Thursday, June 29, 2006

LAST WEEK's Nature

Getting behind myself, I think. Last week's Nature, the issue for 19th June had these:

A piece on the financial state of the PLoS journals; - which are facing a financial crisis, according to Nature;

A piece reporting that a spending bill currently before the US House of Representatives has had an amendment proposed, whereby NIH funded researchers would be mandated to put their work in an open access repository. Currently they are only encouraged to, and most don't.

And a review of a book about malaria in Italy in the 20th century, which argues that there are lessons to be learnt about how to tackle malaria now.

ARGH Biomedical Acronym Resolver

A posting to MEDLIB-L asked if anyone knew of any other acronym websites, but I have to say I did not know about this one. It looks good. The ARGH Biomedical Acronym Resolver is compiled automatically from Medline (so sometimes the same acronym is resolved in two different, but very similar, ways) at the UT Southwestern Computational Biology Group, at UT Southwestern Medical Center, Dallas.

You can put in an acronym and get the expansion - I tried RA, and got a long list, and also BLAST, which is where I got the two variants. You can also put in a phrase and get the acronyms. I tried quality of life and learnt that you need to click the submit button and not just press enter.

ARGH Biomedical Acronym Resolver is at, where there are links to other data mining projects that I will come back to.

Odds ratios, and statistical errors

Two articles I have noticed recently, rather than one article on both things, or linking both!

a paper in Archives of Dermatology, which looked at statistics in papers in Arch Dermatol and in J Am Acad Derm. 364 original studies were found, published in 2003. 155 had statistics in them. 14 percent of these papers had errors in the statistical methods, 26.5 percent had errors in the presentation of results, and 2.6 percent had errors in both. (Information from the abstract). The authors conclude:

"Readers should critically analyze the methods and results of studies published in the dermatology literature."

Neville JA, Lang W, Fleischer AB. Errors in the Archives of Dermatology and the Journal of the American Academy of Dermatology from January through December 2003. Arch Dermatol 2006; 142: 737-740.

Then, a
paper in the same issue of the same journal, looking at the interpretation of odds ratios and their relation to relative risk. (I keep wanting to type "odds rations", for some reason).

Katz KA. The (relative) risks of using odds ratios. Arch Dermatol 2006; 142: 761-764

Stem cells

This week's Nature (29th June) has several papers on stem cells. One of them is a stem cell glossary, which looks useful.

Influenza articles, and sharing flu data

Some recent articles:

Influenza and the challenge for immunology, by Peter Doherty and others, summarising what is known about the interaction between the H5N1 virus and the mammalian host response, published in Nature Immunology.

What came before 1918? - a news item in Science on work by Jeffery Taubenberger on what viruses caused the flu epidemics before the 1918 one. Taubenberger was a member of the team that worked out the genome of the 1918 virus. This work may help discover the origins of that 1918 virus.

A letter in Science on the FLU-ID project, which will share information from veterinary virologists about the virus. This will be done in association with the NIH Influenza Genome Project and GenBank. The NIH Project I am guessing is the one at Genbank is at The same letter comes up in various places in a Google search - search for flu id, rather than flu-id (or it asks if you meant "fluid").

Later note: Nature of 29th June carries an editorial advocating sharing of flu data. It refers to the letter in Science (I think) but also reports moves in the US House of Representatives calling on the US Health Secretary to require sequence data to be deposited in GenBank.

PubMed Basics

This useful leaflet, produced by the National Network of Libraries of Medicine, has been updated. Download it from (PDF format, so you will need Acrobat)

Wednesday, June 28, 2006

New PubMed features

As just mentioned in another posting, PubMed can now display links to related articles, alongside the abstract that you are reading. You used to have to click a link to display related articles. You can turn this feature off and have it looking exactly as it did before.

PubMed has a New/Noteworthy feature, at, which mentions this, and which is also available as an RSS feed. You can also receive updates to PubMed searches via RSS: if you want to see what this might be like, you can see an example in our avian and pandemic flu pages. RSS is an interesting way to keep up to date, as you can get information delivered to you and then look at it when it suits you. I am trying it via Bloglines. If this intrigues you, please contact me to find out more.

Vitamin C and Vitamin E in pregnant women at risk of pre-eclampsia

There is a paper in the Lancet on the VIP trial, which investigates the potential benefits of these vitamins in women at risk of pre-eclampsia.

>> Read the PubMed abstract
>> Read the Lancet article

PubMed now has a new feature which means you can see related articles displayed alongside the abstract you are reading (these used to be hidden under a link). More on this in another posting.

OPSI and National Archives to merge

OPSI is the Office of Public Sector Information, and is what used to be HMSO. It is merging with the National Archives. Read more on the OPSI site.

Registration of clinical trials

The WHO has called for registration of all trials involving humans, according to the BMJ. There is detail straight from the WHO in a piece in the Bulletin of the WHO. The proposal came from a clinical trials day held by the WHO on May 19th.

Later note: The National Academies Press has just published a report of a workshop held by the Board on Health Sciences Policy of the Committee on Clinical Trial Registries. Entitled Developing a national registry of pharmacologic and biologic clinical trials, the book is available for purchase or reading online at

Exporting from journals to RefWorks

If you are reading a paper online, many journals will offer you the choice to export the citation of that paper into reference management software.

Nature journals, I discover, export into EndNote as a default (on our network). Here is how to export to RefWorks instead:

Right click on "Export Citation".
Select "Save target as..." and save the file somewhere.
Go to RefWorks
Select References, Import
Select RIS Format as the Import Filter/Data Source and then database "RIS Format".
Browse to the file and select it.
Click Import.

This imports a link to full text (via the DOI) as well.

Tuesday, June 27, 2006

Influence of the pharmaeutical industry

I have to say that this has always interested me, and so my eye was caught by these:

Commercial influence and the content of medical journals, in the BMJ. Does commercial bias affect the editors of medical journals and help them decide what to include?

Hans Hoogervorst, the Dutch health minister, has ordered an enquiry into the claim of a book that the drug industry influences the content of clinical guidelines.
The BMJ reports this. The book is by Joop Bouma and is called "Slikken: hoe ziek is de farmaceutische industrie?" ("Taking one's medicine: how sick is the pharmaceutical industry", is the BMJ's translation - Slikken is "to swallow"). There is a bit of information about the book on the Scheltema website (online arm of Amsterdam bookshop).

Meanwhile, an article in the AMA's ethics journal, according to the BMJ, is arguing that drug companies funding of CME should end, as it influences prescribing habits.

Finally, Joe Collier's Analysis and comment article in the BMJ, called "The price of independence". Joe Collier was editor of the Drug and Therapeutics Bulletin.


Some recent articles of interest:

A study of the quality of evidence published in medical journals, using the number of RCTs and meta-analyses as the measure - published in the Postgraduate Medical Journal, with accompanying commentary. The commentary records the editors' debates over the publication of the article.

A study of the information sources that are important to surgeons, using a questionnaire. Peer reviewed journals were listed as the second most important source, with the BMJ and Annals of the Royal College of Surgeons of England being read across all sub-specialties. The paper appears in
BMC Medical Informatics and Decision Making as a provisional PDF. Meetings and conferences, by the way, was the most important source.

PLoS Medicine has published an
editorial on open access and public health. It starts with a story told by Arthur Amman, president of Global Strategies for HIV Prevention, about a physician from Africa who altered their practice based on an abstract posted on the Internet. However, the full text of the article would have revealed the deficiencies of the study, and might have led the physician to different conclusions.

Finally, a
BMJ News piece says that search engines increase the use of academic journals more than open access.

I am off to read all these in full!

Thursday, June 22, 2006


Ghana are through to the last 16 - they beat the USA 2-1, and the Czech Republic lost to Italy! See earlier post for context of this post!

Influenza news

Some things I have noticed recently:

An editorial in the Journal of the Royal Society of Medicine, by Kamran Abbasi, the editor, entitled "Bird flu: one dead swan, one billion items of information". This is on open access at He suggests that the "scare" includes an element of distrust created by the quality of information. There is a link to an article in the same issue by Liam Donaldson (which I have not read yet). I would hope that our avian and pandemic flu webpage is one way through all these items of information.

The Guardian recently carried an article by Joanna Blythman arguing that bird flu was caused by intensive farming, and not brought to farming by wild migrating birds. She points to research that suggests that the infection routes are closer to routes travelled by infected material from one farm to another, rather than routes taken by migrating birds. Read the article at,,1791954,00.html Later note: Science has reported a meeting in Rome that concluded that although wild birds do play a role in spreading avian flu, the main culprit is commercial poultry.

EurekAlert (a news service from the AAAS) reports that Blackwell is launching a new journal called Influenza and Other Respiratory Viruses, which is to be edited by Alan Hampson, a member of the WHO Pandemic Influenza Taskforce. Read their news piece at

Finally, Karl Nicholson of this University is involved in a human clinical trial of an influenza vaccine. There is more about this in the University's eBulletin.

I am always adding new links to our avian and pandemic influenza webpage, so please bookmark it if it is of interest.

Meningococcal disease

A paper in Journal of Medical Microbiology looks at the epidemiology of meningococcal disease in England and Wales from 1993-2004, using data from the Meningococcal Reference Unit.

>> Read the paper

ATS/ERS Statement on Pulmonary Rehabilitation

You can read this (if you are a University member on campus!) in the American Journal of Respiratory and Critical Care Medicine.

Journal of Infectious Diseases

I have also been scanning the issue of this title for June 15th (vol. 193, no. 12). It includes a paper on amantadine resistant H5N1 avian influenza virus.

Clinical Infectious Diseases

I have just been scanning the issue for June 15th (vo. 42, no. 12), which is the latest print issue to reach us (later ones are available online). It includes two papers about hepatitis E in Darfur, which was also the subject of one of Alan Cann's VirologyBytes podcasts (see a previous posting from today). It also includes papers on multidrug resistant TB in New York City, and on infections due to rapidly growing mycobacteria. The contents page for this issue is at

Database of antimalarial drug resistance

A paper in the open access Malaria Journal discusses the need for a publically available database, and reviews the resources that are currently available. These include a WHO database that underpins a publication, and national and regional information from Africa. Read the paper at (this is the provisional PDF).

NCBI Toolbar

Without looking, I can't remember if I have mentioned this before. This was a toolbar to give you quick links to all the various NCBI resources. The NLM Technical Bulletin reports that they are no longer able to support the toolbar, although you can keep using it.


Toxicology resources

The National Library of Medicine Technical Bulletin has published a review of all the toxicology resources available from their Toxicology and Environmental Health Information Program. These include a household products database for the public, and information on adverse effects of chemicals, aimed at health professionals. And all sorts of things besides.

>>Read the NLM Technical Bulletin article.

I am keeping half an eye on the World Cup and notice that the USA have equalised against Ghana. I have jinxed all the African sides by picking their players for my Guardian Fantasy Fussball team, I think. But, I notice (and I am going to type this quietly), Ghana are now 2-1 up. Time for the jinx to end? We shall see!

Simple guide to RSS

The BMJ Career Focus has recently published an article by Adel Abdellaoui entitled "A really simple guide to a powerful tool: RSS". It is aimed at the typical doctor but looks to me like it would be useful for lots of people.

>>Read the article.

I am no longer able to install software on my work PC, so have been experimenting with Bloglines, which has a web based RSS reader. There are all sorts of things that have an RSS feed - in preparation for a training session here for postgraduates here, I set up feeds from BBC News, the Weather Channel, my own blog (this one!), a journal, and a newspaper.

Tuberculosis care standards

The problem with bookmarking things for blogging and then returning to them rather later is that I often can't remember where I saw something. However, wherever I saw these, I did see some international tuberculosis care standards on the website of the Francis J. Curry National Tuberculosis Center, in San Francisco.

The documents are: the International Standards for Tuberculosis Care, the Patients' Charter for Tuberculosis Care and version 8 of the Guidelines, Statements and Standards on Tuberculosis Care. All are in English, although French and Spanish versions of the International Standards and the Patients' Charter were promised in April 2006.

You can see these at

Review of NICE's recommendations

James Raftery, professor of health technology assessment at the University of Southampton (UK) has reviewed NICE guidance issued between 1999 and 2005, in an article in the BMJ.

He concludes:

"Overall NICE must be judged to have succeeded in surviving some controversial decisions. Its appeal system has imposed consistency and has so far prevented appellants proceeding to legal challenge. Although clinicians have understandably feared blanket restrictions, these have been fairly rare. NICE continues to be best characterised not by saying no, but by saying yes but... "

Read the paper in the BMJ, 2006;332:1266-1268 (27 May)

Wiki for sharing lab protocols

Another Nature news item reports websites that are being set up to share laboratory protocols and techniques in biology and chemistry. These sites are similar to Wikipedia, and are designed to share details of techniques that apparently journals do not any longer have room to publish.

Nature's publication experiments

Nature has launched an online debate about peer review, which you can find at It is also experimenting with open peer review, where submissions to Nature can be subjected to open peer review. Such submissions will be placed on a preprint server, where people can make comments. Read more about both these experiments at

Nature is also opening up its news items to comment, by attaching a blog to each item in its daily news. There is more about this at

African World Heritage Fund

A belated mention for the UNESCO African World Heritage Fund, which is designed to help countries in sub-Saharan Africa to preserve their cultural and historical heritage. The fund was launched in early May and there are more details on the UNESCO website.


It was interesting to see smallpox making it to the headlines - the Guardian recently ran a story about how easy it was for them to buy a small part of the genome of the virus, and therefore how easy it would be for someone to make the whole virus and perform acts of terrorism with it.

This story was the subject of one of Alan Cann's VirologyBytes podcasts: go to and look for the podcast for 16th June.

Friday, June 16, 2006


This paper, by Abigail Allwood and colleagues from Macquarie University and elsewhere in Australia, in Nature looks at the stromatolites within a rock formation in Australia - stromatolites are fossilised structures of possible biological origin, if I am reading it right, so could be fossilised microbes.

Clinical pathways and COPD

Canadian researchers have published a paper in JAMA that looks at the impact of clinical pathways on the care of nursing home residents with COPD. They looked at whether the use of a pathway could reduce hospitalisation, complications and costs and concluded that it could.

The paper is in JAMA: and the trial is registed in - go to to see full details of the trial.


There is a Nanoparticle Information Library (NIL), designed to help occupational health professionals share information on naonparticles, especially their health impact. NIL is from NIOSH, the (US) National Institute for Occupational Safety and Health. You can do a quick search, or search by structure (film, nano rod, quantum dot, and so on) or element. NIL at the moment has links to other NIOSH resources on nanotechnology.

NIL is at

Score a goal, and boost your team's confidence

Well, there is a football tournament on (and I am waiting with expectation for the results of the Ivory Coast and Angola games later today to see how my Fantasy Fussball team will fare - see earlier football related posting!).

Nature is reporting a paper in the online arXiv that looks at whether a team's scoring a goal results in increased confidence and then a flurry of goals. By looking a large number of results, the researchers found high scoring games occurring more often than they would expect. This suggests, they argue, that teams are encouraged when they score and then go on to score more. Read Nature's report (with a link to arXiv).

Getting paid for publishing in elite journals

Nature reports that researchers in South Korea can earn a financial bonus if they publish in an elite journal. Apparently this is not confined to South Korea, as researchers in China and Pakistan are already able to do this. Not surprisingly, such schemes have their supporters and their detractors. Read more in Nature, and read Nature's editorial as well.

Leicester Research Archive is live

LRA is our open access institutional repository, where we will archive as much of the University's resarch output as we can. I am currently working for half of my time on this project and earlier this week actually put some real information in it! It currently has 15 items in it, with a whole lot more ready to go in when I have sorted out licencing arrangements or got permission from the publisher.

To look at LRA, go to
To find out more about the project, go to

Once there is more material in LRA, we will have a proper launch with press releases and things.

Journal Citation Reports for 2005 available

JCR for 2005 is now available via ISI Web of Knowledge. Go to The JCR is the only source of journal impact factors. If you are in 3Is, and need advice (or would like me to search the JCR for you), please get in touch.

Tuesday, June 13, 2006

The World Cup!

It was only a matter of time! News@Nature is running a World Cup special, with, among other things, pieces on the science of footballs and boots. Some of the items are available only to subscribers (we can see only those items included in a standard journal subscription). Go to

The Chartered Society of Physiotherapy have produced a "2006 World Cup survival guide", on footballing injuries, available in various forms at There is a Flash version, an HTML version, and a printable PDF version.

Finally (and rather peripherally), I am conducting an experiment in the Guardian's Fantasy Fussball, by picking a team made up of as many African players as I am allowed. Watch this space!

Tuesday, June 06, 2006

Anne Frank Day

Anne Frank Day is on June 12th - there is a poster at . The day is a project of the Anne Frank Trust, whose website is at The Trust is involved in work to combat racism and promote diversity.

The Anne Frank Huis in Amsterdam has a website at - the site is available in six languages.

Recent articles that might be of interest

Physical activity and physical self-concept: comparison between children with and without asthma, by Li-Chi Chiang and others, in Journal of Advanced Nursing. You will need University Athens if you are off campus.

Surgical hand scrubs in relation to microbial counts: systematic literature review, by Hsiu-Fang Hsieh and others, also in Journal of Advanced Nursing. The review tries to determine the effectiveness of hand scrubs in relation to bacterial growth on the hands of operating room staff. You will need University Athens if you are off campus.

Emergence of Mycobacterium tuberculosis with extensive resistance to second-line drugs, published in MMWR. This looks at the incidence worldwide of TB that is resistant to second-line drugs (that are used if isoniazid and rifampin based treatments are ineffective).

I am living in my own corpse: the experience of tuberculosis in the poems of A.B. Simic, by M-A Duerrigl and others, in Medical Humanities. Simic (who ought to have inverted chevrons - not sure what they are called - over the S and C) was a Croatian poet. You will need University Athens if you are off campus.

Impact of adverse publicity on MMR vaccine intake: a population based analysis of vaccine uptake records for one million children, born 1987-2004, by V. Friedrichs and others, published in Archives of Disease in Childhood. The authors are from Glasgow and the population database used is for Scotland. You will need University Athens if you are off campus.

Diagnostic insufficiency in Africa, by Iruka Okeke, a letter in Clinical Infectious Diseases. This is about the dearth of clinical scientists in Africa and is in response to a piece in an earlier issue of the same journal. This may not be accessible off campus.

And finally,
Returning home to make a difference is an interview with Dr. Twalib Ngoma, a cancer specialist who came to the UK to study but returned home to Tanzania. The interview is in Careers BMJ.

Monday, June 05, 2006