Wednesday, April 30, 2008

Scopus Affiliation Identifier

It's always a problem identifying work from particular institutions, when searching the literature, as institutions' names are never standardised and are wildly inconsistent. Scopus' way to get round this is the new Scopus Affiliation Identifier.

Basically each institution is given a unique number. I am not sure you can search for this, but there is an "affiliation" search available. I tried this, putting in Leicester. This found eleven institutions:

University of Leicester
Loughborough University
Leicester Royal Infirmary
De Montfort University
Leicester General Hospital
Glenfield Hospital
University Hospitals of Leicester NHS Trust
MRC Toxicology Unit
National Space Centre
Leicester Medical School
University College of Leicester

Under each, the variant names are listed.

You can choose to see the references associated with any of these names, the idea being that every reference from that institution will be found, regardless of the form of name used in the reference.

This seems to work well, although you can't go that extra stage and search for departments using standardised names. This is always a tricky sort of search, but I guess standardising it would be too tricky?

Scopus is at (logging in will be necessary off campus), and the Affiliation search is under the Search button. You can also do Affiliation searches from the Basic and Advanced Search screens, using the drop down box.

Monday, April 28, 2008

Google Custom Search

I have added Flutrackers to the Google Custom Search at, so it now searches that alongside DEFRA, Department of Health, Health Protection Agency, NaTHNaC; and ProMed Mail. It will now pick up things about the Bali influenza simulation (see earlier posting).

Influenza exercise

Another report on the Today programme was about an exercise taking place now in Bali to test plans for dealing with an avian influenza pandemic in humans (if you see what I mean).

Have now found things about this in the Jakarta Post and on Radio Australia, as well as on Flutrackers. (I couldn't find anything earlier).

Have tested my Google Custom Search engine (see on this to no avail. I did wonder if this was because there was nothing there at all, but now that there is, I think it is because I am not searching the right kind of site. The CSE only searches specifically flu related sites.

Gene therapy

Coverage on BBC Radio 4 Today programme this morning about treatment at Moorfields Eye Hospital involving gene therapy for Leber's congenital amaurosis.

The BBC website reports it here:

The trial itself is reported in the New England Journal of Medicine - an editorial is here, linking to two reports, one of the effect of the therapy, and one on the safety.

There is information about Leber Congenital Amaurosis in Gene Reviews.


Drove this morning from Lubenham (Leicestershire) to Mowsley, and, crossing the canal on that road, saw swallows - my first of the year. And, at the junction of that road and the A5199, more similar birds, couldn't make out if they were swallows or swifts - possibly some of each.

Friday, April 25, 2008

Plant genomics

Lots of things about this in Science this week: (on campus access only, as far as I know). Includes a multimedia feature. There is also an article on ecological costs of GM crops, but this appears under "policy forum", not with the things on genomes of plants.


Outside the window, in the trees. Listen to some like them at

800 posts!

Meningitis, and del.ic.ious

A recent Education Guardian piece on meningitis (,,2273536,00.html) highlighted the need to know what it looks like, and the importance of not being afraid to act.

I have done a very librarian-y list of resources, which I suspect is not going to be easy to use, as it isn't apparent what exactly each site is good for (although I have tried to say). A colleague has recently set up a account for us to experiment with, and I thought this was a good excuse to do just that. I have added all the sites, tagged them with "meningitis" and various other things. Splendidly, the meningitis sites all appear together at, and the "related tags" list means you can then click to find the sites that are tagged "patientinformation", "healthprofessionals", "signs", and so on. Neat.

Person to person transmission of H5N1

Three pieces in today's Lancet, vol. 371, no. 9622 - a seminar article on the general subject, and a report of a possible case in China, among them.

Several things on malaria, too, which, given the Lancet's good coverage of global health, and the fact that it is World Malaria Day, is not surprising. And an article on global health websites for students.

University of Leicester members can access the Lancet through - then search for Lancet, vol. 371, no. 9622.

Henry Gray

With an "a" - author of Gray's Anatomy, which was first published 150 years ago this year. I have it in mind to try editing Wikipedia by editing his entry , but perhaps someone else will beat me to it. At least it doesn't say "St. George's Hospital, France" any more!

The BBC "One Show" on Wednesday night had a good piece on him, including a visit to the Royal College of Surgeons (of England - the bit the English media always miss out*), which is mounting an exhibition about the book, and which has some of the original illustrations. The illustrations were done not by Gray, but by Henry Van Dyke Carter.

More on this later, perhaps!

* Spot the person who has worked in Scotland, which has its own Royal College of Surgeons (of Edinburgh)....

World Malaria Day

It's World Malaria Day today.

Malaria, according to the Roll Back Malaria Partnership, is responsible for 2 percent of all deaths worldwide, and 3000 children die of it every day.

Click the button below to find out more.


Wednesday, April 23, 2008

Perioperative hypothermia

NICE have published a new clinical guideline on inadvertent hypothermia, with documents for healthcare professionals and for the public and patients. Look at the guideline here.


Were those three blackcaps in the tree outside the office, pecking at the buds? I think they might have been...

Tuesday, April 22, 2008

Other things in Nature, 17 April 2008

Sequencing of a human genome (James Watson's, in actual fact) in four months using "massively parallel DNA sequencing", and accompanying news and commentary items;

Drug company accused of using ghost writers to write clinical trial papers (referring to a paper published in JAMA);

Evolvability and hierarchy in rewired bacterial gene networks (E. coli);

Genomic and epidemiological dynamics of human influenza A virus

Is the subject of a paper published in Nature online, at, doi: 10.1038/nature06945.

Link to the paper using the DOI here.

Medical blog from Afghanistan

More precisely, a blog from a Canadian physician currently working there -

Sunday, April 20, 2008


Forgot to mention at the time... Last year we often would see a bat in our back garden, just before dark. On Tuesday night we saw it, for (at least for me) the first time this year.

Birds - first swifts

Change of title!

We were driving from Fleckney (Leicestershire) to Kibworth (ditto) on Saturday, after dancing at the Fleckney School Fun Day. We had gone over the canal near Wistow and saw two swifts, the first of the year. And then, right over the road, quite low down, a kestrel. We slowed down - we brake for kestrels, and, rather affronted, it flew over to the side of the road.

Start them young

The bat related entry (which got a date of 11th April, for reasons I don't understand, which is why it seemed to have disappeared) was by my son - in case you wondered about the change of style.

Have not found a way to tell the bat group (they want to know about grounded bats, but not obviously about every sighting). Perhaps they will read the blog!

Friday, April 18, 2008

The first Bat (of the year.)

On April the 18th we saw a Pipistrelle bat (on the way back home from the spar shop) we named it Bert! It stayed around for 5-10 minutes (it was very small!)
Bert flew around the busy road for ages we had to leave him flying around.
We will inform the local bat group.

What tree is that?

I have been trying to identify two of the small trees in my garden (only lived in the house for three years...), using a tree book, and two websites, and the idea of "keys". I have to say I am not getting on terribly well so far, and am finding that the keys don't agree with each other.

One tree might be an elder, the other a rowan. But I am not convinced yet.

Watch this space.

Two items in Science: Croatian Medical Journal, and influenza

Two separate items:

1) Croatian Medical Journal involved in discussions about its future, in light of various allegations of plagiarism published in its pages, or by its editors:

2) A paper on the circulation of seasonal influenza viruses:

Les oiseaux du jour

In the park this morning: a goldfinch? It didn't have a red face, though. [Edit: saw another today, 20th, and reading Simon Barnes Bad birdwatchers' companion on the train, I wonder if it was actually a greenfinch, which is what my son told me they were. It didn't look green, but apparently, they don't, always). Later edit: saw some today (26th) and they did look a bit green.]

And a yellow wagtail (or a grey one), by the side of the river.

This was in addition to the usual wrens, thrushes, ducks (including one sitting on an ivy covered fence), moorhens, dunnocks, robins.

In garden -sparrows, starlings.

Thursday, April 17, 2008


On Today programme (Radio 4) this morning, piece about, Charles Darwin's papers. Coincidentally, was on, yesterday, which is his letters. I think it might be all of them, although they are being published in a series of books as well (vol. 16 due later this year).

Bit in Guardian too -

2009 is 200th anniversary of birth of Darwin, and there do seem to be a lot of books about him appearing.

Wednesday, April 16, 2008

Les oiseaux du jour

In park:

wrens, several, including one really quite cross sounding one (on a branch very close to river);
blackbird bathing in river;
moorhen looking for things in weeds around piece of detritus in river (actually a signpost from the national cycle network...).

Thought last night on way home that there are more blackbirds around in the evening.

And, on late-ish drive from Foxton Locks to home, an owl.

Tuesday, April 15, 2008

Harry Potter and the Copyright Court Case

Lots of coverage of this in the press today - JK Rowling in court in New York to try to stop the publication of an unofficial Encyclopaedia about the books. I'm interested in the fact that the material is already available on a website, and that according to BBC Newsround, Rowling has used the site and found it useful - it appears to have an endorsement from her on the home page. Interesting that the website is not viewed as a threat, or breach of copyright, but that the book is.

One place in the press is here:,,2273675,00.html

Les oiseaux du jour

Yesterday (didn't manage to post yesterday), a robin, sitting on a post, singing very near me. Today, in park, a pied wagtail, as well as usual - ducks, moorhens, wrens, robins.

Sunday, in garden, a large number (well, 15-20?) sparrows, including two attempting to mate, in the tree which houses the bird feeder. We are trying to encourage the sparrows, endangered as they are, so this is very good!

Friday, April 11, 2008


If you were watching Skins last night (and I should tell you that the programme website is labelled "over 18 only", which I am, but you may not be) and wondered about congenital subarachnoid haemorrhages, which Chris had, here are some sites:

BBC Health -

Patient UK -

MedlinePlus -

Low copy DNA

The forensic science regulator has ruled that this technique is sound, although with recommendations about how samples should be handled to prevent contamination. Low copy DNA is a technique used to get a DNA profile from a small number of cells, recently criticised in the case of the man on trial for the Omagh bomb.

The story is covered in the Guardian and on the BBC.

A Forensic Science Service factsheet about the technique is available from here:

I can't currently find the forensic science regulator report.

Les oiseaux du jour

In the garden first thing - sparrows, three woodpigeons. We put up some nesting material (in a ceramic apple, which I hung in one of the small trees in the garden) and it is certainly being taken.

In the park this morning - something flying along the riverbank, but probably not a kingfisher. Otherwise, the usual. On Wednesday night, son and I saw a fox, in the playing field that adjoins the park.

In the park on the way home this evening, what I am fairly sure was a blackcap - audio recording (on rather old BBC Bristol webpage) here.

In the garden after tea (or is that supper?) this evening - a lot of starlings. Lots of blackbirds on the verges of the road, too.

Thursday, April 10, 2008

Nursing in the Third Reich

Interesting piece in the Guardian about nurses' role in the human experimentation carried out in the Third Reich, and present day research and reactions into that.,,2271638,00.html

Induced pluripotent stem cells

Discussion of five questions - anyone can do it, everyone can have their own custom-tailored cells, the cures are on their way, embryonic stem cells are the same as iPS cells, and, iPS cells have no ethical issues - in Nature, at

iPS are created from adult cells.

Bacterial archive destroyed

An archive of infectious bacteria, held at the Pittsburgh Veterans Affairs Medical Center in Pennsylvania, has apparently been destroyed, according to Nature. It looks like this might have happened a little while ago.

There is a piece in Clinical Infectious Diseases, referred to in Nature, which is here: It includes a petition signed by 240 or so people, asking for an enquiry into how this happened.

Quake Catcher Network

Interesting piece in Nature (from a week or two ago - only just had alert of it via Zetoc). Quake Catcher Network is a scheme using the accelerometers in laptops to sense earthquakes, and then relay that information to Stanford University. The central server can then alert other people in the area, but the scheme is really to track quakes. The scheme itself has a homepage at

Il n'y a pas des oiseaux

Apologies for any creaky French grammar. I drove the car to work.

Wednesday, April 09, 2008

Les oiseaux du jour

Pretentious, moi? Not really, I hope. It did occur to me that "bird of the day" might be open to misinterpretation. (Sorry if you are reading this because you found this phrase, and are now disappointed!).

Today, two robins, on a fence either side of the path in the park. One sat within feet of me and sang, for a little bit. I told it my news, as my father always does when robins come to watch him gardening. Is that a Norfolk habit, I wonder?

Also, two very soggy pigeons sitting in a puddle, and what seem to be the usual wrens and thrushes.

Ovid Medline and EndNote

Problem solved! I posted to Thomson's email discussion list, and John East of the University of Queensland Library replied with a solution. There are tags within the filter that EndNote uses to decide which filter to choose to import the references. There was another filter with the same settings for those tags, and EndNote was using that filter instead. That filter (the one for Ovid AutoAlerts) was set to import AU and FA both into the Author field.

I would never have thought of this in a long time! Most grateful to John for his help.

Tuesday, April 08, 2008

Les oiseaux du jour

Nothing out of the ordinary today, but two wrens, both just making chirruping sounds, rather than singing. Probably significant? Last night, two feral pigeons having a disagreement on next door's roof. This morning, plenty of sparrows - some may be nesting in next door's gutter or eaves. I think we have some too, but they resolutely refuse to go in and out of the gutters while I am watching them.

Monday, April 07, 2008

Les oiseaux du jour

Sparrows (trying to encourage them to nest by putting nesting material in garden), starlings (nesting in gutters of next door's house), and, in park, robin, dunnocks (I think), thrush, duck, moorhen, blackbird. Keeping eye out for kingfisher but not spotted yet this year.

Friday, April 04, 2008

Google Custom Search

There is a custom search on the influenza home page, put there kindly by my colleague Janet Guinea. It works, but needs tuning - I have included six or sites, mostly specifically on flu, but two (ProMed-Mail and Nathnac) are not flu-specific. This means that if you search for words like "outbreak", you get outbreaks of other things. I'm reluctant to add search words to the search, as they won't be needed for the other sites and I'd worry that I would lose relevant results.

Updating influenza pages

Just updated the links in our avian and pandemic flu pages. Have not done this for some time, so a few to change. Can't get the PubMed RSS feed to work. Also discovered that if I edit the page generated by MyIntute, using Contribute, and then try to publish it, it has terrible trouble. I ended up creating all sorts of rubbish with variant filenames. Fortunately, none of this junk actually seems to have been published. Have made mental note not to edit that page again!

From Word 2007 (added title within Blogger)

This is a posting written in Word 2007 (which I have installed in an effort to fulfil the requirements of an "expert user" at the University). I noticed you could create a blog posting if you make a new document. Turns out that you are asked to register your blog, and away you go, hopefully. Don't know what happens if you have more than one (as I haven't).

Realised when viewing this that it had no title - have just added one in Blogger. Don't yet know how to do it from Word.

Scopus and RefWorks

And another current problem is this: if you follow a link from Scopus to our link resolver, then save the reference from there to RefWorks, it only imports the first author.

Local link resolver expert, RefWorks on case so far. RefWorks indicate it is an issue with Scopus, so I will go there next.

Update: Scopus report that Scopus sends only the first author's name to the link resolver, so that is why there is only one name to export into RefWorks. Better then not to export from link resolver to RefWorks, I say.

EndNote and Ovid Medline

One of my current problems is this: if I save the Medline (Ovid) filter on my network space, it will work perfectly when used to "direct export" from Medline to Ovid. When I save it to the shared folder, where EndNote looks for these things, it doesn't work. It then disobeys its own set up and imports both sets of author names (FA and AU) to the same EndNote field.

Our local IT services, EndNote and Ovid have all been pestered, to no avail.

Les oiseaux du jour

On the way to the station - starlings and sparrows outside my house, geese flying nearby, in the park: thrush, wren, long tailed tit (duck and moorhen). At station, magpies.