misc.ience

Posts Tagged Medically-related

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 :)

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Beer’s bitterness and your health aimee whitcroft Jan 31

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Yay, more beer-related science!

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.

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.

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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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.

The IgNobel Prize winners 2012: speech jamming, dead salmon brain activity, green hair and more aimee whitcroft Sep 21

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And, ladies and gentlemen, it’s official! The winner’s of this year’s IgNobel prizes have been announced and the webcast of the ceremony showed it to be as good-natured and cheerful an event as ever.

2012 #IgNobel Awardees file out on stage… Credit: @eggheader

Physics: Keller, Goldstein, Warren and Ball for research into the forces that control the shape and movement of a ponytail

Neuroscience: Bennett, Baird, Miller and Wolford for using sophisticated brain scanning technology (fMRI scanners) to detect brain activity in dead salmon as a lesson in the multiple comparisons problem

Fluid dynamics: Krechetnikov and Mayer for research into why people spill coffee when walking around with it

Psychology: Eerland, Zwaan and Guidalupe for research showing that people guess the height of the Eiffel Tower incorrectly while leaning sideways (leaning to the left makes people think it looks smaller)

Chemistry: Petterson et al for solving the mystery of why people’s hair turned green in some houses in Anderslov, Sweden (spoiler: it’s from the dissolved copper in hot showers)

Medicine: Ben-Soussan and Antonietti research into how doctors doing colonoscopies can avoid igniting gases and making their patients explode

Literature: the U.S Government General Accountability Office for producing a report about reports about reports that recommends the preparation of a report about the report about reports about reports. For real.

Acoustics: Kurihara and Tsukada for the creation of the speechjammer, which can, literally, disrupt speech

Anatomy: de Waal and Pokorny research showing that chimpanzees can identify each other (individually!) from photographs of their backsides*

Peace: Petrov for converting old military explosives into nanodiamonds which can later be used as light beacons for cancer treatments such as chemo.

A number of previous IgNobel winners, as well as Nobel winners, made appearances and gave prizes: I particularly loved the grins on the faces of the (now slightly aged) Featherstones, who garnered the 1996 IgNobel Art prize for the invention of the plastic pink flamingo :)

Lest anyone think this is being taken too seriously, the awards also featured two 30 second periods during which people were officially allowed to throw paper aeroplanes onto stage (accompanied by cries of ‘safety first!!’), with some brave soul standing thereon and wearing a bullseye.

More details about the prize winners and their inspiration can be seen in articles from The Guardian and the Washington Post.

One of my favourite elements, apart from the oft-shouted ‘Please stop! I’m bored’ chorus of this year’s _two_ Miss Sweetie Poos, is the 24/7 lectures.

In these, a top researcher is asked to explain their subject twice: first, a completel technical description in 24 seconds (they very seldom get to complete their abstract). And second, a clear summary, understandable by anyone, in just seven words.

Some of this year’s:
Mass spectrometry? “It weighs the bits in your junk”.
The research last year about bacteria living on arsenic? “Only arseholes believe arsenic can support life”.
Why the universe keeps us enrapt? “Because it’s the only one we’ve got”.

There was also a very funny, if odd, opera in three parts titled “The Intelligent Designer and The Universe”. It featured dress-making :)

And keep an eye out on the IgNobel website, where they’ll post the screencast and the full list of winners :)

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The IgNobels 2012 live! Now!

Quiet! I was talking!

IgNobel banter

The teapot effect, end of (one of my favourites)

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* The link points to the New Scientist article about it because the paper itself is behind a paywall, and costs $113 US PLUS TAX!!!!

This is your brain on implants (spoiler: it’s better) aimee whitcroft Sep 14

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Today, the Journal of Neural Engineering published rather an interesting paper. In it, they showed that they had been able to restore (and in some cases, improve) decision-making ability in primates through the use of an implanted prosthetic.

Sounds like something out of science fiction, doesn’t it?

The location of the PFC. Credit: Wikipedia

The region of the brain responsible for decision-making and complex cognition is called the prefrontal cortex (PFC). Damage or disease which disrupts the very precise neural firing necessary for proper function in this area can lead to a range of problems with attention, decision-making and movement selection.

And that doesn’t just mean people aren’t sure what kind of cooldrink they want for lunch, or get distracted easily. These are also known as the ‘executive functions’ – being able to think about the future consequences of one’s actions, for example, or the ability to differentiate between good and bad, or knowing how to behave in a way that’s socially acceptable. Decisions which, if made poorly, can lead to unpleasant outcomes.

Researchers at Wake Forest Baptist Medical Center have taken a step forward towards being able to treat this sort of damage in people.

They were able to use an electronic prosthetic system to tap into the PFC of their test subjects – 5 rhesus macaques – and restore or, in some cases, improve neural function in this area.

Diagram of NHP brain showing PFC recording locations (accessing cortical areas 46, 8, 6). Hampson et al, 2012

For the study, the scientists trained their subjects to match multiple images on a screen until they were correct most – 70-75% – of the time on the easiest trials. A screen would show the monkeys an image, and then go blank for up to two minutes before the monkey was then shown a range of images, and had to choose the image which matched the original.

While the monkeys were conducting the exercise, a prosthetic neural implant recorded the firing patterns of a number of the neurons in the PFC. More precisely, the implant recorded the neural impulses only when the monkeys had made a correct match. The details for the mathematical model used – a multi-input multi-output nonlinear (MIMO) model – are available in the paper.

Then, the monkeys were given a potent drug which is known to disrupt cognitive activity. And, I must admit, this is where I giggled a bit – they gave the monkeys cocaine :P * snort *

It worked, though – the monkeys’ ability to correctly match images decreased by some 13%. Which is where that implant comes in – when it detected that the monkeys were likely to make a ‘wrong’ decision, and ‘played’ back the neural recording taken when the animals were choosing correctly.

Let’s be clear about that – the implant ‘played’ its recording BACK into the neurons whose activity it recorded. And ye gods, but it worked. In fact, not only did it restore the cognitive function that those naughty, naughty lines had taken away, but it actually _improved_ cognitive function by about 10% above normal. Even when the schnarf was still in the monkeys’ system!

According to the paper, it’s “the first successful application of neuroprosthesis in the primate brain designed specifically to restore or repair the disrupted cognitive function.”

So, next steps?

The study’s lead author, Dr Robert E. Hampson, says “based on the findings of this study, we hope in the future to develop an implantable neuroprosthesis that could help people recover from cognitive deficiencies due to brain injuries,”

As with anything of this sort, there’s always the caveat that it worked in the animal model, and has not yet been tried on humans. But still, it seems promising!

The full paper is available, free, online, at http://iopscience.iop.org/1741-2552/9/5/056012.

Reference:

Hampson, Robert E. (2012-09-13) Facilitation and restoration of cognitive function in primate prefrontal cortex by a neuroprosthesis that utilizes minicolumn-specific neural firing. Journal of Neural Engineering, 9(5), 056012. DOI: 10.1088/1741-2560/9/5/056012

TOSP Episode 21: February 21st 2012 aimee whitcroft Feb 20

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We’re back! And with a minimum of difficulties this week :)

This week, Elf and aimee talk of a new soft motor, ROBOBEES, a teeeeeensy chameleon (squee!), hacking yoghurt, some very ancient art, ROBOBEES, investing in yourself, knitting needles and water bubbles and space, quantum computing for beginners, sequencing genomes on a USB stick-sized device (!!!!) and ROBOBEES.

…..

You can read the rest of this entry on the Sciblogs The Official Sciblogs Podcast site

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misc.ience

Posts Tagged Medically-related

Marvellous MRI music vid aimee whitcroft Feb 15

Beer’s bitterness and your health aimee whitcroft Jan 31

A very kitchenesque CT scanner aimee whitcroft Jan 14

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

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

UnderSkin, the Tube and schematic mapping aimee whitcroft Sep 26

The IgNobel Prize winners 2012: speech jamming, dead salmon brain activity, green hair and more aimee whitcroft Sep 21

This is your brain on implants (spoiler: it’s better) aimee whitcroft Sep 14

TOSP Episode 21: February 21st 2012 aimee whitcroft Feb 20

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