Stuff that occurs to me

All of my 'how to' posts are tagged here. The most popular posts are about blocking and private accounts on Twitter, also the science communication jobs list. None of the science or medical information I might post to this blog should be taken as medical advice (I'm not medically trained).

Think of this blog as a sort of nursery for my half-baked ideas hence 'stuff that occurs to me'.

Contact: @JoBrodie Email: jo DOT brodie AT gmail DOT com

Science in London: The 2018/19 scientific society talks in London blog post

Saturday, 9 February 2013

Mildly diverting subtitle glitch on my television - also mildly amusing

While my hearing's fine I like subtitles for two reasons - I often find that I get more info about what's going on if I have them on including names and places and how things are spelled and, on adverts and some television programmes they tell you what the music is and subtitle the lyrics too.

I've noticed on a few occasions that the subtitles are for a completely a different programme... here are a couple of examples which made me laugh.

Why do the subtitles get decoupled from the programme though - what's going on? Will the wrong subtitles come from the same channel type (eg would I only get BBC subtitles for a BBC programme and ITV subtitles for an ITV channel?) or is it anything to do with which channel multiplex the two programmes are on, or something else?
Owly Images


Owly Images 



Comedy giraffes - mis-subtitled BBC David Attenborough programme from jobrodie on Vimeo.

David Attenborough's Africa featuring giraffes that are seemingly participating in a very different programme. It's me trying not to giggle in the background.






#Burzynski - is this normal clinical trial practice?

The year before last I wrote a blog post expressing surprise at how many trials the Burzynski Clinic had running and after recent events (rumours that the Burzynski clinic is under unprecedented scrutiny from the FDA, but note this caveat tweeted by @medtek) I wondered what had changed.

Back in November 2011 I found 61 trials, this year by searching for the name Burzynski it seems there are now 62 (however the last one, this trial, actually relates to a completely different Burzynski so no change in numbers at all, h/t @dianthusmed).

It also appears that there have been more trials but not all of them registered, according to a paragraph on a page from 1998 on Quackwatch's website, highlighted to me by @jonmendel
"Working outside peer review, Burzynski is conducting 71 concurrent, preliminary phase II trials that cover most cancer indications-an unheard of number for a single investigator, and for a drug which is yet to be proven effective for any indication."

What struck me was that the ones I looked at on the first page (of 'unknown' status) all follow the same format of "Antineoplaston therapy in treating X (patients) with Y (type of cancer)" and all on the first page (shown below) are followed by this line (indicating the type of treatment given) appears below all of them: Interventions:     Drug: antineoplaston A10;   Drug: antineoplaston AS2-1

From the first page of results (brown = status unknown for more than two years, red = withdrawn, purple = terminated, green = completed - though is it published and what happened?):
  • Antineoplaston Therapy in Treating Patients With Stage IV Adrenal Gland Cancer
  • Antineoplaston Therapy in Treating Patients With Residual or Recurrent Anaplastic Astrocytoma
  • Antineoplaston Therapy in Treating Patients With Brain Tumors
  • Antineoplaston Therapy in Treating Children With Brain Tumors
  • Antineoplaston Therapy in Treating Children With Low-Grade Astrocytoma
  • Antineoplaston Therapy in Treating Patients With Anaplastic Astrocytoma 
  • Antineoplaston Therapy in Treating Patients With Recurrent or Refractory Mixed Gliomas
  • Antineoplaston Therapy in Treating Patients With Primary Malignant Brain Tumors
  • Antineoplaston Therapy in Treating Children With Primary Malignant Brain Tumors
  • Antineoplaston Therapy in Treating Children With Visual Pathway Glioma
  • Antineoplaston Therapy in Treating Patients With Refractory or Recurrent Intermediate-Grade Stage II, Stage III, or Stage IV Non-Hodgkin's Lymphoma
  • Antineoplaston Therapy in Treating Patients With Recurrent or Refractory High-Grade Stage II, Stage III, or Stage IV Non-Hodgkin's Lymphoma
  • Antineoplaston Therapy in Treating Patients With Mantle Cell Lymphoma
  • Antineoplaston Therapy in Treating Patients With Primary Central Nervous System Lymphoma
  • Antineoplaston Therapy in Treating Patients With Advanced Mesothelioma
  • Antineoplaston Therapy in Treating Patients With Stage IV Melanoma
  • Antineoplaston Therapy in Treating Patients With Multiple Myeloma
  • Antineoplaston Therapy in Treating Patients With Recurrent or Refractory Waldenstrom's Macroglobulinemia
  • Antineoplaston Therapy in Treating Patients With Metastatic, Recurrent, or Refractory Neuroblastoma
  • Antineoplaston Therapy in Treating Patients With Neuroendocrine Tumor That Is Metastatic or Unlikely to Respond to Surgery or Radiation Therapy
Are all these trials running at the same time? The way the titles are written it seems as if the antineoplastons A10 and AS2-1 are being trialled in children and adults with a fairly broad range of cancer types (or stages of a particular cancer type).

Searching for antineoplaston A10 brings up 61 hits and searching for antineoplaston AS2-1 brings up 60, so possibly there's at least one Burznyski trial listed in the 62 that has nothing to do with antineoplastons (could be someone with the same name of course).

Is that usual where the type or stage of cancer has a very poor prognosis and no-one has the luxury of time to wait and see how these ANPs perform in one situation before trying them in the next?

For comparison I had a look at GLP-1 and spotted a few that had similar titles, but there seemed to be much more variance in title, and trial status. One is even listed as having results...

Feb 2012 - Searching just for the antineoplaston A10 trials, we get 61 of which:
  • 0 are recruiting
  • 50 are of unknown status
  • 7 are withdrawn
  • 2 are terminated
  • 1 is completed
  • 0 are active, not recruiting
  • 1 is not yet recruiting
Note that Unknown status incorporates some of the other categories
UNKNOWN (RECRUITMENT STATUS)
A clinical study in ClinicalTrials.gov with a status of Recruiting; Not yet recruiting; or Active, not recruiting and whose status has not been confirmed within the past 2 years. Studies with an Unknown recruitment status are considered open studies or closed studies, depending on their last recorded recruitment status.

Nov 2011 - Here's what I found in November 2011 (but I think I searched on Burzynski rather than antineoplaston A10 so there's a caveat there)
  • 10 are recruiting
  • 35 are of unknown status
  • 7 are withdrawn
  • 2 are terminated
  • 1 is completed - it began in March 1996 and was completed in 2005. Its clinical identifier is NCT00003509 and this does not appear anywhere in PubMed.
  • 5 are active, not recruiting
  • 1 is not yet recruiting

While writing this post @majikthyse also published a post on the Burzynski Clinic which makes very interesting reading.

Comments relating to conspiracy theories or personal attacks on anyone will be ignored.

Wednesday, 6 February 2013

I hope lots of medical research charities will sign the #alltrials petition

UPDATE 9 February 2013: The AMRC (Association of Medical Research Charities) signed the petition yesterday morning - but of course I'd still like to see other health / patient charities (AMRC members and non-members) signing up.

Update 12 February 2013: A whole bunch of medical research charities have signed as part of a big gang of patient groups, including my beloved former employer Diabetes UK - hooray :D
http://www.alltrials.net/supporters/pin-statement/


"Trials with positive results are twice as likely to get reported as negative results," Goldacre said. "You can't make informed decisions about which treatment is best for the patient on the basis of just half the results, especially as it's the unflattering ones that are withheld."
Source: GlaxoSmithKline to publish clinical trial data, The Guardian, 5 February 2013
There seems to have been widespread under-reporting of clinical trial data along with an incomplete record of registered trials in the first place. This makes it harder to track what happened next. It also means that healthcare professionals only have part of the picture available to them when looking at which medications to consider for their patients.

The #alltrials petition calls for all clinical trial reports to be published, not just the positive stuff.

I've heard of the petition mostly through following Ben Goldacre on Twitter where he's been enthusiastically tweeting about organisations who have signed, including a surprise entry from GSK (GlaxoSmithKline) today who are pretty much 'big pharma' by any definition, or haven't signed in the case of the Association of the British Pharmaceutical Industry, aka ABPI.

The Wellcome Trust has signed the petition and they are a big funder of medical research, they're also members of the Association of Medical Research Charities (AMRC) as are lots of other lovely charities and I hope those charities might also sign this petition.

Signing is A Good Thing and as Ben says in his recent blog post "The eccentric position is now not supporting alltrials.net. There is no serious defense for withholding information about clinical trials from doctors and patients. It is simply unethical, and it harms patients."

All Trials
Click to visit the AllTrials site

It's important to have all the information to know which drug to prescribe (or which drug to take) but it's also important to know about other problems with drugs that might show up only after the drug is on the market when many more people are taking it. This is 'postmarketing surveillance' (the drug is now on the market and regulatory people keep their beady eyes on it to spot any problems).

Conveniently I heard a discussion about precisely this topic on Radio 4 this evening - Dr Margaret McCartney and someone from the MHRA (Medicines and Healthcare products Regulatory Authority) were discussing, with host Dr Mark Porter, how anyone - you don't have to be a doctor to do this - anyone can use the MHRA's Yellow Card scheme to report any side effect that they experience when taking any medicine.

The scheme was opened up to the public a few years ago - previously it had been just healthcare professionals that would fill these cards in. Now anyone can fill in the 'card' online. The MHRA has noticed that the number of these filled-in reports is dropping and is keen to raise awareness of the yellow card scheme.



Saturday, 2 February 2013

Quick random thoughts on Vitamin D

I'm writing this at a conference so treat it as provisional as I'm on battery power and not doing my normal fact-checking. Bits in pink are bits I need to reference.

It's a while since I've really looked in any depth at the evidence for, or against, Vitamin D as something that people might want to use as a supplement. My interest in it stems from my time at Diabetes UK when there were a few questions from people about its particular value as something that might generally 'help' either in preventing diabetes from starting, or reduce complications or other helpful things.

At the time I first started looking into this I don't think there had been any intervention trials where people (with a particular type of diabetes) were split into groups, one lot given Vit D and the other not and the outcomes compared.

There were plenty of studies looking at Vitamin D status (eg how much Vitamin D or its metabolites is zinging around in your blood) and outcomes, which were interesting, but I never really felt I understood what Vit D status tells you. Vit D exists in several forms - there are one or two coming in via diet but they are immediately tweaked first by the liver to another form and then the kidney to another one (or possibly the other way around!). Your skin is also capable of rustling up a bit of Vitamin D all by itself.

So what's in your blood could be a consequence of what's in your diet or from the sun, or from what's going on with the enzymes that do this conversion. I also can't help wondering if, given that Vitamin D is a fat-soluble vitamin, gaining or losing weight makes a big difference to Vitamin D concentrations in the blood.

How good a predictor for health outcomes or diabetes complications etc is how much Vitamin D (metabolites) you have in your blood? Dunno.

But then I thought... fat soluble vitamins

I seem to remember that Vitamin A, essential for retinal goings on etc, can be a bit of a problem if you have too much of it. Vague recollections of giving polar bear livers a swerve as the content of Vitamin A can floor you. Vitamin A is fat soluble.

Vitamin E was touted as some life saving thing for people who'd had heart attacks I think? There was a trial looking at Vit E with some other vitamins or medication and it turned out that it wasn't such a great idea to use this. I mean obviously you need some of it but 'some of it being good for you' doesn't translate, not that surprisingly, to 'lots more of it is therefore also good for you'. Vitamin E is fat soluble.

Vitamin K plays an important role in blood clotting and I was surprised to learn recently that eating too much spinach (rich in Vitamin K) was perhaps contributing to unexpected INR (international normalised ratio - which is how the speed of blood clotting is measured) in someone using warfarin. High Vitamin K foods interact with warfarin, which can be potentially a bit of a problem. Vitamin K is fat soluble.

Are fat soluble vitamins something we want to be a bit more careful with, in terms of hoovering them up as supplements? I suppose to answer that I need to avoid positive confirmation bias of happening to know off the top of my head which are the fat-soluble vitamins and find out what dangers there are from all the water-soluble vitamins. To be honest I thought most of them just got peed out but I expect I should mug up on it.

Anyway, unintended consequences and all that - apparently Vitamin D supplementation can negatively affect your lipid profile. I suppose I should go and look up the reference for that, I hate it when people don't cite stuff properly...



How to share your Twitter archive via your public Dropbox

This is a lot easier than I thought it was going to be, and it worked instantly. I'm still investigating the 'ethics' side of sharing all four plus years of my tweets publicly - not that I've said anything terribly exciting but I might need to think about the people I've intereacted with*. So I'm not sharing the link to my tweets quite yet.

You will need
1. Think about tweets you've sent and whether there's anything in there that might embarrass your friends, let alone yourself. Just because you can now share your past tweet history it doesn't mean that you should.

Download
2. If you've not downloaded your Twitter archive you'll need to do that first. Go to your Settings page or if you're logged in just click https://twitter.com/settings/account, scroll down the page until you see the 'Request your archive' link, click that and wait for an email to arrive. Once it arrives click on the link to download a zipped file of your tweets and accessory information (making them look nice on screen and searchable). Unzip the file.

Further details on downloading and playing with your Twitter archive can be found here.

2.5. Double click on index.html and your offline Twitter archive will open. You can search your old tweets and see what's there, or browse by clicking on the month in the panel on the right. Each tweet gives you the option to view the 'live' version on Twitter - where you can delete it if you wish, or copy its URL / embed it into blog posts or Storify etc.

Make available to others
3. Move the 'tweets' folder into your Public folder in Dropbox.
Might as well move all of the folder contents but I may work out which are the minimum essential files to move - to be honest the readme.txt file doesn't really participate in accessing your tweets

4. [Optional] You can rename the tweets folder if you want, not really essential. You can also rename the index.html file - again not essential but if lots of people are sharing their Twitter archives in this way then it doesn't hurt to stick your Twitter name in the address.

Share public link so others can see and search your tweets
6. Right-click / or Ctrl+Click for Mac (not cmd click) on whatever you've now called your index.html to bring up the menu, click on the Dropbox menu option and then 'Copy Public Link' which is now copied to your clipboard and can be pasted in a tweet or blog post or wherever you want to put it.

It will look a bit like: https://dl.dropbox.com/u/12345678/tweets_folder_name/your_name.html#

Once you've shared the link don't change the name of the file on Dropbox - or if you do you'll need to reshare the new link.

*A tweet is not an island. When you click on it to expand or 'view conversation' you can see the discussions that have gone on around it. Of course all these conversations probably happened in the public sphere (given that any tweet sent from a not-locked account is public) but I think it is a little different when you suddenly make the pointers to tweets that are several months or years old more easily available again. That's not to say historic tweets have been particularly well hidden - topsy.com can find all sorts of old stuff.

I don't know if tweets sent four years ago by someone who's since made their account private will now inherit their new privacy status (or vice versa) but I want to find out a little more about it before unleashing all my tweets, and manual RTs of other people's tweets (which will persist even if they've deleted the original) etc.

It would be interesting if I knew how to make this password protected, then could share just with mates and researchers. Don't think that option is available at the level of Dropbox but I'm sure there's a way around it.

Random observations
I wonder if people will have their Twitter archives subpoenaed - it's suddenly become possible for everyone with an account to gain access to all of their previous tweets (including the option to find and delete tweets from much further back than the default 3,200 that you can scroll back through). Presumably far easier to get them from an individual than from Twitter, though I am not a lawyer.