Tuesday, December 19, 2006


Coming out of blog-silence (caused by lack of time, and general disorganisation) to list these sources of information on PVL MRSA (Panton Valentine Leukocidin), the strain of MRSA that was featured on the BBC radio news yesterday.

Interim guidance on diagnosis and management of PVL-associated Staphylococcal infections in the UK (Department of Health)

Panton-Valentine leukocidin positive MRSA in 2003: the Dutch situation (a report in the online journal Eurosurveillance)

and, perhaps most relevantly at this time,

Hospital-associated transmission of Panton-Valentine leukocidin (PVL) positive community-associated MRSA in the West Midlands (a report in CDR Weekly, from the Health Protection Agency)

There may, of course, be material in things about MRSA in general:
this quick search of INTUTE would be a good place to start.

For research literature on PVL,
click here for a search of PubMed (but remember that PubMed does not always link to University of Leicester full text)

Monday, November 13, 2006

Seasonal and pandemic influenza: at the crossroads

I have a Web of Science alert running, which sends me references to new literature on avian and pandemic flu. It has alerted me to this supplement to the Journal of Infectious Diseases:
Seasonal and Pandemic Influenza: At the Crossroads, a Global Opportunity, suppl. 2 to vol. 194, and available online from
http://www.journals.uchicago.edu/JID/journal/contents/v194nS2.html. The supplement is sponsored by a number of bodies including CDC and NIAID.

National Knowledge Week for COPD

This week is National Knowledge Week for COPD, an initiative of the National Library for Health. The NLH Respiratory Specialist Library has a page of specially written articles, with supporting evidence. These cover statistics, physiotherapy, palliative care, spirometry, and more.

Friday, November 03, 2006

All Party Parliamentary Group on Global Tuberculosis

Today's BMJ reports the inaugural meeting of this group, chaired by an MP from each of the major parties. The Register of All Party Groups gives more information about membership and purpose.

Wednesday, November 01, 2006

Avian and pandemic influenza

"My" webpage on this subject has moved to a new URL, as part of the redesign of the Library's website.

You will find it now at http://www.le.ac.uk/library/clinical/influenza.html.

The page has also been archived as part of the UK Web Archiving Consortium project, which is nice!

Tuesday, October 24, 2006

Vaccines and the incidence of autism

Noticed this some time ago: review article on the changing epidemiology of autism, and whether this is in any way due to vaccines.

Vaccines and the changing epidemiology of autism
B. Taylor

Child: Care, Health and Development 2006 32:5, 511

is the article and University members can find it here

Microbial database of protein sequence analyses

Noticed this in BMC Bioinformatics: MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization. Read more at http://www.biomedcentral.com/1471-2105/7/459

Analgesic effect of watching television

No, not in general, but using TV as a way to distract children while they are undergoing venipuncture. The authors, based in Italy, studied 7-12 year old children undergoing this procedure. Some were not distracted at all, some were in the same room as a television ("passive distraction") and some were actively distracted by their mothers. TV watching was more effective than the active distraction, perhaps, the authors say, because the mothers were emotionally involved in the procedure. The study appears in Archives of Disease in Childhood.

ATS statement on grading the quality of evidence

The American Thoracic Society has published a statement on grading the quality of evidence in its recommendations. Read it at http://ajrccm.atsjournals.org/cgi/reprint/174/5/605


I can't now remember how I found this site, but this site is operated by people living with HIV and contains some useful looking community forums, explicit in places, as you might expect, but using the web to share information.

AIDSmeds.com is at http://www.aidsmeds.com/

Thursday, October 12, 2006

Ig Nobel prizes

Today's Nature and the Guardian earlier this week both cover this year's prizes. Research into why woodpeckers don't get headaches, and into a sound based repellent that teenagers can hear but older people like me can't, and into how dry spaghetti breaks, was dul honoured.

Read more in Nature
Read more in the Guardian

Conclusiveness of Cochrane Reviews

A paper in Acta Paediatrica, by researchers from Israel, looks at the conclusivesness of Cochrane Neonatal Reviews. They find that the majority are conclusive, the that they emphasise the need for further studies. The sample size and number of studies influences the ability of the review to be conclusive. Newer reviews are more likely to be conclusive than older ones.

Read the article at Acta Paediatrica 2006, 95, 1209-1212 -

Friday, September 29, 2006

BMJ, 30th September

Tomorrow's BMJ includes:

a clinical review article on management of meningococcal disease in children - http://bmj.bmjjournals.com/cgi/content/full/bmj;333/7570/685

a news piece on the current outbreak of E. coli O157:H7 associated disease in the USA, caused by spinach - http://bmj.bmjjournals.com/cgi/content/short/333/7570/673-c?etoc

another news piece, this time reporting a survey of doctors that indicated that most did not feel the government was prepared for an "avian influenza pandemic" - http://bmj.bmjjournals.com/cgi/content/short/333/7570/674-a?etoc

an article arguing that reliance on RCTs is not helpful in resource poor settings. For example, when studies (which were not RCTs) began showing that oral rehydration therapy was effective to counter dehydration caused by diarrhoea, the WHO started an ORT programme. There were no RCTs until ten years after this date. The authors argue that clinical experience and other sorts of studies can be an effective evidence base. http://bmj.bmjjournals.com/cgi/content/short/333/7570/701?etoc

And then there are some letters about extreme drug resistant TB (which I have mentioned before) and about plagiarism. One of those looks at keeping records of studies in a field, and how that can help spot studies that don't quite fit, or which repeat already known data; another looks at citations - where it is not clear how a citation supports an assertion, and where it is not clear if an assertion is supported by any citation; and the last looks at using Google to detect plagiarism.

Entire table of contents is at present at

The joy of cataloguing

I was also struck by this Guardian item. A graduate student has found an up-till-now lost poem by Robert Frost, which was written in pencil by the author inside a copy of one of his poetry collections. That particular copy was given to a friend, and it ended up in the Library of the University of Virginia. The student, Robert Stilling, was reading some of Frost's correspondence, in the Library, and made the connection between a letter mentioning the book, and the actual copy of that book held in the Library.

This all goes to show:

You never know when something in the Library collections (or the medical literature, either, for that matter) will become important;
Cataloguing some material in detail is important: presumably the library catalogue (or catalog) recorded the provenance of that patricular copy of the book.

Marc Abraham's "Improbable Research" column last week talked about library materials being lost because they were not catalogued accurately. He was talking about Irish Gaelic materials being catalogued as if "Na" was the first word of the title, when in fact it means "The". I have found this so many times over the years, even with titles in French and German, let alone more unusual languages. Filing "The Lancet" under "The", even...

More at:

http://books.guardian.co.uk/news/articles/0,,1883689,00.html (Frost)

http://education.guardian.co.uk/egweekly/story/0,,1880490,00.html (Improbable Research)

Connectivity Map

Today's Guardian has a very small item about this, which it describes as a "Medical Google" and the "human connectivity map". It refers to an article in Science, and I suspect it is this:


This is the "Connectivity Map", a reference collection of gene expression profiles. The profiles come from cells treated with various small molecules, and it is hoped that the Map will aid the discovery of connections between diseases, physiological processes and the actions of drugs.

Thursday, September 21, 2006

Extreme drug resistant TB

Wednesday 13th's Guardian carries a report of extreme drug resistant TB (XDR-TB) in South Africa. They report what happened at a hospital in Tugela Ferry in Zulu kingdom. When antiviral drugs eventually became available, doctors noticed a great improvement, but there was a group of patients whose immune systems responded well, but who did not get any better. XDR-TB is resistant to every first line drug.

The article discusses concerns over what will happen if the disease spreads, and about what the government is doing about it. Apparently the national health minister did not attend a meeting last week of WHO, CDC and South African experts to discuss what to do about XDR-TB.

Dr. Alan Cann also discusses XDR-TB on his blog http://microbiologybytes.wordpress.com/

See also:

Nature for 14 September
Lancet for 16-22 September
Science for 15 September

Monday, September 18, 2006


That last post, on JAMA's theme issue on malaria, was the 600th to this blog.

JAMA theme issue on malaria

JAMA is planning a theme issue on malaria, and is asking for papers. Those received before 15 December 2006 stand the best chance of publication.

Read more at http://jama.ama-assn.org/cgi/content/extract/296/10/1289

How prepared are we for an influenza pandemic?

Iain Stephenson, of this very hospital, is the author of an editorial on this subject, in the Lancet of 16-22 September.

Wednesday, September 13, 2006

Legionnaires' disease

Today's Guardian reports an increase in the number of cases of legionnaires' disease, with the HPA investigating 120 cases reported to it since the start of August. This is twice the number reported in the corresponding period last year.

The HPA's general information on the disease is at http://www.hpa.org.uk/infections/topics_az/legionella/menu.htm, with a press statement about the increase in cases at http://www.hpa.org.uk/hpa/news/articles/press_releases/2006/060912_legionnaires.htm

Tuesday, September 12, 2006

Infectious diseases: preparing for the future

Science (8th September) reports a Foresight project that has produced a report on this. The project compared the UK, China and sub-Saharan Africa. It looked especially at detection of infection and identified eight areas where improved detection would help:

1. New diseases (SARS, BSE) and variants (H5N1)
2. Infections resistant to antibiotics
3. Zoonoses, including foodborne infection
4. HIV/AIDS, malaria and TB
5. Epidemic plant diseases
6. Acute respiratory infections, including influenza
7. Sexually transmitted infection
8. Animal diseases

Read Science's report of this at http://www.sciencemag.org/cgi/content/summary/313/5792/1392. The Foresight papers (and other things) are at http://www.foresight.gov.uk/Detection_and_Identification_of_Infectious_Diseases/Index.htm

Thursday, September 07, 2006

Acinetobacter baumannii

One day soon I will get round to posting all the things in my "to be blogged" folder. I am very behind again.

Meanwhile, a supplement to Clinical Infectious Diseases has crossed my desk: Serious infections in the intensive care unit: Pseudomonas aeruginosa and Acinetobacter baumannii, which appears to concentrate on antimicrobial resistance. It is Clinical Infectious Diseases 2006, 43 Suppl. 2, and University members (on campus) can access it here.

Wednesday, August 02, 2006

Pandemic influenza

Two things from a search alert that runs for me in PubMed (ask me if you would like to know how to do this):

First, a paper in Primary Care Respiratory Journal that summarises the literature about any imminent influenza pandemic from a primary care perspective. Their conclusions:

"We need to update ourselves and keep our staff and patients informed to make infection control measures part of our daily activities. In areas where there are contacts with animal reservoirs of influenza A, patients need to be reminded that they need to protect themselves from being infected."

The paper is available online through ScienceDirect (if you are a University of Leicester member or member of another institution with a subscription). There is no link (at the moment anyway) from PubMed directly to the article.

Second, a letter in the British Journal of Anaesthesia looking at the preparedness of intensive care units in the south east of England (or "south east UK", as the authors term it) for a pandemic. The authors found hospitals with no contingency plans, so urge that all hospitals develop one. There is a link to full text, which ought to work if you are a University of Leicester member.


The latest issue of id21 Insights, a web magazine "enabled" by DFID and produced by the Institute for Development Studies at the University of Sussex, has a malaria theme. It looks at household and community responses to malaria in Africa, with several articles about mosquito nets, and others about cultural and social factors, and about malaria control in refugee camps.

SciDev.Net reports a programme that will use home computers to investigate how malaria spreads. Africa @ Home will use spare capacity of home PCs to run a simulation of how malaria spreads.

SciDev.Net also reports a paper published in Nature Chemical Biology, in which researchers used a drug library to find drugs with possible activity against the malaria parasite. The Johns Hopkins Chemical Compound Library provided the information, and this library is now being expanded. Researchers report that astemizole (an anti allergy drug) looked as if it might have this activity: it proved effective in mice. Read more about this in SciDev.Net.

This issue of id21 Insights is at http://www.id21.org/insights/insights-h09/index.html. You can read more about Africa @ Home at http://www.scidev.net/News/index.cfm?fuseaction=readNews&itemid=2990&language=1.

Child Health Information and Learning Discussion Group

This is an email discussion group, hosted by Dgroups (which hosts the HIF-Net list, which I belong to, and which alerted me to this).

The list hopes to stimulate debate about how to improve child healthcare worldwide. Full details about how to join and what sort of thing to post are at http://www.dgroups.org/groups/CHILD2015/index.cfm.


Two items in the New England Journal of Medicine (may not be available in full online) caught my eye:

A "Perspective" column in the 27th July issue (355:339-41) about the health effects of illiteracy. The column reports a patient who was not taking their medication properly, despite having it explained carefully (the physician thought) and having a note written for them. It was the medical student who suspected that the patient might not be able to read, and this proved to be the case. No one else out of the team of people who had met the patient had thought of this.

"Perspective" column in the issue for the 20th July (355:229-31) looks at language barriers to health care in the United States, focusing on the case of a 12 year old boy with Spanish as a first language and with little English. His mother, who described the symptoms, had no English. The physician had no Spanish. This obviously led to some confusion, and there are descriptions of other cases where inappropriate care was the result.

Research Councils policies on institutional repositories

Revised posting, revised 2nd August:

For some time, the UK Research Councils have been deliberating about whether researchers they fund should place their research into open access repositories. After a consultation, they have decided to leave the decision up to each individual research council.

The Medical Research Council will mandate researchers to place their publications into PubMed Central, from October 2006. The Economic and Social Research Council will encourage people to put their publications into the "ESRC awards and outputs repository" (I am not clear at this precise moment exactly what this is). The Biotechnology and Biological Sciences Research Council will require publications resulting from research that they fund to be put in an "appropriate e-print repository". For University of Leicester researchers, this "e-print repository" is Leicester Research Archive.

The other councils have yet to decide or are awaiting the results of a RCUK investigation into publishing as a whole.

You can read more about this in these places:

ScieCom Info (in Swedish) - this is a bulletin compiled by Ingegerd Rabow, project leader of Svenskt Resurscentrum for vetenskapelig kommunikation, based in Lund.

SPARC Open Access Newsletter

The Guardian

and on the RCUK website, which links to statements from each council.

and, in Science of 7th July and the BMJ of 14th July.

New bit:

The ALPSP (Association of Learned and Professional Society Publishers) have responded to the RCUK statement, and you can read about it via the UK Serials Group's Serials e-news.

Knowledge for practice, MRSA, personal protective equipment to prevent respiratory infection

A lazy shorthand title, so I can mention three pieces from the latest CMAJ, all in one entry!

First, knowledge. The idea of "clean, clear knowledge" is one that NHS staff may have seen, as it is a slogan that has been used to promote the National Library for Health (ask me, if this is new to you!). Sir Muir Gray, director of the project, writes this guest editorial in CMAJ, about developments in providing this knowledge to Canadian practitioners. Read the editorial - in English - en francais.

Then, MRSA. The same issue of CMAJ (that for the 18th July) has a practitioner's guide to community acquired MRSA. Presumably some of the information will apply only to Canada (notification, what to prescribe), but hopefully some of it will apply in other countries too.

Lastly, respiratory infections. That same issue has a
commentary looking at personal protective equipment (gloves, gowns, masks). It refers to an article in the same issue which compares two different systems.

Presenting data

An article in BMJ Career Focus, by Grant Hutchison, looks at presenting data using graphs, with discussion of use of colour and labels. Read it at http://careerfocus.bmjjournals.com/cgi/content/full/333/7560/36

Meningitis Learning

This was mentioned in a magazine my son brought home from school. Meningitis Learning is a site made by the Meningitis Trust, and has information about the disease and its signs and symptoms. There are sections for primary and secondary aged children, and also for teachers. Go to http://www.meningitis-learning.org/index.html


Silence on this site due to the blogger being on the Isle of Mull, Scotland, for a fortnight.

Friday, July 14, 2006

Some tuberculosis things I have seen

A "Perspectives" piece in the New England Journal of Medicine issue about health care workers transmitting tuberculosis.

The competitive cost of antibiotic resistance in Mycobacterium tuberculosis, in Science.

An editorial on tuberculosis and social exclusion, in developed countries, in the BMJ.

And lastly, The Big Picture Book of Viruses, a catalog(ue) of images of viruses, arranged by virus name or family, or by genome type, host, or disease. The site is produced by the research lab of Dr. Robert Garry at Tulane University, New Orleans.

Some microbiology things I have seen

Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae, by Marc Prudhomme and colleagues, published in Science for 7th July.

ENTER-NET, an international surveillance project for human gastrointestinal infections, namely Salmonella and E. coli. The website includes quarterly reports back to 1998.

"Perspectives" piece in the New England Journal of Medicine on hand hygiene, arguing that we need a systems approach to hospital acquired infections, which deals with systems failures that lead to contamination, but that individuals also need to accept responsibility for their part in transmission and wash their hands. (This might also have a systems element, as the piece points out).

The recommendations of the Advisory Committee on Immunization Practices on the Prevention and Control of Influenza (a posting on MEDLIB-L alerted me to these).

A review in Trends in Microbiology about marine microbial diversity. Easiest way to get to this is to copy this line:


go to http://dx.doi.org, and paste it in.

Open access update

Leicester Research Archive is now included in OAIster, which indexes the contents of open access repositories. Thanks to them for that.

Nature this week reports moves to encourage researchers to try to keep the rights to their published article, by using documents that can be added to the standard copyright transfer agreement that publishers give them to sign.

And a letter in Science for 7th July looks at the success (or otherwise) of the NIH's policy asking people to place their work in PubMed Central - the uptake has been small, and some things have been archived before the embargo period is over.

Enhancements to MedlinePlus

The excellent MedlinePlus has added clickable body maps to its health topics section. MedlinePlus contains links to consumer health information, and is produced by the National Library of Medicine. The body maps provide another way to get to the information you want: it is the words in black that are the links, or you can point at the appropriate anatomical bit.

Monday, July 10, 2006

Access to BIOSIS

We are losing access to BIOSIS, the biological sciences bibliographical database, through EDINA, but gaining access through Web of Knowledge. Please contact me if you have any questions. Access via EDINA ends at the end of July.

Meadow and Southall cases

There is an article looking at these two cases, in Pediatrics. The article concludes that both doctors gave "responsible" opinions, and that the conduct of the hearings in both cases was unfair. Read the article (June 2006, 117(6), pp. 2247-51).

PLoS Clinical Trials

Another new open access journal from the Public Library of Science. The journal is now accepting submissions, and aiming for a launch in March 2006.

Later note: this is now launched (thanks to the Librarians' Rx for this). The blog entry is at http://www.library.ualberta.ca/mt/blog/librariansrx/archives/004906.html, the journal at http://clinicaltrials.plosjournals.org/

Mercy Ships drug formulary

Mercy Ships is a Christian organisation that runs hospital ships, that visit developing countries (see http://www.mercyships.org.uk/). It has produced a drug formulary, which lists the drugs which it tries to make available to its ships. The list is based on the recommendations of the WHO Model Essential Medicines List.

The formulary is downloadable, as one file, or in sections, from http://www.ms-information.org/medical/programsframe.htm. There are also Powerpoint presentations about the formulary, available from the same site.

Antimicrobial resistance data

This has been on my list of things to blog for some weeks... At last, here it is!

http://www.bsacsurv.org/index.jsp is the home of the British Society for Antimicrobial Chemotherapy survey of antimicrobial resistance. Two surveys are being run, one covering lower respiratory infection and the other bacteraemia. Results are presented here for the use of microbiologists and medical professionals, and you can find data for particular organisms and for particular antimicrobial agents. The methodology of the project is presented in articles in Journal of Antimicrobial Chemotherapy, which are referenced on the site itself (in the disclaimer). The site includes data on the resistance of MRSA to other antimicrobials.

Saturday, July 08, 2006

Salmonella and chocolate

Today's Guardian reports (in the third of three stories of interest that I saw at lunchtime!) that the "scare" over salmonella montevideo in chocolate is spreading, because the "crumb" that contained the bacteria has been used by other manufacturers. Here are some things to read about the story, or about the bug:

Today's Guardian
CDR Weekly (for 22 June 2006) (there are also links from the HPA home page, for S. montevideo, but they seem to me to lead to material about S. ajioba, which Saturday's Guardian is reporting about also: more details later!)
The Food Standards Agency website (this includes a list of products recalled by Cadbury's)

Friday, July 07, 2006


Science reports that the recent cases of avian influenza in Indonesia were due to human-to-human transmission, but that there is no sign that the virus is becoming more dangerous. They also report the death in 2003 of a man in China which was put down to SARS but which has been found to be die to avian influenza. I mentioned this a few days ago in another posting.

Science and Nazism

I read the work of Dietrich Bonhoeffer (or some of it), the theologian, some years ago, and discovered that his father was a psychiatrist. Working in a prominent medical library at the time, I was able to get some material about his father, Karl Bonhoeffer, who had worked in Berlin. He was an interesting man (I was going to write an article about him, but haven't done it yet). He seems to have argued in favour of sterilising mentally ill people - as did many people, and not just in Nazi Germany. But he seems not to have been a sympathiser of Hitler, and was apparently indirectly involved in a plot to kill him, when a bomb designed to do that was driven to the train station in his car.

So, my eye was caught by a piece in Science about the Dutch born chemist Peter Debye. A recently published book in Dutch took a harsh view of Debye, documenting behaviour that might indicate Nazi sympathies. The University of Utrecht has removed his name from one of its institutes. But there have also been pro-Debye books (the publication of one of which has just been halted), and others have argued that signing letters "Heil Hitler" (as he apparently did) might just have been something people did without necessarily believing in Hitler's doctrines.

Read the piece in Science.

There is also material in Wikipedia (in
English, and in Dutch - the Dutch link is not working at the moment), and I found this article in De Volkskrant written at the time of the decisions of Utrecht and Maastricht universities to stop using his name.

New NLH Specialist Library for theatre staff

The National Library for Health now has a Surgery, Theatres and Anaesthesia Specialist Library, with links to resources for any member of the theatre team. Perioperative management, surgery, infection control, safety, theatre management and equipment are among the topics covered. You can browse the Library, or search it. There is a related blog, at http://theatreslibrary.blogspot.com/.

The Library itself is at http://www.library.nhs.uk/theatres/

Contaminated surgical instruments

The Guardian today reports a NICE study which finds that hospitals don't always keep sets of instruments together. This is designed to make it easy to trace instruments if one particular instrument is found to be contaminated.

This finding was discovered by a team drafting guidance on preventing transmission of CJD. This would appear to be the 2nd draft of the 2nd consultation on Patient safety and reduction of risk of transmission of Creutzfeldt-Jakob disease (CJD) via interventional procedures, available via http://www.nice.org.uk/page.aspx?o=cjdconsultation2

On a related matter, a paper in the most recent Annals of the Royal College of Surgeons of England looks at the quality of new surgical instruments - do they work properly, do they break, and so on. Fifteen percent of the instruments examined (at hospitals in London) had a problem. Local quality control, the paper concludes, is vital. (This link is to Ingenta: you will need a subscription - which Leicester has - to read the full paper).

Whooping cough

The Guardian also reports this BMJ paper, which finds a high incidence of whooping cough among children taken to their GP with a persistent cough. Although vaccination against it is common, vaccinated children can still get a milder form of the disease. The BMJ paper, by Anthony Harnden and colleagues from Oxford (and elsewhere) is in fact a BMJ Online First paper.

Read the Guardian
>> Read the BMJ paper

Tuesday, July 04, 2006

Cochrane Library enhancements

Cochrane Library has made some enhancements, which you can read about here. There is also a useful summary of these changes, in the Royal Children's Hospital (Melbourne) Update at http://www.rch.org.au/library/update.htm (thanks to my colleague Sarah Sutton for this).

On a related topic, we have access till the end of the year to the Wiley journal Evidence Based Child Health, which presents new and updated reviews from the Cochrane Library. If you are University of Leicester and find this journal useful, I would be interested to know. The journal is within Wiley Interscience, or you can go straight to
http://www3.interscience.wiley.com/cgi-bin/jtoc/112100413/. I am here.

Human TB gene

Researchers have identified a gene that could determine West Africans' susceptibility to TB, according to a report on SciDev.Net. The research is published in PNAS, and investigated whether the SP110 gene was associated with TB symptoms.

>> Read SciDev.Net
>> Read the PNAS paper

Space Shuttle launch

The Space Shuttle Discovery is scheduled to launch this evening (British Summer Time). This is the first launch since the one that we were lucky enough to see on our holiday last year, so I am following it with some interest.

There is full information at http://www.nasa.gov/mission_pages/shuttle/main/index.html

Monday, July 03, 2006

Who should you cheer for?

Can't decide who to support? (I know, it is getting a bit late...) . This World Development Movement website presents significant data about each country in the World Cup finals, to help you decide who to support. Data includes life expectancy, national income per person, military expenditure, debt, and (here is my excuse for mentioning it here!) health expenditure.

Go to http://www.wdm.org.uk/whoshouldicheerfor/ before it really is too late!

Athens problem?

Are you University of Leicester, using Athens to gain access to resources off campus? If you are, and you are having problems, please get in touch. I am particularly interested in problems accessing Taylor and Francis, as I am trying to resolve that for someone at this time. But problems with other things would be of interest as well. Thank you.

Some papers that caught my eye

Here are some recent papers that caught my attention:

CRB-65 predicts death from community acquired pneumonia, by T. Bauer and others, in Journal of Internal Medicine 2006; 260: 93-101. CURB is a score comprising confusion, blood-urea nitrogen, respiratory rate and blood pressure.

Censorship of medical journals, by S. Hickey, a letter in BMJ 2006; 333: 45. This argues that because Medline has no explicit guidelines to help it decide what journals to index, it tends to ignore journals that don't "conform to the conventional paradigm". A rapid response points out that it doesn't index papers from certain statistical journals, and so will miss papers of obvious medical importance. As the writer of the rapid response points out, these papers are picked up in Web of Science. The immediate message from this present librarian is: sometimes you need to search in more than one database to ensure that nothing is missed.

The BMJ reports a NEJM letter in which Chinese scientists report that a man who died of suspected SARS in November 2003 in fact died of H5N1 avian influenza. The BMJ letter is here, and the NEJM letter is available free here.

Nature presents a composite picture of the scientific research that was going on during the longest day, 21 June.

Future immunological meetings

There are websites devoted to forthcoming meetings, but the journal Immunology has a column. Go to http://www.blackwell-synergy.com/doi/full/10.1111/j.1365-2567.2006.02422.x for the latest list of future meetings. There are links to websites for the meetings concerned.

The same journal also has a "Forthcoming papers" column -
http://www.blackwell-synergy.com/doi/full/10.1111/j.1365-2567.2006.02423.x for this issue's column.

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
http://invention.swmed.edu/argh/, 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 http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html. Genbank is at http://www.ncbi.nlm.nih.gov/Genbank/index.html. 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 http://nnlm.gov/training/resources/pmtri.pdf (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 http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNewsm, 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 http://www.nap.edu/catalog/11561.html

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
http://www.jrsm.org/cgi/content/full/99/5/213. 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
http://www.guardian.co.uk/birdflu/story/0,,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 http://www.eurekalert.org/pub_releases/2006-06/bpl-wet060106.php

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 http://www.journals.uchicago.edu/CID/journal/contents/v42n12.html

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 http://www.malariajournal.com/content/pdf/1475-2875-5-48.pdf (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.

Read more at http://www.nlm.nih.gov/pubs/techbull/mj06/mj06_technote.html#8

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 http://www.nationaltbcenter.edu/international/

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 http://www.nature.com/nature/peerreview/index.html. 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 http://www.nature.com/nature/peerreview/index.html.

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 http://virologybytes.blogspot.com/ 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: http://jama.ama-assn.org/cgi/content/abstract/295/21/2503 and the trial is registed in clinicaltrials.gov - go to http://www.clinicaltrials.gov/ct/show/NCT00157612?order=1 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 http://www2a.cdc.gov/niosh-nil/

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 https://lra.le.ac.uk
To find out more about the project, go to http://www.le.ac.uk/li/lra

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 http://wok.mimas.ac.uk. 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 http://www.nature.com/news/specials/worldcup/index.html

The Chartered Society of Physiotherapy have produced a "2006 World Cup survival guide", on footballing injuries, available in various forms at http://www.csp.org.uk/director/physiotherapyexplained/features/worldcup.cfm. 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 http://www.annefrank.org.uk/Anne_Frank_Day_poster.pdf . The day is a project of the Anne Frank Trust, whose website is at http://www.annefrank.org.uk/. The Trust is involved in work to combat racism and promote diversity.

The Anne Frank Huis in Amsterdam has a website at http://www.annefrank.org - 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

Thursday, May 25, 2006

The Aberdeen typhoid outbreak of 1964

I worked in Aberdeen before moving to Leicester, and knew about this, so my eye was caught by a piece in Lancet Infectious Diseases about E.S. Anderson, who worked at Colindale and was involved in investigating this typhoid outbreak. His work investigated the strain of Salmonella typhi that was responsible for the outbreak, in which over 500 people were affected and in which a can of corned beef (a large one) was implicated.

PubMed search on the subject pulls up some interesting looking further reading. There is also a research project at Aberdeen investigating the event.

Hurricane Katrina

I made a couple of entries late last year about this, listing things about it. Pediatrics has just produced a supplement called "Hurricane Katrina, Children, and Pediatric Heroes: Hands-on Stories by and of Our Colleagues Helping Families During the Most Costly Natural Disaster in US History". Go to http://pediatrics.aappublications.org/content/vol117/issue5/#SUPPLS2 to read more.

Early introduction of solid food and development of allergic disease

This is the subject of a systematic review in Archives of Pediatric and Adolescent Medicine. It concludes that early solid feeding may increase the risk of eczema, but that there is little data to support a link with other allergic conditions.

Read the paper (password may be need to read full text: University members can contact me)

Epidemiology of group A Streptococcus in Ethiopia

Clinical Infectious Diseases has published a major article on this subject, looking at the GAS isolates taken from schoolchildren in Addis Ababa, Gondar and Dire Dawa. The authors are from Addis Ababa, Gondar, Harar and the Karolinska Institut in Stockholm.

>> Read the paper (full text available on campus only)
>> Read about the Leicester Gondar Link


Ganfyd is a collaborative medical textbook, a wiki, to which anyone can contribute. It is for medical professionals. Ganfyd is at http://ganfyd.org/

Tuesday, May 23, 2006

Malaria and climate

Researchers working as part of the AMMA (African Monsoon Multidisciplinary Analysis) project have built a thatched hut in Niger, West Africa, to monitor climate, soil conditions and other factors that have an influence on mosquito behaviour. The project hopes to examine the effect of these factors on malaria epidemics.

One of the researchers is Dr. Paul Monks of the Department of Chemistry here, and there is more information in the University eBulletin.