Pneumococcal vaccination and risk of myocardial infarction

Lots in this most recent issue of CMAJ! This, a study that hypothesises that pneumococcal vaccine would protect people from myocardial infarction. It seems that it might, but you can't take my word for it. Since CMAJ is an open access journal, you can read the study for yourself.

Clostridium difficile

Two items about this , in the most recent CMAJ:

One, on patterns of antibiotic use and C. diff - which finds community acquired C. diff infection in a significant number of people who had not used antibiotics.

The other, a commentary on community acquired C. diff, written by authors from Leiden.

Listeriosis

In August this year, Canada apparently experienced the worst epidemic of listeriosis in the world, with 43 cases, and 16 deaths, caused by cold cuts of meat from a particular factory. There is an editorial about this in the most recent CMAJ, with a public health oriented primer. The editorial discusses some of the public health changes that might have aided the epidemic. Being the CMAJ, of course, the editorial is also in French.

Genome of Penicillium chrysogenum

The genome of the fungus that produces penicillin has been sequenced, according to a report on the BBC (discovered via the BBC Health feed that I get in Twitter). The genome has been published as an advance online publication in Nature Biotechnology and may lead to the discovery of new antibiotics, according to the BBC report.

If you are University of Leicester but off campus, try this link instead -login with CFS username and password when prompted. If any problems, of course, contact me.

New features in My NCBI - My Bibliography - updated

The My NCBI feature of PubMed has had some enhancements. There is an announcement about this, and yesterday afternoon (UK time) there was an announcement on PubMed that My NCBI would be missing for some hours while the changes were made.

The changes are there this morning (UK time!). My NCBI has a new look (and a new feel, doubtless). There is a "I forgot my password" feature, and you can elect to have your password remembered or to remain signed in at all times. The features that were there before are still there - saved searches, collections, filters - but there is now a "My Bibliography" feature, which appears with the collections and saved searches under "My Saved Data".

My Bibliography enables you to gather PubMed citations to your own publications. I tried this, for my own publications (all 2 of them!). You can choose more than one name, if you appear in more than one form, and the search box fills itself in, in the same way that the index boxes do, in PubMed itself, so you can see what forms of name exist within PubMed. You can apply filters - year of publication, grant number, and so on - and you could search by PMID. Once you have put your citations into My Bibliography, you can sort that list by title, first author and date, and you can remove citations.

You can add Other Citations to My Bibliography, this only searches PubMed and is designed to give you a place to collect other citations, not your own. This seems to suggest that there is no way to add citations that are not included in PubMed. There also seems to be no way to output the citations in My Bibliography into lists. There also seems to be no way to export from My Bibliography into things like EndNote, but since you can export from PubMed into EndNote, that seems not to matter a lot.

New bit - Laika Spoetnik has a posting about what happens if you try to save a search in My NCBI and that search has a line like #1 AND #2 in it. Read the posting if you have problems - and Laika suggests contacting the PubMed helpdesk as well, in case this is a bug.

EndNote X1 tips

This posting is to augment the information at http://www.le.ac.uk/li/research/bibliographic.html and I shall add to it as I realise things. What is on this page applies only to University of Leicester members.

Updated - 1. EndNote 9 has now gone from CFS. You must download EndNote X1. Instructions for doing this are on the link above. Exporting from Web of Science into EndNote (using the "Save to EndNote..." button) appears to fail if you have not installed EndNote X1.

2. You then need to install the EndNote X1 toolbar - go to Start - All Programs - CFS Software 2 - EndNote X1 - Install Word toolbar. Note that Word 2007 has its own referencing facilities (on the References tab) - I personally think this will be too limited for the sort of use we want to make. This References tab is nothing to do with EndNote. If you had EndNote 9 and Word 2007, EndNote appeared on the Add-Ins tab. Once you have installed the EndNote X1 toolbar, it will appear on its very own tab.

3. You can delete the old EndNote 9 toolbar and custom menu, by right clicking them. I can't see a way to uninstall EndNote as such. I have seen the installation of the EndNote X1 toolbar bring up a dialog box asking if you want to uninstall the EndNote 9 toolbar. I don't think this happened to me when I installed X1.

4. You might also have spotted that Word 2007 has a "references" tab. This is Word's own citation tool, which looks to work quite well, but is very basic, only having a very small number of unalterable styles, and it seems that you have to add all your references manually. I'm teaching the Word referencing tool soon so will have more structured thoughts soon.

Accessing full text journals via PubMed

This may be of interest to University of Leicester members. If you are at a different institution, then your access to resources may be different and you need to talk to your library.

Leicester now has a proxy server, which makes off campus access to databases and journals easier. PubMed, however, is not behind the proxy server.

What this means is:

- if you are on campus, and follow a link from PubMed to full text, that link will work if we have on campus access to the journal in question.

but

- if you are off campus, there is no way that the journal will be able to identify you as University of Leicester, and so very probably the link will not work...

...unless you do this...

- go to the Leicester Digital Library at http://www.le.ac.uk/library/digital/index.html and click the Login to electronic resources link.
- login with your CFS username and password
- you will then be taken to the A-Z list of databases
- go to P and choose PubMed
- follow the links as you would normally do. Now you are identifiable as University of Leicester, and so full text ought to work.

If you have any problems, tell me! Leave a comment on the blog or email me.

Link between antibiotics in pregnancy and cerebral palsy

This Lancet study was picked up by the press last Thursday - it looks at the development of children born to mothers who were administered antibiotics in premature labour. The antibiotics were being given to delay premature birth, and the Department of Health is advising that they only be given in the event of infection.

The Society for General Microbiology news page has a summary and links to the story in four national newspapers. The Lancet article is here, with links to several related things.

(Note: the SGM news page link may cease to work when there is later news - you need to navigate to the news for the 18 September. The Lancet link uses the DOI and whether it will work for University users off campus I am not exactly sure. If you find out, please let me know by leaving a comment).

Asthma in the Lancet

The Lancet for 20-26 September, 372(9643) is full of articles about asthma. This includes original research and commentaries of one sort or another. The research includes a paper on paracetamol and asthma, which I think was picked up in the press (I heard it mentioned by someone at a party at the weekend - they could of course be avid Lancet readers).

University of Leicester members can access the Lancet via ScienceDirect.

MetaBase: database of biological databases

I read somewhere of Ecoliwiki, a wiki about E. coli (not a surprise), and this led me to MetaBase, a user contributed list of biological databases. The initial data comes from the database issue of Nucleic Acids Research, and there are conditions of use (see http://biodatabase.org/index.php/Help:About#Database_Description)

You can search it, or browse it by category. I searched for "human genome", and found no page matches, but got links through to title matches. Some of the links to those titles appear to be faulty, and need another click to get to the correct resource. Once you have the details of a resource, though, you get a database description, a link to the database itself, and contact details if they are known.

Ecoliwiki's details are here. There is also a guide to using MetaBase.

Protocol for handling research misconduct

The BMJ also carries a news item on this - a draft protocol from the UK Research Integrity Office - UKRIO offers advice to universities and research organisations on research conduct. The document (downloadable from the link above) contains the P-word (plagiarism, not peanuts!), without going into detail about what it is, just including it as one of the examples of misconduct.

BMJ news item here.

Coffee creamer used as infant food

Obviously, anything to do with infant feeding is close to my heart at the moment, although I am very much a minor player. So, my eye was caught by a study in the BMJ, looking at a popular brand of coffee creamer available in Laos, and whether it is used as an infant food or not. The creamer logo portrays a baby bear in an apparently breastfeeding position.

Most of the paediatricians surveyed said that they were aware of parents who had used the creamer as infant milk, and most of the adults surveyed said they thought it contained milk (which I assume it does not, although I could be wrong). The creamer does have a warning on the can about not using it to feed babies , which 80% of people surveyed had not read.

Read the article here.

Which prompts me to check - is there still a boycott of a well known food manufacturer because of its policies on promoting (real) baby milk? Yes, there is.

NIH takes down two open access genetic databases

My eye was caught by a report in Biotechniques news that the NIH had removed access to two genetic databases following research that indicated that you could extract an individual's data from a set of pooled data.

I had not been able to work out exactly which databases - see below for something I have just read that might shed light.

**Later note** - this story is discussed in Science, whose report suggests that it is not whole databases that have been pulled, but some data from within particular databases. Some data has been pulled by the NIH from dbGAP, and from a cancer genetics database called CGEMS (http://cgems.cancer.gov/, which is currently displaying a news item saying that some data is temporarily unavailable for public posting). The Wellcome Trust has pulled data too - the Science report does not give details.

The story is also reported in the LA Times, Peter Suber's Open Access News, and (mentioned by Suber) Nature News. The research itself is in PLoS Genetics.

AIDS Ephemera

I was working at Charing Cross and Westminster Medical School (as it then was), in London, in 1986-1987, relatively soon after HIV (also, as I recall, called at the time HTLV-3) was identified as the cause of AIDS. And so my eye was caught by this online exhibit from the NLM, of (American, I think?) posters, badges, booklets and the like. The material was exhibited at the NLM in 2002. The virtual exhibit is here.

More about changes to Ovid

I have since found a posting on Laikas MedLibLog about this, and Laika has obviously looked at this properly! So, I can now report that you can move the search history box so it is under the search box - drag it using the grey rectangle in the top right hand corner of the search history. You can also close either or both results managers - although they will both be open in any new Ovid session.

Laikas posting is here (in English and ook in Nederlands) and is gratefully acknowledged. She talks about other things besides, so please read her posting for more!

I also discover that you can customise the limit tick boxes that appear on the main search screen. But those choices seem to disappear in any new session. I have not investigated whether it remembers the choices if you are logged into your personal account.

PubMed's Drug Sensor

This was implemented in PubMed in mid August. Search for a drug that is included on a list of 200 or so, and on the Summary Results screen (the list of references), you will see links to other resources about the drug. Currently the link is to PubMed Clinical Q and A, which is one of the items on the NCBI Bookshelf.

This is a separate thing from what you see when looking at an individual item from a list of results, when there may be a link to more information about the drug in MedlinePlus, which will appear under a heading "Patient Drug Information".

More about Drug Sensor

Citation mapping in Web of Science

I had meant to blog about this before going off, and had made some notes. But meanwhile, a review has appeared in Issues in Science and Technology Librarianship, so I think I will refer to that and move on:

Simboli BD. Web of Science's "Citation Mapping" Tool. Issues in Science and Technology Librarianship 2008; 54. http://www.istl.org/08-summer/electronic-1.html [Accessed 26 August 2008]

Changes to Ovid

Back after paternity leave. Ovid has made some minor changes to its interface. At a quick look these seem to be:

The results manager is now above and below the search history and search box - overkill, perhaps? I have to say I quite liked it where it was, at the side, but I am sure I will get used to this new position.

There is a multifield search - allowing you to combine author and title, or journal and date, for example. I can't remember if the "search fields" option was there before. Our Ovid still defaults (at our request) to Advanced Ovid Search

The search box has moved so it is under the search history.

Currently there seem to be problems with logging into personal accounts. My existing password was declared invalid when I tried to use it. On advice of colleagues, who have been through all this already, I requested a new password. I logged in with it, and tried to change it. There are no rules given, but when I tried to change it back to the old password I discovered that a password needs to be between 6 and 8 characters. (My old one was 10). I chose a new one, and that was declared invalid, as was the next one. Again, on advice of colleagues, I tried logging in with the first of those new ones, and it worked. We are following this up with Ovid, but meanwhile, the advice needs to be: request a new password, login with it, change it to another one but ignore the warning that the new one is invalid. Try it out before deciding it is.

(Note: you only need a personal account to save searches or search alerts, not to use Ovid).

Pests in hospitals, and the reporting of medical science

I was interested to hear (and see) the BBC Breakfast News coverage of the figures obtained by the Conservative Party about the number of instances of pests in hospitals. I found myself wondering: did the figures count calls to the pest controllers, or actual pests found? There were 20000 incidents of "pest infestation" (according to the Guardian's report) in the period starting January 2006. I wonder how many hospitals there are in England (or wherever the figures apply to) - if there are 1000 hospitals, and the figures cover 2 years, then this is 10 instances of pests (or calls to the pest squad) per year per hospital. 20000 sounds shocking - 10 per hospital sounds different. The Guardian does point out that there were hospitals that called pest controllers 50 times in the period.

Of course, rats in the maternity ward is no joke, but the way things like this are portrayed is very interesting.

Channel 4 has an interesting deconstruction of this issue, which raises some other interesting things about the figures - the fact that hospital's estates includes outdoors as well as buildings, and therefore that foxes, dead pigeons, and so on will occur and need to be dealt with, and the mismatch between these figures and the ratings of the Healthcare Commission, for two.

Microbes on Mars

Just before going off on paternity leave (see previous post) my eye was caught by a "Cross-talk" column in the Lancet Infectious Diseases, in which Bernard Dixon talks around this. He refers to work that was done looking for microbes in the clean rooms at the Jet Propulsion Laboratory in California and at the Johnson Space Center in Houston. Samples were examined for evidence of Archaea, and evidence was found.

Dixon suggests that the question had been raised before of whether microbes from Earth could hitch a lift into space, and that there are protocols to try and prevent them doing so. But if Archaea can survive in clean rooms, should instruments and so on on spacecraft bound for Mars be screened for them? If microbes are found on Mars, how will we know that they didn't come originally from Earth?

The Lancet Infectious Diseases article is:

Dixon B. Spacebugs. Lancet Infectious Diseases. 2008; 8(8): 466. DOI: 10.1016/S1473-3099(08)70165-8

I've been following the Mars Phoenix Lander via Twitter - http://twitter.com/MarsPhoenix