Wednesday, July 23, 2008

Put those antibiotics down!

Heard on the radio news this morning that doctors are being told not to prescribe antibiotics for coughs and colds - nothing new there, I thought. This turns out to be a new NICE guideline on respiratory tract infections. The BBC reports NICE as saying that this is the first practical guideline to help practitioners to decide when to prescribe, and indeed, the quick reference guide to the guideline does give a care pathway to help doctors assess the person sitting in front of them.

The NICE guidance - full guidance and quick reference guide, and things for patients, is here and I shall be expecting it to make an appearance in our EBP sessions with medical students early next year (assuming we don't change the subject).

Tuesday, July 22, 2008

Changes to Web of Knowledge

Web of Knowledge has had its quarterly upgrade. Enhancements include:

"Citation Map" - visual map image displays - I need to have a longer look at this to understand what it does!

If you right click a link to, say, an author name, you can now open this link in a new tab or new window.

You can now use the browser back button to go back from Full Record to Summary page - previously the Back button meant you needed to refresh the screen.

DOIs are displayed when you are looking at single records.

Full Records and Output Sort by Times Cited for results in the All Database search

Search by Address in the All Databases search

Monday, July 21, 2008

House of Lords committee on the spread of pandemic diseases

Caught a mention of this on the radio this morning - it is the House of Lords Intergovernmental Organisations Committee, which has issued a report on the spread of pandemic diseases. One headline was that it apparently considers the WHO to be ill equipped to deal with the threat of a pandemic.

The Telegraph is reporting it, as is the Times, and the Committee page without the report is here. The report itself, called Diseases know no frontiers, is here.

Later note: BBC has picked this up, at

Friday, July 18, 2008

Nobel Prize games

Discovered this through the Biotechniques Weekly Newsletter. There are some multimedia online games based on the discoveries that have been awarded Nobel Prizes. I have just spent too long on the Robert Koch and TB game - I did manage to stain the expectorant, look at under the microscope and see the bacteria, but very slowly. Your virtual guide is called Wilma, and she has a nice line in responses when you try to do something stupid like pick up the bench, or pour the expectorant down the sink. The games are at - the "Nobel Prize in..." links at the top of the screen link to more games too. They cover peace, literature and economics (world trade) as well as chemistry, physics, medicine - including malaria and DNA and the genetic code, as well as TB.

Science: drug resistance

The latest issue of Science is a special issue on this topic, with articles about C. diff, TB, and antibiotics and antibiotics in natural environments.

There is also an article which I plan to read, about what scientists are citing now that so much is available online.

Science contents page

Thursday, July 17, 2008

Archives of Pediatrics and Adolescent Medicine vaccine themed issue

The April 2009 issue of the Archives of Pediatrics and Adolescent Medicine will be on the theme of vaccines. Papers are now invited - topics may include trials, safety, interventions that might increase vaccination rates, and a lot else.

"Manuscripts received by September 15, 2008, will have the best likelihood of being included in this theme issue".


Was led to this very useful looking website by a link from the Evidence Direct site at the Royal Melbourne Hospital.

HuGENavigator is "an integrated, searchable knowledge base of genetic associations and human genome epidemiology" - HuGENet is a CDC based project.

HuGENavigator includes:

Phenopedia - search this for genes associated with a disease

Genopedia - search this for diseases associated with a gene

Literature - search the literature (no, you don't say!), since 2001, with links to PubMed records. This has to be some sort of filtered search (searching for macular degeneration finds 171 records, where a straight search of PubMed for the same timespan finds 6500) - I can see that it searches MeSH and text, and that you can use "query detail" to deselect MeSH terms or tell it not to search free text, but haven't seen any more details as yet.

Investigator - search for a gene or disease to look for people working in an area (shows number of papers with that author as first or last author)

Gene evidence - are there genes that might be associated with a disease - not sure how this differs from Genopedia above, unless Gene evidence is looking for probable associations, not definite investigations?

Trend/Pattern shows you trends in literature, diseases or genes studied, and gives you a graph - this does show how this area has grown, even if it doesn't show you much detail.

Lastly, there is Risk, which enables you to evaluate the predictive ability of genetic markers. You would need more knowledge than I to be able to say more about this!

Some time ago I did a handout on clinical genetics resources, for a visit I made to staff at the Clinical Genetics Centre at the Leicester Royal Infirmary. I have revised it since, for genetics students, and have revised it again today to include HuGENavigator. The handout is at

Tuesday, July 15, 2008

Quality of indoor air and health

Is the subject of a review article in CMAJ: (open access! hurrah!).


Algaebase (Biotechniques again) is a database of images and bibliographical references to algae, 120000 species of them. You can search by genus or species from boxes on the home page, or search the literature, images, common names, distribution and other things from the Search option on the home page.

The database is compiled by Mike Guiry at the National University of Ireland and copyright and conditions of use are outlined here. Some papers about Algaebase are listed on the About page.


Also found in Biotechniques' WebWatch column, iHOP brings together all sorts of information relating to the gene you have searched for - once you have located the gene in the species you are interested in, you get links to information in UniProt, OMIM, and the NCBI databases.

There is a paper in Nature Genetics - doi: 10.1038/ng0704-664, about iHOP, and a PubMed search just for the word "ihop" finds more papers about its uses, but not the Nature Genetics one itself as it has no abstract.

Structural exon database

Found in WebWatch in Biotechniques, the Structural Exon Database, SEDB. Introductory page says:

"Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms."

To be able to use the datasets, you need to install Friend on your PC, but various searches seem to be possible without it: GenBank accession search, sequence searching, and using BLAST.

SEDB is hosted by Northeastern University in Boston, MA and is described in a paper in Bioinformatics, doi: 10.1093/bioinformatics/bth150. (DOI found in the PubMed record - see previous posting on this blog!)

Imported malaria

Richard Lehman again - this time in the BMJ, and an article on malaria imported to the UK. This paper was picked up also in the news at the end of last week - this, found via Intute Newsround, and this, found via Google News, and this, on the BBC.

The number of proven cases of malaria in the UK has risen in the last 20 years, with the majority of cases being found in people returning from visiting family, especially in South Asia or Africa.

The BMJ, by the way, now publishes online first, so things may turn up in the press on any day, not just Friday. BMJ references now look like this: It looks like they retain this kind of format once the article appears in a print edition of the journal - I have just had a quick look at one research article from the latest edition, and it retains the a... number, and the pages of the PDF are numbered "1 of 9", "2 of 9" and so on.

TB vaccine development

Richard Lehman's very readable Journal watch alerts me to this review in the Lancet, which looks at the immune responses which might be important, and at approaches to developing new vaccines. Start with this DOI: 10.1016/S0140-6736(08)61036-3

Monday, July 14, 2008

PubMed includes DOIs

PubMed now includes DOIs in its records - see NLM Technical Bulletin article for more details. In the tagged MEDLINE format, the DOI is in a field called LID, according to this bulletin. I have done a quick PubMed search and found the DOI appearing as AID, however.

A quick test suggests that AID goes to the DOI field in RefWorks, and the Electronic Resource Number field in EndNote 9.

Tuesday, July 08, 2008

Yec'hed mat!

Hear, hear, to the sentiments of the Nature editorial on the Academie Francaise's views on the status of France's minority languages, Breton among them. Nature says: "... regional and minority languages, like endangered species, merit protection. Languages that aren't revitalized through constant exercise die out."

On a recent holiday in Brittany, I was disappointed not to have the nerve to try out (or the application to learn many words) any Breton, but it was very good to see road signs in the west of Brittany in Breton and French.

O bydded yr hen iaith barhau!

Research Council funding

Two things that I noticed on the same day:

1 - an interview on the BBC Today programme with the head of the STFC, about their recent funding awards - money for large pan-European projects, apparently, and little for basic research in universities. There is an audio piece from a Today journalist here.

2 - an editorial in Nature about the drive to fund projects that involve industry, at the expense of basic research.

The first made my ears prick up (while I was growing up, my father taught Physics). The second caught my eye (two facial metaphors for the price of one) - there is a place, of course, for collaboration with industry, but I do think industry and business should not determine what happens in education, and overemphasis (note my emphasis) on collaboration of this sort could do that. Of course, higher education can find application through industry, but education is not only vocational.

Wednesday, July 02, 2008

Changes to PubMed

Updated 14th July 2008

Lots of discussion about this on the MEDLIB-L list, and lots of detail of the changes on Laika Spoetnik's blog - Part III of her discussion is here with links to the previous two parts.

I wrote this, to go to the departments I liaise with:

1. The sidebar has gone from the summary results screen (to make way for “forthcoming features”. I don’t know what these are yet!). In some library circles this change is generating some controversy – if you don’t like it, let me know!

2. Advanced search. This allows you to search by field (author name, journal title, etc.), to set limits and to see your search history (limits and search history are available via the “old” routes too). Look for the “Advanced search” link next to the search box.

3. Changes to automatic term mapping (ATM). Previously, if you searched for a journal title or author name, but that title or name was the same as a MeSH term, you would get a subject search instead of what you wanted. To address this, a change has been made to the way ATM works. Previously, automatic term mapping would map your search terms to MeSH and to “text words” (words in titles and abstracts). It will now map to MeSH and “all fields”.

I think this might now introduce irrelevant references into your search, if your subject matches a journal or author name, but it does address the original issue. There is some controversy in library circles about this change, and so I would be interested to know if this has adversely affected your searches at all, or to have any comments. There are full details of the change at

New information about ATM: there is now a FAQ about it:

4. Citation sensor: matches searches with citations if you use terms that can be interpreted as year, author name, journal title. Citation sensor results are displayed in a yellow area on the results display. This will not work if you use [au] and other tags in your search.
More details about citation sensor are at:

5. Title sort for results (does not ignore articles). Sorting results was possible before, but the title sort is new. You should know that it does not ignore initial articles, so a paper entitled “A new method…” will file under A, not N.

I have since discovered that the "old" spellchecker that used to say "Did you mean..." and offer a link to what it thought you meant has seemingly been replaced - I typed pharmacokinetics cucumin and it automatically told me there were zero results, but that it had searched pharmacokinetics curcumin instead, and showed me those results.