Browsing

Checklists for surgical safety

2010-02-18T12:41:00.004Z

Just caught a piece on Radio 4's You and Yours consumer programme about using checklists in the NHS, with a speaker from Patient Safety First, which turns out to be an NHS body. The list is undertaken before surgery, by the team doing that surgery. I am not clear why the piece made it onto the radio today rather than any other day - maybe there was a space today, rather than anything being launched today. The Patient Safety First site links to a case study of checklists being used at Barts and the London, and a web search turns up an adaptation for the NHS in England and Wales of the WHO checklist, which has been around for a little while. Atul Gawande has also just written a book about using such lists in the USA, which I am waiting to see.

Anyway, today is as good a day as any to mention it - it is an important topic of interest to all those who work in operating theatres. The list being described on the radio asks all the perioperative staff to introduce themselves to each other, as well as asking people to check that they have all necessary X rays and so on, and checking that everyone knows the site of the surgery. The WHO list does these things.

Here are some links:

Case report on Patient Safety First site;
WHO checklist adapted for the NHS in England and Wales;
WHO site including English language checklist and manual;
Atul Gawande's book at University of Leicester Library

Changes to PubMed

2010-02-05T20:07:00.004Z

These changes, announced in a recent NLM Technical Bulletin, are now live:

"Limits" now appears as an option on the one line search screen - it did appear only on the Advanced Search screen for a while.

If you switch from one line to Advanced search, the one line search that you have been doing is now cleared - it used to stay there.

The Advanced Search screen will change - instead of the present three lines, with option to add more, there is a "search builder" - I had thought that this would enable you to add as many lines as you like, with the appropriate Boolean operators in between but in fact it seems to add your search terms to the basic search box, with the Boolean operators you choose. This seems a little like the "send to search box with..." that appears in the MeSH browser.

This post replaces the original, which had an inappropriate comment added that I could not work out how to remove.

Citizen science

2010-02-01T12:43:00.004Z

Added to in March 2010.

Well, it was the same story yesterday as it is every year. I decide not to do my bit for the RSPB Big Garden Birdwatch in the morning, but later in the day. Later in the day, of course, all the birds have vanished. Yesterday, just one blackbird, one wren and two sparrows were present, even though earlier there had been more sparrows, and, of course, outside the front of the house, where I was not counting, there were more too.

I am sure there are good explanations for this, although there is not really a good explanation for my continued refusal to do the survey in the morning!

This birdwatch is an example of "citizen science", science data gathering using as many people in the general population as want to. This enables interested people to participate in scientific research, and might, I guess, also increase those people's knowledge.

The RSPB are interested in seeing how many of particular birds appear in your garden (or park) at one time. You can only count your garden, and you can't count things that just fly over. When you report the results, you can give information about your garden - size, distance from fields, types of trees, that sort of thing. Because you can't count other people's gardens, we have to ignore the trees that we can see from our house, and this means ignoring the crows that are nesting nearby, but the hope is that the owner of those trees is also counting.

Some time ago BBC Radio 4 ran a series on Citizen Science, and the programmes are still there to be listened to. The series covers other initiatives - SETI@Home uses home computers to analyse radio frequency data from space for patterns, and other initiatives do similar things to molecular structures looking for ones that might make good medicines. These use computers' "idle time".

Wikipedia also has an entry (that needs work) that lists some initiatives, primarily American ones.

Addition: Have just (29 March) come across this, in Research Information. It discusses a JISC project, as well as giving more examples of citizen science.

Haiti: health information

2010-01-18T22:28:00.015Z

Revised 23 February 2010.

In the hope that the information might be found by someone who can use it, here are some links to health information in Haitian Creole, and some related things that might be useful.

Information posted to the MEDLIB-L and HIFA2015 discussion lists has been useful here.

The NLM have a webpage specifically for this emergency, containing numerous links to health information in Creole and French, and information on relevant topics.

National Resource Center on Advancing Emergency Preparedness for Culturally Diverse Communities - currently has links on its homepage to translated material (including Medlineplus in Creole, and in French), the CIA Factbook and organisations that are helping. They also have a separate page of resources in Haitian Creole.

Hesperian Foundation have produced Haitian Creole editions of: Where There is No Doctor ; Where Women Have No Doctor ; Sanitation and Cleanliness booklet . These are all PDFs - Where there is no doctor is particularly large.

The Stanford Health Library's Multilingual Health Information site has further Creole things. The CDC site has natural disaster information in Haitian Creole, and links to mass casualty information in English here. And information in French here.

More things added 19th January 2010:

Websites in response to crisis in Haiti, from NNLM MidContinental Region

Posting to Afro-Nets about Hesperian publications (may include things not listed above)

Refugee Health Information Network, items in Creole.

Two pages from CDC, in English, but potentially useful: earthquakes, and handling human remains.

There is a disaster health information discussion list maintained at the NLM.

And another thing added 23 February 2010:

MedlinePlus have a page of resources in Haitian Creole (Kreyol).

EndNote and 2010

2010-01-08T12:12:00.002Z

Just noticed EndNote not importing publication years properly in a batch of Web of Science records I was working with. The date was not being imported at all.

This turns out to be this known issue with EndNote - http://www.endnote.com/support/Faqs/Import/faq20.asp

We have EndNote X1. I have just checked the batch of records in question and discover that for 2009, the publication year is indeed present.

The EndNote FAQs give details of how to globally change a batch of records. You could, of course, also edit individual ones.

Another use for E. coli

2009-12-17T21:22:00.006Z

Interesting item in SciDev.Net about using genetically modified E. coli to detect landmines.

The bacteria have the gene for an enzyme called luciferase (this is present in fireflies, for one), which naturally produces light in some bacteria and fireflies. When TNT is present, this gene is switched on, and the bacteria glow. This can happen within hours of the bacteria being introduced to the region under investigation. Plants can be modified in the same way, but take weeks or months to produce results.

The work is not yet commercially available - European Union regulations on genetically modified bacteria need to be observed.

There is a protein in the cell membrane that senses TNT, according to the item. The work was done at the University of Edinburgh, by Alistair Elfick at the Centre for Biomedical Engineering.

Luciferase has also been used in bioluminiscent imaging, to detect tumour cells, although I can't immediately find anything published about its application to landmines.

Trailblazing

2009-12-03T20:29:00.002Z

Is the name of a new site from the Royal Society. Being a twice former resident of Scotland, which also has a Royal Society, I can never resist adding "of London" to the name, so I will do so now - a new site from the Royal Society of London.

That Royal Society is 350 next year. The first library job I had after qualifying was at another Royal Society, the Royal Society of Medicine, in London. Its library had volumes of the Philosophical Transactions of the Royal Society, one of the first scientific journals, back to 1665, the first year of its publication. It was fascinating - Leeuwenhoek, Newton, Hooke, Herschel, as they wrote.

Well, this site gives you facsimile copies of landmark papers from the last 350 years, with commentaries, all on a nice timeline which also gives you some of the events in the wider world. So, Leeuwenhoek is there, along with the Boyle's account of the first blood transfusion (from one dog to another - I imagine the dogs' thoughts are not recorded!), and a paper by Watson and Crick which I didn't know about - more detail than the famous one in Nature. The most recent is one from 2008 by James Lovelock, "A geophysiologist's thoughts on geoengineering".

Trailblazing is at http://trailblazing.royalsociety.org/ target="_blank".

Google in consumer news

2009-11-26T12:17:00.002Z

On my days not at work I quite often listen to You and Yours (Radio 4). Today they were talking about Google. Today they also mentioned another story that they had covered.

Today it was this: if you search for the name of a well known florist that can deliver to your chosen recipient, among the sponsored links is the name of another one. The first is suing the second. I tried this with the example given (this blog only advertises when I want it to!), and it is indeed so. I have just tried searching for my usual daily newspaper, and it is the only sponsored link that appears. The same happens if I search for the maker of our car.

The other story (which I did not hear and which I can't find quickly on the You and Yours site or in the last couple of programmes on Listen Again) concerned an offensive image of Michelle Obama, which appeared at the top of the list of results. This is reported elsewhere on the BBC, and the report goes into the way that Google ranks results, which of course is all to do with popularity.

Nasal spray and Burkholderia cepacia

2009-11-20T21:44:00.002Z

Vicks has recalled some of its nasal sprays because of possible contamination with a soil bacterium, Burkholderia cepacia, which can cause problems to people with impaired immune systems or cystic fibrosis, and has caused hospital acquired infections.

There is news and details of the recalled products, including lot numbers, on WebMD - this includes details of the recalled products in the US, Germany and the UK. The story is also covered on PJ Online, and the MHRA alert is here.

For more on B. cepacia, try these:

Cystic Fibrosis Foundation (USA)
Burkholderia cepacia complex MLST databases (multilocus sequence databases - allelic and isolate information)
Health Protection Agency
CDC

Worms in space

2009-11-18T21:27:00.003Z

My eye was caught yesterday by this article in the Guardian, describing the voyage into space (on the shuttle Atlantis) of some nematode worms from Bristol. Apparently some worms that were on board Columbia, when it broke up on re-entry in 2003 - the container which held them was discovered several weeks later.

According to the press pack for the mission (STS-129, which is also taking parts for the International Space Station), there are two experiments (known as CERISE). One will investigate the effect of microgravity on RNA interference, and the other (the one described in the Guardian) the effect of the space environment on protein phosphorylation and signal transduction in muscle fibres. A search of the NASA site (www.nasa.gov) for the word "nematode" will find some other experiments that have been carried out on C. elegans in space.

This mission is STS-129 and there is a launch blog here. There is lots more about C. elegans on the Caenorhabditis elegans WWW server maintained at the University of Texas Southwestern Medical Center in Dallas.

Later note : just discovered this NASA resource, "Ask a C. elegans expert", part of their Web of Life site.

Developing countries and the media

2009-11-17T20:22:00.003Z

I shall allow myself the liberty of going slightly off the usual subjects. I was reading the very interesting Developments magazine, produced for DFID, on the train the other morning. One article which caught my eye described training film makers in Kenya to make films on environmental issues in a way that would catch the attention of Kenyan villagers or school children. These are short films, involving and made by local people, different from documentaries or conservation films made by people visiting the country. The project, funded by the Darwin Initiative, involves Dr David Harper of Leicester's Department of Biology.

The other thing on a related topic concerns TV coverage of developing countries, a report commissioned by the CBA-DFID Broadcast Media Scheme and the International Broadcasting Trust. It found: news coverage of developing countries is limited and may often involve voices from outside, not inside the country. People may not watch documentaries, but they may read novels that change their perception. TV dramas (The No. 1 Ladies Detective Agency is mentioned) may be presented as rather "soft" and "Sunday night", but programmes like Long Way Down and Top Gear may present a rather more realistic and full portrayal of developing countries - I do remember being very taken with the Long Way Down programme that took Ewan Macgregor and Charlie Boorman through Ethiopia. There is more about the report here.

Animals containing human material

2009-11-10T09:42:00.004Z

The Academy of Medical Sciences has launched a new study of this, reported on the BBC Radio 4 Today programme this morning. This caught my ear, as it includes consideration of animals that contain a gene sequence of human origin.

There is material about this study on the AMS website - a press release, some responses from partner organisations, and a fact sheet. The press release includes the scope of the study: "... to: examine the scientific, social, ethical, safety and regulatory aspects of research involving non-human embryos and animals containing human material".

Still here

2009-11-10T09:41:00.001Z

Just have not been blogging. Until today. Will attempt to make this the first of many posts, not just a single posted excuse.

World TB Day

2009-03-23T15:02:00.003Z

World TB Day is tomorrow, 24 March. More here, and there is also a blog. The theme carries on from last year and is "I am stopping TB".

Malaria resources

2009-03-17T09:14:00.001Z

Prompted by the coverage of malaria during the recent Comic Relief programmes, here are some useful looking resources largely found through Intute:

Malaria Foundation International – mission "to facilitate the development and implementation of solutions to the health, economic and social problems caused by malaria". Site includes links to the 2008 World Malaria Report and the WHO Global Malaria Action Plan, as well as foundation projects.

Malariasite – comprehensive site.

Malaria – Wellcome Foundation site, includes very short guides to the parasite, mosquitoes and the extent of the problem, and interactive life cycle of the malaria parasite.

Malaria Past and Present - Nobel Prize organisation site. Details of historical figures in the field (Alphonse Laveran, Ronald Ross, Paul Muller), and interactive mosquito game and parasite game.

Medicines for Malaria Venture –partnership between the public sector and the pharmaceutical industry, which aims to discover new effective and affordable drugs.

POSTNote – Tackling malaria in developing countries – UK Parliamentary Office of Science and Technology document examining progress towards the Millennium Goal of halting the spread of malaria by 2015.

European Malaria Vaccine Initiative – EU/European Commission body which contributes financially and technically to vaccine development.

SciDevNet – SciDev.Net provides news and information about science and the developing world.

Malaria: an online resource - from the Royal Perth Hospital, Australia. Diagnosis, treatment, prophylaxis, and photomicrographs of blood films ("teach and test").

Malaria – MedlinePlus interactive tutorial with PDF summary.

Roll Back Malaria Partnership – partnership between WHO, UNICEF, World Bank and UN Development Programme.

Insecticide treated malaria nets: a WHO position statement]

Malaria Consortium – organisation aiming to improve treatment and prevention of malaria. Provided support to Comic Relief 2009.

Incidence and statistics

Malaria Atlas Project – the project aims to map the extent of P. falciparum and P. vivax malaria.

World Malaria Report 2008 – WHO report detailing cases of malaria and deaths from the disease, and implementation of WHO measures against malaria. Site also includes profiles of endemic countries and a link to the WHO Global Health Atlas of infectious disease. The WHO also has a general malaria site.

UNICEF – statistics on prevention, treatment and incidence.

Genomic information

Plasmodium falciparum genome projects - Wellcome Trust Sanger Institute. Site includes links to genomic information on other Plasmodium parasites.

Anobase – the Anopheles database. Genomic and biological information particularly about Anopheles gambiae.

PlasmoDB – genomic and proteomic data about the various species of Plasmodium.

TIGR – Institute for Genomic Research – TIGR's parasites database includes sequencing information for P. vivax, P. falciparum and P. yoelii. Sequencing is ongoing.

Molecular Movies

2008-12-23T09:41:00.002Z

Molecular Movies is a directory of animations of processes at the cellular level, including, for example, immunity relevant to Crohns Disease, the lifecycle of malaria, transcription, the structure of DNA. The "about" link seems to be broken, so it isn't clear whose site this is, although the email address for enquiries is at a company called Digizyme. There are also tutorials for those creating animations, and a link to a blog that announces developments and additions to the site.

Yale Image Finder

2008-12-23T09:27:00.003Z

Yale Image Finder is from the Krauthammer Lab at Yale, searches the images in 34000 open access articles from PubMed Central.

It searches the text within the images, but you can also search on image captions or on the article text. I tried it using the search string streptococcus pneumoniae. Searching the default of "image text (high recall)" found many genome and phylogenetic tree images, and a screenshot of the ISABEL diagnostic program. Searching "image text (high precision)" found the same (I assume) 18 images. Searching captions instead found more, including an image of S. pneumoniae infection. You can search within, say, captions and full text.

There is more detail on how this works in a paper in Bioinformatics.

BioText, from Berkeley, searches image captions and article full text.

Tidying my desk I found a paper from Bioinformatics from 2004 describing FigSearch, a text mining system for figures from full text biological papers, developed at the University of Oslo. But the URL is no longer found, and a search of the UiO site finds nothing. A Google search for FigSearch finds lots of things about it, but not it itself. If you know where it is, please leave me a comment.

Caesarian increases asthma risk

2008-12-02T13:12:00.002Z

Is the headline given to this Thorax paper by the BBC, which also reports that the association was even stronger in children who had two parents with allergies.

The study is: well, I can't actually find it in Thorax, or anywhere else, so perhaps the BBC (and all the other media sources that appear in a search of G**gle for the author's name and the word "asthma") have got an advance copy.

I will try to come back to this another day and fill in the gaps. Meanwhile if you can find the Thorax paper, leave me a comment. Especially if I have missed it.

FACTA

2008-12-01T11:50:00.002Z

FACTA is not in this context the Fabricated Access Covers Trade Association or the Fair and Accurate Credit Transactions Act, but a tool from the National Centre for Text Mining at Manchester, which uncovers associations between biomedical concepts mentioned in Medline articles. Enter a search term, and you will be presented with lists of associated concepts covering genes, diseases, drugs, and other things (which things are shown depends on the tick boxes that are selected when you search). You can then click to see "snippets", which highlight your search term. I tried it with HFE (the gene associated with hemochromatosis, the example from the Gene Gateway Workbook, described in a previous posting) and got 1564 hits connecting it with the disease.

Any of the associations are links so that you can see their own associations.

FACTA is described in a open access paper in Bioinformatics:

Yoshimasa Tsuruoka, Jun'ichi Tsujii, and Sophia Ananiadou. 2008. FACTA: a text search engine for finding associated biomedical concepts, Bioinformatics, Vol. 24, No. 21, pp. 2559-2560 (there is a link on the FACTA site to this).

Genetics websites

2008-12-01T11:29:00.003Z

Two I found (again can't remember where).

The Personal Genome Project wants to recruit people willing to share their own genome sequence in the interest of furthering research. 10 people have enrolled so far and the website tells you about them, and about who runs and funds the project.

Gene Gateway (Exploring Genes and Genetic Disorders) is a site from the Oak Ridge National Laboratory. There is a poster that outlines disorders that have been mapped to particular chromosomes, and the website offers a workbook and materials that accompany that. The very useful looking workbook uses hereditary h(a)emochromatosis as an example to show how to use OMIM, NCBI Viewer, Swiss-Prot, and other things. ORNL, in Tennessee, was founded during World War 2 to carry out plutonium production for the Manhattan Project.

Mathematics websites

2008-12-01T11:22:00.002Z

Due to bad record keeping, I can't now remember where I saw these.

The Mathematical Association of America's Minutemath website is rather fun, especially because I can actually do some of the problems. There is a daily problem, with an interactive solution which can offer hints before you see the answer, and which gives you an idea of the difficulty (which could be quite depressing, I guess). The MAA also have a Number a Day site, which chooses a different number each day and gives you a fact about it or a property of it.

Google Scholar and material in repositories

2008-12-01T09:15:00.004Z

Thanks to Wouter Gerritsma's blog "Wouter over het web" for this, which I have not seen mention of anywhere else. (The post is in Dutch and any misinterpretation is entirely my own!).

Google Scholar will now give a link to freely available versions of an item, with this link appearing next to the title of the item. It will still tell you how many versions of an item it has found, and if you click that information, give links to all those versions, whether free or not, but next to the title, in your main results list, there will be a link to any free version.

Wouter's blogpost has a screenshot showing an item with a link to the repository of the University of Utrecht. I tried this with the search calcium signalling bacteria, and this finds a copy of the paper by Norris et al in the Journal of Bacteriology in 1996 in Leicester Research Archive.

This, I think, is a very interesting development. There are of course search engines that search only open access material, and I have started slipping OAIster into some classes that I do, but this development to a search engine that we know a lot of people already use is very interesting. Will it push up traffic from Google Scholar to LRA - we shall see.

Drosophila resources

2008-11-27T15:17:00.003Z

Here are some web resources relating to the genetics of Drosophila, the fruit fly:

Berkeley Drosophila Genome Project

Drosophila Heterochromatin Genome Project

Ensembl

Flybase

Homophila (thanks to Max Casu for drawing this to my attention) - compares human and fly genomes. Care with spelling if typing in the URL!

Interactive Fly - this has an A-Z index of genes

NCBI Entrez , perhaps in particular: Gene; Nucleotide; SNP; Taxonomy. Gene searches Flybase (see above) and provides links to PubMed

NCBI Map Viewer, graphical view of the D. melanogaster genome

WWW Virtual Library: Drosophila

The state of mycology

2008-11-27T08:54:00.003Z

Radio 3 news (I had changed channels by now) reported concern over the state of mycology in the UK, with many mycologists coming up to retirement. There is concern that the UK will not be able to take advantage of the prospects for the field.

Today obviously reported this as well, as there is an audio clip here.

The state of school science

2008-11-27T08:48:00.004Z

Interesting discussion on BBC R4 Today programme between Richard Pike of the Royal Society of Chemistry and John Holman of the National Science Learning Centre. RSC have done an experiment in which they gave questions from science exams from the last 30 years to present day school students and saw how they did. They think the results show that it is possible to get a good GCSE grade now with superficial knowledge of maths. NSLC was surprised that the experiment did not have a control (although it would be difficult, as they said, to go back in time to test past students).

An RSC press release, with link to their report and a petition to 10 Downing St about reversing the decline in school science, is here.

And the Guardian reports it here, with the chance to try some of the questions. Now, let's see...

More about PubMed

2008-11-19T16:56:00.002Z

The NLM Technical Bulletin also describes some other changes - in the summary format, article title will appear first and be the link to a more detailed format, and the icons that denote full text or abstract available are going to disappear. There is a screenshot in the NLM Technical Bulletin article.

Changes to PubMed - advanced search

2008-11-19T16:54:00.001Z

This, from the NLM Technical Bulletin, confirms that the tabs in PubMed are moving to the advanced search screen, and outlines some of the other changes that are afoot.

Advanced search (which I have to say I have not used a lot) is moving off beta and becoming... whatever things become after beta! Not gamma, I imagine.

Changes to PubMed - advance information

2008-11-10T16:57:00.002Z

A long gap since the last posting - apologies. I was in Mull for some of the time, but mostly it is just idleness and bad planning that has led to the silence.

PubMed now displays "clipboard" next to the search box, if you have added items to the Clipboard, and this is preparation for the retiral of the tabs. The possible implication, reading the NLM information, is that these features will go to the advanced search screen?

The "recent activity" box - cause of some debate on medical library discussion lists - can now be closed.

Pneumococcal vaccination and risk of myocardial infarction

2008-10-09T10:14:00.002+01:00

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

2008-10-09T10:10:00.002+01:00

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

2008-10-09T10:05:00.002+01:00

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

2008-09-30T09:40:00.004+01:00

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

2008-09-26T09:17:00.006+01:00

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

2008-09-25T15:07:00.008+01:00

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

2008-09-23T09:35:00.004+01:00

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

2008-09-22T11:17:00.003+01:00

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

2008-09-22T11:09:00.003+01:00

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

2008-09-22T11:01:00.002+01:00

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

2008-09-12T16:29:00.002+01:00

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

2008-09-12T16:22:00.002+01:00

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

2008-09-06T05:40:00.003+01:00

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

2008-08-28T11:53:00.003+01:00

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

2008-08-27T10:31:00.002+01:00

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

2008-08-26T14:40:00.002+01:00

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

2008-08-26T14:05:00.002+01:00

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

2008-08-26T13:59:00.003+01:00

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

2008-08-07T20:52:00.002+01:00

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

2008-08-05T22:16:00.005+01:00

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

Not much on this blog lately, is there?

2008-08-05T22:15:00.001+01:00

See another blog for the reason why!

Put those antibiotics down!

2008-07-23T08:44:00.003+01:00

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

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

Changes to Web of Knowledge

2008-07-22T10:25:00.002+01:00

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

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

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

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

DOIs are displayed when you are looking at single records.

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

Search by Address in the All Databases search

House of Lords committee on the spread of pandemic diseases

2008-07-21T08:12:00.005+01:00

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

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

Later note: BBC has picked this up, at http://news.bbc.co.uk/1/hi/health/7516850.stm

Nobel Prize games

2008-07-18T13:31:00.003+01:00

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

Science: drug resistance

2008-07-18T13:29:00.002+01:00

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

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

Science contents page

Archives of Pediatrics and Adolescent Medicine vaccine themed issue

2008-07-17T16:17:00.003+01:00

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

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

HuGENavigator

2008-07-17T09:24:00.004+01:00

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

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

HuGENavigator includes:

Phenopedia - search this for genes associated with a disease

Genopedia - search this for diseases associated with a gene

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

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

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

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

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

Some time ago I did a handout on clinical genetics resources, for a visit I made to staff at the Clinical Genetics Centre at the Leicester Royal Infirmary. I have revised it since, for genetics students, and have revised it again today to include HuGENavigator. The handout is at http://www2.le.ac.uk/Members/khn5/other-stuff

Quality of indoor air and health

2008-07-15T11:21:00.001+01:00

Is the subject of a review article in CMAJ: http://www.cmaj.ca/cgi/content/full/179/2/147?etoc (open access! hurrah!).

Algaebase

2008-07-15T09:58:00.003+01:00

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

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

iHOP

2008-07-15T09:51:00.003+01:00

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

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

Structural exon database

2008-07-15T09:45:00.004+01:00

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

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

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

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

Imported malaria

2008-07-15T09:00:00.003+01:00

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

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

The BMJ, by the way, now publishes online first, so things may turn up in the press on any day, not just Friday. BMJ references now look like this: http://www.bmj.com/cgi/content/abstract/337/jul03_2/a120. It looks like they retain this kind of format once the article appears in a print edition of the journal - I have just had a quick look at one research article from the latest edition, and it retains the a... number, and the pages of the PDF are numbered "1 of 9", "2 of 9" and so on.

TB vaccine development

2008-07-15T08:56:00.003+01:00

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

PubMed includes DOIs

2008-07-14T15:32:00.003+01:00

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

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

Yec'hed mat!

2008-07-08T15:15:00.003+01:00

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

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

O bydded yr hen iaith barhau!

Research Council funding

2008-07-08T15:08:00.002+01:00

Two things that I noticed on the same day:

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

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

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

Changes to PubMed

2008-07-02T13:08:00.004+01:00

Updated 14th July 2008

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

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

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

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

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

I think this might now introduce irrelevant references into your search, if your subject matches a journal or author name, but it does address the original issue. There is some controversy in library circles about this change, and so I would be interested to know if this has adversely affected your searches at all, or to have any comments. There are full details of the change at http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html

New information about ATM: there is now a FAQ about it: http://www.nlm.nih.gov/services/pubmed_atm_change.html

4. Citation sensor: matches searches with citations if you use terms that can be interpreted as year, author name, journal title. Citation sensor results are displayed in a yellow area on the results display. This will not work if you use [au] and other tags in your search.
More details about citation sensor are at: http://www.nlm.nih.gov/pubs/techbull/mj08/mj08_pubmed_atm_cite_sensor.html

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

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

Noma

2008-06-26T17:21:00.001+01:00

Not something I had come across before seeing this article in Lancet Infectious Diseases. It is a nasty necrosis of the tissue of the mouth and face, with an unknown cause, but malnutrition and a bacterial agent are thought to be involved. It is also known (note to any medical students reading this: this is a synonym!) as cancrum oris.

There has been a Noma Day, and the website contains information about the NoNoma Federation and its activities.

You can probably search Google for more information as well as I can (but if you use the synonym you will probably not find the restaurant in Copenhagen or the lighting company, or many other fascinating but irrelevant things…), but there is a useful page in the MedlinePlus Health Encyclopedia which my Google search did not find.

Biosecurity, laboratory safety

2008-06-25T13:04:00.002+01:00

Another half heard Today piece (no good at multitasking). BBC Health's Twitter feed has this in it - I think that must be it.

This is the report of the innovation, universities, science and skills committee of MPs into the foot and mouth outbreak in Pirbright last year. It says that funding uncertainty has meant that the lab facilities themselves are neglected.

Surgical safety

2008-06-25T12:44:00.002+01:00

Half heard a piece on the BBC Radio 4 Today programme this morning about this, and think it was about this:

http://www.who.int/mediacentre/news/releases/2008/pr20/en/index.html,

a new WHO checklist to ensure that all necessary things are carried out before and during an operation. It identifies three phases of an operation - "sign in" (before anaesthesia is induced), "time out" (before any incision is made), "sign out" (before patient leaves the operating room). There are certain tasks to be performed in each phase - for example, in sign in, checking that the correct site is marked, and in sign out, counting the swabs.

This information is from the WHO Press Release (link above), I have not found the list itself.

Journal Citation Reports - 2008 data soon

2008-06-18T10:02:00.000+01:00

Updated 18th June - JCR 2007 data for sciences and for social sciences is scheduled to be released 17th June 1 pm, EDT.

This should mean it is there now - which it is!

The PEACE study

2008-06-17T11:51:00.001+01:00

This is a randomised controlled trial of the effect of carbocisteine on acute exacerbation of chronic obstructive pulmonary disease, although I can't immediately see why it is called PEACE. However, that aside, it is in the Lancet, doi: 10.1016/S0140-6736(08)60869-7. Access should be possible for University of Leicester members, who are welcome to contact me if they have problems.

The reference:

Jin-Ping Zheng, Jian Kang, Shao-Guang Huang, Ping Chen, Wan-Zen Yao, Lan Yang, Chun-Xue Bai, Chang-Zheng Wang, Chen Wang, Bao-Yuan Chen, Yi Shi, Chun-Tao Liu, Ping Chen, Qiang Li, Zhen-Shan Wang, Yi-Jiang Huang, Zhi-Yang Luo, Fei-Peng Chen, Jian-Zhang Yuan, Ben-Tong Yuan, Hui-Ping Qian, Rong-Chang Zhi, Nan-Shan Zhong, Effect of carbocisteine on acute exacerbation of chronic obstructive pulmonary disease (PEACE Study): a randomised placebo-controlled study, The Lancet, Volume 371, Issue 9629, , 14 June 2008-20 June 2008, Pages 2013-2018.(http://www.sciencedirect.com/science/article/B6T1B-4SRFCCJ-11/1/5bd9c035756f67be393458fb2f7a4a2a)

Reading at length

2008-06-17T11:45:00.002+01:00

Have the reading habits of the web destroyed our ability to read long things and read in detail? This is the argument put forward in an article in Atlantic Monthly by Nicholas Carr.

Read the article

Thanks to the very useful Library Link of the Day for this.

UK Clinical Research Collaboration

2008-06-16T16:05:00.002+01:00

I seem to have started receiving the Biotechniques Weekly Newsletter, and it has alerted me to this collaboration, with a website at http://www.ukcrc.org/. It "is a partnership of organisations working to establish the UK as a world leader in clinical research, by harnessing the power of the NHS". It has published a report on funding in microbiology and infectious disease research (http://www.ukcrc.org/publications/news/midrreport.aspx)

Blackwell journals move to Wiley Interscience

2008-06-16T16:02:00.001+01:00

Blackwell Synergy is closing on June 27th, and all journals moving to Wiley Interscience. There is more about this at http://www3.interscience.wiley.com/aboutus/wiley-blackwell/transition_end-users.html, including information about what will happen to alerts and bookmarks.

Les oiseaux du jour

2008-06-16T16:00:00.003+01:00

OK, it is a bit pretentious and I maybe ought to stop it, but l'oiseau of yesterday was, in my own garden, a green woodpecker - noticed the red head and gold bars before the green, but there it was, nonetheless. I am not counting the ospreys seen on a Father's Day (or is that Fathers' Day?) trip to Rutland Water.

CAMERA - what's in the sea?

2008-06-16T15:57:00.002+01:00

It has been quiet, hasn't it?

CAMERA is "Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis", aimed at researchers in marine microbial ecology. The site is a collection of tools and data, and is at http://camera.calit2.net/. Thanks to Kevin Ahern's Webwatch column in Biotechniques for this site.

Birds

2008-05-20T17:01:00.003+01:00

Rather a random collection of thoughts:

I think there are sparrows nesting in my roof (or under the tiles), which is Very Good. And we have a regular visit from at least one bat, at dusk.

And, forgot to mention, on a recent trip to Rutland Water (which I appear not to have blogged about), heard, but did not see, a cuckoo. My first cuckoo ever, I think, let alone the first one of spring.

Researcher ID

2008-05-20T16:55:00.002+01:00

I had an "invitation" to sign up for this Thomson Reuters service, allied to Web of Science. Basically it assigns you a unique ID, and gives you the chance to make a page about yourself and your publications. You need to sign into Web of Science first, then create an account in ResearcherID. This seemed fairly straightforward. I have had a WoS account for so long that my password doesn't obey their rather strict rules, but had to create a password obeying those rules for ResearcherID.

You can then import your publications list from EndNote (I did this) and also search WoS for things what you wrote. Not too complicated in my case, as there are not too many K Nockels, and I can easily spot the two things in WoS that are mine.

Researcher ID will calculate your personal metrics - no, not shoe size, but citation data. Zero, in my case.

ResearcherID is at http://www.researcherid.com/, where you can search for people, and see their publications.

Friends of the Suriname Medical Library

2008-05-16T11:46:00.002+01:00

Justus Krabshuis brings this to my attention - a website to gather donations for textbooks for the Medische Bibliotheek Suriname at the Anton de Kom University Library in Surinam. You can pledge to sponsor a particular book (there is a wishlist) or to contribute generally.

The website is at http://www.mbsuriname.org/index.html

Support for those affected by earthquake in China

2008-05-14T09:02:00.002+01:00

This is support available to members of the University of Leicester - a reminder of that support is at http://www2.le.ac.uk/ebulletin/bulletin-board/2000-2009/2008/05/nparticle.2008-05-13.1111858097

National Knowledge Week for Rhinitis

2008-05-13T14:56:00.002+01:00

Is this week, 12-16 May, with resources available via http://www.library.nhs.uk/ent/ - click Contents under National Knowledge Week for Rhinitis.

25 years since discovery of HIV as cause of AIDS

2008-05-13T13:59:00.003+01:00

When I was working in my first library job, a one year post between University and library diploma, there was much talk of AIDS, not all of it terribly enlightening. There had recently been the two research groups that had isolated HIV - HTLV-3, I think was a name that was given to it by one group - and I had work colleagues who could stop themselves thinking about it seriously by viewing it only as a "gay disease" (straight colleagues, presumably - perhaps there still are such people). Anyway, I am made to ramble like this by an editorial in Science, looking at where HIV and AIDS research has got to in those 25 years.

The editorial is:

Bernstein A. AIDS and the Next 25 Years. Science 2008; 320(5877): 717. Available at: http://www.sciencemag.org/cgi/content/summary/320/5877/717

This will work on campus only for University of Leicester members.

Scalpel injuries in the operating theatre

2008-05-13T13:53:00.002+01:00

Hitch with subscription prevents me from seeing full text, but an editorial in the BMJ discusses this:

Watt AM et al. Scalpel injuries in the operating theatre. BMJ 2008; 336:1031. Available from http://www.bmj.com/cgi/content/extract/336/7652/1031?etoc

The role of healthcare workers in MRSA transmission

2008-05-08T11:00:00.004+01:00

Is discussed in a paper in the Lancet Infectious Diseases - are healthcare workers the source of the infection, or a vector, or something else?

Conclusions (looking quickly) seem to be that they are important as a vector, but possibly not as a source.

I think I am a little worried by the search strategy, which doesn't seem to include alternative terms for "MRSA", just "MRSA" (does this matter, I wonder?), and doesn't seem to include specific healthcare workers, only the phrase "healthcare worker(s)". The authors did however use the Outbreak Database, http://www.outbreak-database.com/, which was new to me. Not sure if this is a current database - it seems to have started with information from a Medline search done up until 2002. The search page doesn't seem to be working at the moment.

Paper is:

Albrich WC, Harbarth S. Health-care workers: source, vector, or victim of MRSA? Lancet Infectious Diseases 2008; 8(5): 289-301.

Link accessible to Science Direct subscribers (University of Leicester members, this is you!):
(http://www.sciencedirect.com/science/article/B6W8X-4SFS83N-X/1/727e6be35322303f2c8443ac0203fd89)

University of Leicester members: I can advise if you have problems with this link.

Buzzards and ducklings

2008-05-08T11:00:00.000+01:00

Saturday 3rd May - two buzzards circling over the house then flying off to the East. And, on the river, the first ducklings I have seen.

Sunday 4th May - starlings feeding young in next door's roof?

Posted this on Sunday 4th and it ended up dated 20th April, for some reason.

Later edit: baby thrush in nest outside office, and blackbirds busy nest building in back garden.

Stenotrophomonas maltophilia

2008-05-07T12:28:00.002+01:00

A study by the Sanger Institute makes the papers today, including the front page of "Metro", which I don't usually read, but which did catch my eye.

This microbe ("new hospital superbug"), also known as pseudomonas maltophilia, likes wet areas like shower heads and taps, and IV drips, and can affect hospital patients who have lung diseases, cystic fibrosis, or who are on chemotherapy. It usually colonises, rather than infects, and to infect must bypass normal host defences.

Here are some links:

The story in the Guardian
Emedicine
British Society for Antimicrobial Chemotherapy
Sanger Institute project to sequence genome of S. maltophilia
Information on cysticfibrosis.com

And the map of the genome referred to in the Guardian story is in this:

Crossman LC et al. The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biology 2008 Apr 17;9(4):R74 http://genomebiology.com/2008/9/4/R74

Not sure immediately where the figure of 1000 reports of "steno" blood poisoning a year come from: if you know, you can leave me a comment!

Scopus Affiliation Identifier

2008-04-30T16:27:00.003+01:00

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

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

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

Under each, the variant names are listed.

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

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

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

Google Custom Search

2008-04-28T13:09:00.002+01:00

I have added Flutrackers to the Google Custom Search at http://www.le.ac.uk/library/clinical/influenza/index.html, so it now searches that alongside DEFRA, Department of Health, Health Protection Agency, NaTHNaC; and ProMed Mail. It will now pick up things about the Bali influenza simulation (see earlier posting).

Influenza exercise

2008-04-28T12:46:00.000+01:00

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

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

Have tested my Google Custom Search engine (see http://www.le.ac.uk/library/clinical/influenza/index.html) on this to no avail. I did wonder if this was because there was nothing there at all, but now that there is, I think it is because I am not searching the right kind of site. The CSE only searches specifically flu related sites.

Gene therapy

2008-04-28T09:21:00.004+01:00

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

The BBC website reports it here: http://news.bbc.co.uk/1/hi/health/7369740.stm.

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

There is information about Leber Congenital Amaurosis in Gene Reviews.

Swallows

2008-04-28T09:18:00.002+01:00

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

Plant genomics

2008-04-25T16:55:00.002+01:00

Lots of things about this in Science this week: http://www.sciencemag.org/content/vol320/issue5875/index.dtl?etoc (on campus access only, as far as I know). Includes a multimedia feature. There is also an article on ecological costs of GM crops, but this appears under "policy forum", not with the things on genomes of plants.

Goldfinches

2008-04-25T16:10:00.000+01:00

Outside the window, in the trees. Listen to some like them at http://www.rspb.org.uk/wildlife/birdguide/name/g/goldfinch/index.asp

800 posts!

Meningitis, and del.ic.ious

2008-04-25T15:57:00.002+01:00

A recent Education Guardian piece on meningitis (http://education.guardian.co.uk/egweekly/story/0,,2273536,00.html) highlighted the need to know what it looks like, and the importance of not being afraid to act.

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

Person to person transmission of H5N1

2008-04-25T11:37:00.003+01:00

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

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

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

Henry Gray

2008-04-25T09:28:00.002+01:00

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

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

More on this later, perhaps!

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

World Malaria Day

2008-04-25T09:19:00.002+01:00

It's World Malaria Day today.

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

Click the button below to find out more.

Perioperative hypothermia

2008-04-23T16:57:00.001+01:00

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

Birds

2008-04-23T16:56:00.001+01:00

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

Other things in Nature, 17 April 2008

2008-04-22T15:57:00.002+01:00

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

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

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