COVID-19 pandemic: Serpentinization-induced lithospheric long-wavelength magnetic anomalies in Proterozoic bedrocks in a weakened geomagnetic field mediate the aberrant transformation of biogenic molecules in COVID-19 via magnetic catalysis“

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Re: Vitamin D?

Post by raven » Tue Nov 03, 2020 5:44 pm

jdc wrote:
Sun Nov 01, 2020 11:17 pm
sTeamTraen wrote:
Sun Nov 01, 2020 8:33 pm
Doesn't the US already put Vitamin D in milk and flour/bakery products? Would their already appalling death rate be even higher if they didn't?
I can answer your first question. OK, part of it. I dunno about flour.

Most cow’s milk sold in stores in the U.S. is fortified with vitamin D. I checked with the CDC. (They were a bit annoyed about me phoning. I think they were having dinner.)

Nutrition data website seems to reckon around 100iu (25% RDA) for a cup of milk (244g in English money). https://nutritiondata.self.com/facts/da ... ducts/69/2 and https://nutritiondata.self.com/facts/da ... ducts/71/2
Here in the UK, spreads/margerines quite often have added Vit D. As do fortified breakfast cereals, and most oat- and nut- milks I've come across. (Mind you, it's usually D2 in the vegan milks, which is apparently less easily absorbed than D3.) Dunno if that's enough to prevent deficiency though.

I think fortification isn't mandated generally because it's possible to over do it with Vit D, and they're erring on the side of caution.

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