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Posts Tagged Medically-related

Future Timeline – a visual representation Pt 2 aimee whitcroft Aug 23

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After some agonising, I’ve decided to go with the easy route.

Confused? See Pt 1 for an explanation of what this is all about :)

So, here’s the full thing, in two formats:

1) Future Timeline – visual (a webpage, sorry about some of the mashed formatting. Time mutter grumble grumpy grumble)

2) A PDF (see below)

Remember, in both versions EACH ENTRY is hyperlinked back to the fuller explanation for it :)

I’m not going to have the time this weekend to try other ways of doing it, but if anyone would like to chat with me about turning it into something a bit more Web, get in touch!

Future Timeline – a visual by aimee_w

Future Timeline – a visual representation Pt 1 aimee whitcroft Aug 23

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Future Timeline is an extremely interesting site.  Calling itself a “speculative timeline of future history”, it has page upon page of really interesting content. Some of it is very much based on fact, while others is based more on supposition and hypothesis.

It’s an excellent exercise for casting one’s mind forward.

Unfortunately, however, the structure of the website means it’s impossible to get an overview of trends and changes. Something which, I hope, I’ve been able to help with. At least a little.

I’ve taken every entry in the website, assigned each a category, and sorted and colour coded it. I also kept all the hyperlinks, so one can click on any entry to be taken to the fuller explanation about it. This necessitated having to check ALL of them, as some got mushed somehow. Arg.

Below you can see some of the iterations I went through (this was a somewhat time-intensive project).

Next step? Figuring out how best to get it online :) Stay tuned!

UPDATE: Here it is!

A Perfectly Archetypical Title for This Journal aimee whitcroft Jun 21

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Wow, the weather’s foul. And it’s enfoulenating the moods of many, I imagine. So a brief, funsy Friday frivolity :P

From the Pipeline column, a list of The Perfect Papers For Each Journal.

Some of my favourites include:

For Science:
“People Only Read One or Two Papers Out of Any Issue of This Journal, and This Isn’t One of Them, is It?”

For the Journal of Medicinal Chemistry:
“Big Pharma Here, With a Gigantic Flaming Viking Funeral for a Project That Chewed Up Eight Years, And Here’s All We Have to Show For It?”

“Small Academic Lab Here, With A Series of Rhodanines and Polyphenols That Are Seriously Hot Leads for At Least Ten Diseases”

For Tetrahedron Letters
“Remember Us? Here’s a Four-Page Paper About Some Reaction With No Experimental Whatsoever. Where Else Can You Find. . .Oh, Right. Never Mind.”

“The Four Thousand And Forty-Seventh Way to Prepare Nitriles From Oximes”

And there are lots, lots more. Check out the original post for the full listing :)

Which are your favourites? And do you have any journals/titles you’d like to add? If so, well, that’s (kinda) what the comment section of this blog is for :)

Stay safe and warm!

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And on a separate note – a great article about Lego, New Zealand researchers and Bad Science Journalism.

 

The danger of science denial aimee whitcroft May 30

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This, ladies and gentlemen. THIS.

Journalist Michael Specter gives an impassioned TED Talk on the danger of science denial. A brilliant talk, and something to be shared as widely as possible. _Especially_ with the anti-science people you know!

Vaccine-autism claims, “Frankenfood” bans, the herbal cure craze: All point to the public’s growing fear (and, often, outright denial) of science and reason, says Michael Specter. He warns the trend spells disaster for human progress.

Click here to view the video on YouTube.

[And no, I will never forgive Mbeki for what he did. Never.]

Marvellous MRI music vid aimee whitcroft Feb 15

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Hooray for CNET!  not only do I use them whenever I’m looking at new tech to buy, but they’ve also pointed me at an extraordinary music video.

British musician Sivu (James Page) spent 2-3 hours holed up in an MRI machine at St. Bartholomew’s Hospital in London for his new single, ‘Better Man Than He’.

The single will be released later this month, but we get to watch the video – weird, fascinating and oddly beautiful that it is – now. And the track itself isn’t half bad, either :)

YouTube Preview Image

 

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Related posts:

All kinds of trippy goodness – food as scanned by MRI

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Beer’s bitterness and your health aimee whitcroft Jan 31

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Yay, more beer-related science!

ResearchBlogging.org

This time, it’s around the chemistry involved in that lovely bitterness in beer. As it turns out, this bitterness is provided by a class of chemicals* called alpha acids, which are to be found in the resin of mature hops.

For those living in New Zealand and enjoying the local craft beer industry’s obsession with hoppy beers – you know what I’m talkin’ about, bitterness-wise :)

From Urban, J.et al, 2013, Absolute Configuration of Beer′s Bitter Compounds

Anyhoo, one of the major such acids is called humulone, and it’s about this that we’ll be talking. During the brewing process, humulone degrades into two isomers**, which are both far more soluble than humulone itself. Up until now, there’s been a great deal of confusion about these isomers and their formation.

And so in have stepped the scientists and, in this case, their ability to perform x-ray crystallography. The technique takes the crystals of a compound, and then bounces x-rays off of them – how the x-rays diffract gives valuable information on the compound’s physical structure.

And what this group found was that the common notions around humulone (and its derivatives’ structure) have been…incorrect.

Why is this important? Well, it’s simple. There have, increasingly, been claims that beer (and what makes it bitter), in moderate amounts, can be beneficial for a number of illnesses and complaints***.  Some of the claims have linked specific alpha acid isomers  (i.e. specific bitternesses) with specific benefits.

The problem is, though, that the configuration of these isomers, and how they’re formed, has been a source of confusion for decades. In turn, this prevents the development of any good structure-function relationships for these compounds. If we knew exactly what does what, we can get better at getting the most goodness out of our beer habits. Hell, we may even be able to give people supplements, say, containing only the beneficial compounds. Why anyone would want to lose out on drinking lovely, lovely pints in the process is beyond me, but that probably says more about me than anyone else :P

Or, as the authors put it:

Excessive beer consumption cannot be recommended to propagate good health, but it has been demonstrated that isolated humulones and their derivatives can be prescribed with documented health benefits.#bib21” rel=”references:#bib21” shape=”rect”>21 The absence of correct stereochemical assignment for these compounds has prevented verification of the actual species responsible for biological activity.

So there you have it. With a bit of luck, one day we’re going to know exactly which alpha acid isomers are good for what. Can you imagine being prescribed certain types of beer? It’s certainly a less bitter pill to swallow for many, as it were :P

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And yes, I did indeed toy with doing an ‘up-goer fiver’ on this :P

Also, amuse that this was published in a German journal…

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References:

Urban, J., Dahlberg, C., Carroll, B., & Kaminsky, W. (2013). Absolute Configuration of Beer′s Bitter Compounds Angewandte Chemie, 125 (5), 1593-1595 DOI: 10.1002/ange.201208450

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Related posts:

Drink up! Beer benefits bones…

The Periodic Table of Beer?

Beer, anxiety and depression – their origins

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* Yep. CHEMICALS. You know, the stuff everything’s made from. Not ‘chemicals’ in the sense of ‘ew, chemicals, they’re bad for you’.

** Isomers are, basically, different forms of the same thing – to be more precise, they’re compounds ‘ isomers are compounds with the same molecular formula but different structural formulas’ (thanks, Wikipedia). Sometimes they’re mirror images of each other, and sometimes it gets quite a bit more complicated than that.

*** See Beer: Can it help fight off the common cold?, for example. Also, read the paper this post talks about for more examples of other complaints beer has been linked to helping fight.

A very kitchenesque CT scanner aimee whitcroft Jan 14

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From awesomely-educational website Hack A Day comes a particularly wonderful,  if oddly gruesome, piece of science/tech hacking.

Rotating CT chicken, courtesy of Ben Krawsnow. Watch it dance.*

 

Mad chap Ben Krasnow has built a ‘build something mad on your kitchen table’-type version of a CT scanner. CT scanners, as you will remember, take X-rays of an object and then put them all together to get a 3d composite view of the innards of said object.  They get used a great deal in medicine, for example.

And they tend to be giant (in hospitals, at least).

Anyhoo, Ben built his and, in order to keep it small, simply rotated his subject rather than rotating the machinery. He used only an x-ray tube, a stepper motor, a large ring bearing, and an Arduino microcontroller, plus a phosphor screen and camera.

The subject?  A frozen chicken. Watch the video below to see how he did it.

YouTube Preview Image

 

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For some reason, I find it weirdly unsettling…

 

How will the End of the World affect clinical trials? aimee whitcroft Dec 21

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Yes, sure, my first response was also ‘not well – dead patients are often difficult test subjects on which to continue clinical trials’.

A date inscription in the Mayan Long Count on the east side of Stela C from Quirigua showing the date for the last Creation. It is read as 13.0.0.0.0 4 Ajaw 8 Cumku and is usually correlated as 11 or 13 August, 3114 BCE on the Gregorian calendar. The date of 13.0.0.0.0 4 Ajaw 3 K’ank’in is usually correlated as 21 or 23 December 2012. Source: Wikipedia

Thankfully, however, the Canadian Medical Association Journal has looked more deeply into this most pressing of issues.

ResearchBlogging.org

In fact, as the paper’s introduction states:

There is a great deal of speculation concerning the end of the world in December 2012, coinciding with the end of the Mesoamerican Long Count calendar (the “Maya calendar”). Such an event would undoubtedly affect population survival and, thus, survival outcomes in clinical trials. Here, we discuss how the outcomes of clinical trials may be affected by the extinction of all mankind and recommend appropriate changes to their conduct. In addition, we use computer modelling to show the effect of the apocalypse on a sample clinical trial.

They go on to say, in effect, as part of Good Clinical Practise guidelines, research methods need to updated to expedite all current clinical research, lest the research results and analysis not be of benefit to anyone.

The full paper is linked to at the bottom of this piece – it’s open access, and an hilarious read.  Titles include “Stuff we did”, “Stuff we found out”, “Chit chat” and “Mostly true background”. Those of us used to wading through research papers will, of course, recognise their more prosaic analogues (Methods, Results, Discussion and Background).

Their results found that for the control group, death continued as usual but for the obliteration/end of the world group, well, things were a bit different!

For the control group, death occurs at a predictable and fairly uniform rate. However, MaD leads to a statistically significant, and clinically relevant, difference in survival between the control and obliteration groups (we’re pretty sure that, were it calculated, p would definitely be something really significant, and certainly less than 0.05). Oddly, despite censoring for major known sources of bias (e.g., astronauts currently aboard the international space station, as well as zombies, the undead, the Grateful Dead, Dungeons and Dragons players, men who have read Fifty Shades of Grey and other similar beings likely to be unaffected by the apocalypse), the obliteration group does not fall to 0. We have dubbed this slow rise in the obliteration curve the “zombie repopulation.”

There’s lots more detail, of course, including looking into the effect of the end of the world on a trial of two different drugs, and thEre are graphs and everything!  Clearly excellent science :)

Their conclusion?

If we have been thinking clearly, then it is apparent that the end of the world will have catastrophic effects on statistical analyses of survival outcomes. We therefore recommend that all clinical trials should stop immediately, as MaD will negate all potential trial results.

BUT really – go and enjoy the full paper – it’s a lovely piece of satire :)

I’m off to Canada until early Jan, but will resume blogging on my return.  In the meantime, enjoy the End of Times and, should that not happen, have an excellent holiday season!

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From those of us for whom it’s already midday on Dec 21st, well, we’re still here!

Also, it may be worth pointing out that this notion of the End Times came from us, not the Mayans.

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Reference:

Wheatley-Price P, Hutton B, & Clemons M (2012). The Mayan Doomsday’s effect on survival outcomes in clinical trials. CMAJ : Canadian Medical Association journal = journal de l’Association medicale canadienne, 184 (18), 2021-2 PMID: 23230049

More fraud behind paper retractions than you might have thought aimee whitcroft Oct 02

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A subject that’s come up in discussion with my friend a couple of times recently has been the increase in retractions of scientific papers from journals. I’ve always staunchly defended allegations this might be due to naughty scientists.

I am  now having to make my own retraction about that.

According to research (as yet unretracted) in Nature last year, the number of retractions has increased by over tenfold in the last decade, to more than 300 a year. At the time, the article talked about how it was difficult to analyse what was causing this increase.

 

Retractions. http://blogs.nature.com/news/files/retraction%20numbers%20pic%20blog.png/caption

 

Today, famed science writer and scientific tattoo collector* Carl Zimmer published an article in the Washington Post with a very upsetting piece of news: while it’s generally been thought these retractions were due to error, it now turns out more may be due to misconduct and fraud than many of us had thought.

Which makes me want to go and kick something. Possibly a disingenous scientist. But more on why I’m so angry later on this rant piece.

A new study, published in PNAS, went and looked a little deeper than previous studies. Looking at the 2,047 retracted papers related to the biomedical and life sciences in PubMed, they found that misconduct (of which fraud was a major component)**  was responsible for fully 67.4% of the retractions where they could determine the retraction’s cause.

That’s appalling.

Now, one must remember that this still accounts for a very small percentage of the papers submitted. Quoting from Zimmer’s article:

Dr. Benjamin G. Druss, a professor of health policy of Emory University, said he found the statistics in the paper to be sound but added that they “need to be kept in perspective.” Only about one in 10,000 papers in PubMed have been officially retracted, he noted. By contrast, 112,908 papers have had published corrections.

I can’t read the paper (hello paywall), so I can’t say whether the total increase of retractions is in line with the increase in paper publication over the years (i.e. is the proportion of retraction increasing too?). However, the authors do stipulate that the number of retractions due to fraud has increased tenfold since 1975. UPDATE: having now read the paper (gonna protect my source), it would appear that “research publications: retractions for fraud or suspected fraud as a percentage of total articles have increased nearly 10-fold since 1975″. So, the abstract could have been a bit clearer, then :)

While the percentage of retractions when put against publications is still very small, this development is extremely worrying.

It’s being postulated by some that the increasing pressure on scientists to ‘Publish or Perish’ is pushing them too far – where a published paper can mean the difference between tenure and unemployment, suddenly the temptation to cheat can become unbearable. Thankfully, the problem’s been noticed and there aren’t tonnes of people already talking about how broken the current publishing system is, and what could be done to fix it (eagerly, as a rule, opposed by the journals).

The Publish or Perish culture is also extremely unfair to scientists who, for example, work very practically, or who work in organisations which focus on applied rather than research work.

Finally, however, and possibly most scarily – this simply fuels anti-science sentiment and propaganda. Those out there who believe that scientists lie and twist the truth in the ongoing battle for research grants are going to seize upon this as proof positive that they’re right. Science, and scientists, cannot be trusted. Something which, to be sure, is demonstrably untrue, but for which even the smallest numbers will be triumphally used.

So. For shame, to the scientists who cheat. You do yourselves, your work and your science a great disservice. But for shame, too, to the systems which encourage these scientists to do so.

Both need a long, hard look.

Further update:

The full paper also shows some other interesting numbers: amongst these, that journal-impact factor shows “a highly significant correlation with the number of retractions for fraud or suspected fraud.

Additionally, below are the numbers for country of origin for retraction types. These graphs would, I think, have been more useful had they included information about how many papers in total each country had been published, allowing us to see the proportional representation of each country, but yes. Still interesting.

 

Fang et al (2012). Misconduct accounts for the majority of retracted scientific publications. PNAS. Click to enlarge.

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Related posts:

The (threat) challenge to science publishing

Geopolitics and science activity: 30 years’ worth

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* Well, he collects pictures of them. I have no idea whether he collects them personally :P

** The breakdown of this misconduct is as follows: “fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%)” (quotation from paper abstract)

UnderSkin, the Tube and schematic mapping aimee whitcroft Sep 26

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A beautiful piece of medical art has cropped up and being doing the rounds again the last few days.

Titled ‘UnderSkin’, and made in 2010 by illustrator/designer Sam Loman, UnderSkin shows the human anatomy in the style of the very famous London Underground map.

 

The original UnderSkin design by Sam Loman. Credit: Sam Loman. See just-sam.com to buy prints of the updated version. Click to enlarge.

 

I must say, it’s a beautiful piece of work, showing the locations of and linkages between our respiratory, arterial/venous, muscoloskeletal, lymphatic, digestive, nervous and other systems. And, should you want to put it on your wall, you can buy an updated print directly from Sam (go on! support great work!).

But while it looks, superficially, very much like that Tube map, there’s one, large difference. And it’s that this is far more accurate, at least in terms of where things are. Because, if nothing else, where things are is _important_ in anatomy.  One cannot have people simply carving randomly into bits. Things go badly.

The Tube map, first designed by Harry Beck in 1931 and continuously improved/worked on ever since, isn’t geographically accurate at all. Rather, it shows the _relative_ position of each of the stations along the line, and their connective relationships with each other and fare zones, rather than their geographical position. Which means, amongst other things, that you can’t trust it to tell you how far away something is, or quite, well, where.*

 

The London Underground map, 2012. Warnings: things are not quite where they appear. Click to enlarge.

 

So yes. Enjoy.  And go buy a print from Sam. She deserves it, don’t you think?  Also, check out her other art (I especially like the Medical stuff, admittedly) :)

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* I found this out myself, when living there. Something could seem like it was going to miles and miles on the tube, but upon getting out and walking I discovered that my destination was a couple of blocks away: something particularly common in the hive that is Central London.

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