Friday, 25 July 2014

To Chemistry World... and beyond!

I've started a new gig guest blogging for Chemistry World. Over there I'll be doing that thing where I praise (or poke fun at) academic journal cover art. So head on over there now and check out my first post about a crazy colour explosion in Chem Soc Rev.

Chemistry World Blog

Thursday, 10 July 2014

Just who's been talking about your work?

Want to know who's been tweeting about your work, or what news articles are out there on that latest bit of research? Altmetric are now making that easier than ever. 

Article level metrics

Wiley are piloting an "article level metric score" with Altmetric for every one of their articles in the Wiley online library. These scores give a level for how much the article is shared online. I only recently noticed this development after seeing a Tweet from Matteo Cavalleri (@physicsteo) about these Altmetric ratings. A pretty cool idea.

Next to each article is a little Altmetric icon and a score for that article. In their FAQ section, they explain how it's all figured out in three easy steps:

1: Volume - Your score rises as more people mention it, which makes sense. But you only get 1 mention from each person per source, so you can't fake boost the score by tweeting the same thing over and over.

2: Sources - Different sources contribute different amounts. So a newspaper article is worth more than a blog post (even a fine one such as this), but then a blog is worth more than a mere tweet.

3: Authors - The score depends on who is saying it. So loud-mouths talking about every article under the sun are worth less than a specialist sharing with their specialist peers.

So with this new information at hand, I went to check out my latest paper.

Altmetric score

Looking at this article recently published in Angewandte Chemie, it has a score of 28, which to me sounds pretty good. Clicking on the link then gives you a breakdown of what that all means. So for this particular paper there were three news articles and five Twitter mentions. The news stories were all new to me. Being an author of the work you think I might have known, but no. A break down of the tweets states that four were from the public and one from a scientist. I'm pretty sure all the tweets came from scientists so I'd love to know whose work Altmetric doesn't think is worthy of scientist status! 

The news articles were all based on the same press release from an Angewandte but one link was to a Chinese website. A (possibly bad) Google translate of the opening sentence gave, "Eye for an eye, but also treat the person in his body", which was definitely not in the original English press release!

But hey Altmetric, I also talked about the paper on my own blog recently, so that's another one to add to the list, maybe need to expand your search a little. (--Update-- This blog is now recognised! Nice one Altmetric, sorry for ever doubting you.)

Alternate versions

Interestingly, Angewandte also does a German version of the journal (technically this is the original and the other is an international version). Looking at the paper in the German edition tells another story. The score is up to 34!

There are four news outlets this time and one blog. No tweets for this one but one extra blog (still not mine). Two of the same news pieces from the international version were there and one of the new ones was from a German website (a faithful translation this time).

So Angewandte is actually artificially lowering their scores by having two versions. Maybe something for the Altmetric team to consider here; combining the mentions somehow. Or I could just do it for them and add up the scores, which gives me an impressive looking 28 + 34 = 62. That's how science works right?

Monday, 7 July 2014

The making of a cover

I'm on the cover! One of my scientific ambitions has just been fulfilled.

From the moment I began my PhD I had but one aim... finish the PhD. Well I managed that last year, but I also had other ambitions for my scientific career and one of them was to have my work featured on a journal cover. The first time I dived into the scientific literature and saw these cover designs, I knew straight away that I had found my calling in life. Ok, so this is a slight exaggeration, but I do think they are really cool.

Authors use all sorts of ways to demonstrate their work visually. But obviously some fields of research lend themselves more easily to the use of pretty pictures than others. My work with protein interactions was certainly one of these areas.

The first sketch

It was in July last year that I had a break through. My proteins were binding in the way that I wanted and things were finally all coming together. As a quick summary, the work involved attaching 5 carbohydrates to a non-toxic mutant of the cholera toxin protein. That modified protein could then be used as an inhibitor of matching size to the original toxin. The carbohydrates of the inhibitor bind to the wild-type cholera toxin, therefore inhibiting the wild-type from sticking to your cells.

I was sat in the back of a seminar a week or so after getting my latest results, when my thoughts wandered onto how I could visualise the work. In my mind there was only one way to show the interactions and that was by anthropomorphising the proteins. I sketched down a first rough cartoon. The noble inhibitor was obviously going to try to catch the evil toxin. I don't remember much of the seminar, but I think this was still time well spent.

original sketchThe modified protein, our hero, had 5 large arms to catch the bad guy, oh and a police badge giving him the authority to hunt down these no-good toxins. As for his nemesis, well this guy had to wear the stereotypical black stripes and face mask of a robber as well as holding onto a swag bag to keep all his loot. As if this did not yet make it completely clear that he was not to be trusted, he also has evil eyebrows, a sure sign of a villain.

My initial sketch was not complete fantasy. The 5 arms represented the addition of carbohydrates to the protein. The swag bag represented for the toxic subunit that the wild-type protein possesses. The big googly eyes represented, oh no wait, they were just big googly eyes.

Writing the paper for this work was put on a list of things to do for quite a while and with it went the protein policeman. I was away at international conferences (holidays), I then had my thesis to write and after that a change of country. So it wasn't until February that the first draft of the paper appeared and as with any publication, a TOC (table of contents) image was needed. Here, the protein enemies resurfaced.

From notebook to TOC

First TOC image
The cholera toxin protein is fairly well known, with many crystal structures. Therefore, it was quite an easy task to scan through the protein data bank and pick out a nice structure as a starting point. A ribbon representation of the protein structure was chosen to start with as I believe this is the most recognisable protein depiction. Using Pymol, I then built in the alkane chains and added the carbohydrates around the protein. There was no choice for the colours, there is a standard scheme in the Turnbull lab; red = cholera toxin, orange = non-toxic mutant. The proteins were structurally accurate, the eyes and mouths were added for effect.

The initial design got the thumbs up from the lab group although it certainly needed a little refining. So after trying a few different positions and angles, the protein ribbon was changed in favour of a surface representation and a decent image was taking shape. The mask was added back in for the villain. A whistle and a police badge were given to our hero. Not the most serious piece of work, but we were confident that the actual research was good enough so that we could relax a little with a silly image.

From TOC to cover

I really wanted to try for a journal cover. We had some great work (I thought) and a great idea to build the TOC image into a full picture. The paper had been submitted to Angewandte and so the image had to be based on their standard circular design.

Final Cover!We went through 15 versions of bacteria for a background. Red, yellow and blue bacteria, some more realistic than others. I also tried out a Petri dish with bacteria growing across the plate but a consensus was made for an image with some large green bugs. The proteins stood out in the foreground and the colours worked well. Bacteria was used because the work is about protein modification and binding, and of course we couldn't perform any of the work (or have need to) without some little E. coli factories churning out all that protein.

A final change was to put some actual science into the image. Straight through the middle, separating the two enemies is a curve from one of the ELLA (enzyme-linked lectin assay) experiments reported in the paper. It gives the inhibitory potential of our good guy binding to the baddie. A fitting central divide.

All the best pictures have something a little bit ambiguous about them and here I feel that confusion is provided subtly by the police badge. The acronym refers to the top detective agency at Leeds University. CTPD, of course, standing for the Cholera Toxin Police Department. At this institution they only hire the most specialised proteins to catch the toxins.

The paper was accepted with great reviews and even recommended as a VIP paper. Excellent news! After much celebration we submitted the cover design. The editors were very quick to respond and accepted our image. More excellent news! I was amazed by how incredibly smoothly everything had gone. For my first first-author research paper this was fantastic.

I'm not sure if the image is quite bad enough to make it into TOCROFL, that will be the aim for my next paper. And after that my next scientific ambition is to get an SI unit named after myself, so we'll see how that works out.

You can find the paper "here" and our awesome cover design "here".