Tuesday, December 23, 2008

Molecular Movies

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

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.

Tuesday, December 02, 2008

Caesarian increases asthma risk

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.

Monday, December 01, 2008


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

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

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

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.

Thursday, November 27, 2008

Drosophila resources

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

Berkeley Drosophila Genome Project

Drosophila Heterochromatin Genome Project



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

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

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...

Wednesday, November 19, 2008

More about PubMed

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

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.

Monday, November 10, 2008

Changes to PubMed - advance information

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.

Thursday, October 09, 2008

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.


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.

Tuesday, September 30, 2008

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.

Friday, September 26, 2008

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.

Thursday, September 25, 2008

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.

Tuesday, September 23, 2008

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.


- 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.

Monday, September 22, 2008

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.

Friday, September 12, 2008

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.

Saturday, September 06, 2008

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.

Thursday, August 28, 2008

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.

Wednesday, August 27, 2008

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.

Tuesday, August 26, 2008

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).

Thursday, August 07, 2008

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.

Tuesday, August 05, 2008

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

Not much on this blog lately, is there?

See another blog for the reason why!

Wednesday, July 23, 2008

Put those antibiotics down!

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

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

Tuesday, July 22, 2008

Changes to Web of Knowledge

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

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

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

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

DOIs are displayed when you are looking at single records.

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

Search by Address in the All Databases search

Monday, July 21, 2008

House of Lords committee on the spread of pandemic diseases

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

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

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

Friday, July 18, 2008

Nobel Prize games

Discovered this through the Biotechniques Weekly Newsletter. There are some multimedia online games based on the discoveries that have been awarded Nobel Prizes. I have just spent too long on the Robert Koch and TB game - I did manage to stain the expectorant, look at under the microscope and see the bacteria, but very slowly. Your virtual guide is called Wilma, and she has a nice line in responses when you try to do something stupid like pick up the bench, or pour the expectorant down the sink. The games are at 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

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

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

Science contents page

Thursday, July 17, 2008

Archives of Pediatrics and Adolescent Medicine vaccine themed issue

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

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


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

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

HuGENavigator includes:

Phenopedia - search this for genes associated with a disease

Genopedia - search this for diseases associated with a gene

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

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

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

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

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

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

Tuesday, July 15, 2008

Quality of indoor air and health

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


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

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


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

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

Structural exon database

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

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

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

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

Imported malaria

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

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

The BMJ, by the way, now publishes online first, so things may turn up in the press on any day, not just Friday. BMJ references now look like this: 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

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

Monday, July 14, 2008

PubMed includes DOIs

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

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

Tuesday, July 08, 2008

Yec'hed mat!

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

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

O bydded yr hen iaith barhau!

Research Council funding

Two things that I noticed on the same day:

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

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

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

Wednesday, July 02, 2008

Changes to PubMed

Updated 14th July 2008

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

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

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

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

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

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

Thursday, June 26, 2008


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.


Wednesday, June 25, 2008

Biosecurity, laboratory safety

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

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


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.

Wednesday, June 18, 2008

Journal Citation Reports - 2008 data soon

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!

Tuesday, June 17, 2008

The PEACE study

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

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.

Monday, June 16, 2008

UK Clinical Research Collaboration

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

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

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?

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.

Tuesday, May 20, 2008


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

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.

Friday, May 16, 2008

Friends of the Suriname Medical Library

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

Tuesday, May 13, 2008

National Knowledge Week for Rhinitis

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

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

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

Thursday, May 08, 2008

The role of healthcare workers in MRSA transmission

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!):

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

Buzzards and ducklings

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.

Wednesday, May 07, 2008

Stenotrophomonas maltophilia

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
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!

Wednesday, April 30, 2008

Scopus Affiliation Identifier

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.

Monday, April 28, 2008

Google Custom Search

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

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

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.


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.

Friday, April 25, 2008

Plant genomics

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.


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

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

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

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

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.


Wednesday, April 23, 2008

Perioperative hypothermia

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.


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

Tuesday, April 22, 2008

Other things in Nature, 17 April 2008

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);

Genomic and epidemiological dynamics of human influenza A virus

Is the subject of a paper published in Nature online, at http://www.nature.com/nature/journal/vaop/ncurrent/full/nature06945.html, doi: 10.1038/nature06945.

Link to the paper using the DOI here.

Medical blog from Afghanistan

More precisely, a blog from a Canadian physician currently working there - http://www.cmajblog.blogspot.com/.

Sunday, April 20, 2008


Forgot to mention at the time... Last year we often would see a bat in our back garden, just before dark. On Tuesday night we saw it, for (at least for me) the first time this year.

Birds - first swifts

Change of title!

We were driving from Fleckney (Leicestershire) to Kibworth (ditto) on Saturday, after dancing at the Fleckney School Fun Day. We had gone over the canal near Wistow and saw two swifts, the first of the year. And then, right over the road, quite low down, a kestrel. We slowed down - we brake for kestrels, and, rather affronted, it flew over to the side of the road.

Start them young

The bat related entry (which got a date of 11th April, for reasons I don't understand, which is why it seemed to have disappeared) was by my son - in case you wondered about the change of style.

Have not found a way to tell the bat group (they want to know about grounded bats, but not obviously about every sighting). Perhaps they will read the blog!

Friday, April 18, 2008

The first Bat (of the year.)

On April the 18th we saw a Pipistrelle bat (on the way back home from the spar shop) we named it Bert! It stayed around for 5-10 minutes (it was very small!)
Bert flew around the busy road for ages we had to leave him flying around.
We will inform the local bat group.

What tree is that?

I have been trying to identify two of the small trees in my garden (only lived in the house for three years...), using a tree book, and two websites, and the idea of "keys". I have to say I am not getting on terribly well so far, and am finding that the keys don't agree with each other.

One tree might be an elder, the other a rowan. But I am not convinced yet.

Watch this space.

Two items in Science: Croatian Medical Journal, and influenza

Two separate items:

1) Croatian Medical Journal involved in discussions about its future, in light of various allegations of plagiarism published in its pages, or by its editors: http://www.sciencemag.org/cgi/content/full/320/5874/304a

2) A paper on the circulation of seasonal influenza viruses: http://www.sciencemag.org/cgi/content/abstract/320/5874/340

Les oiseaux du jour

In the park this morning: a goldfinch? It didn't have a red face, though. [Edit: saw another today, 20th, and reading Simon Barnes Bad birdwatchers' companion on the train, I wonder if it was actually a greenfinch, which is what my son told me they were. It didn't look green, but apparently, they don't, always). Later edit: saw some today (26th) and they did look a bit green.]

And a yellow wagtail (or a grey one), by the side of the river.

This was in addition to the usual wrens, thrushes, ducks (including one sitting on an ivy covered fence), moorhens, dunnocks, robins.

In garden -sparrows, starlings.

Thursday, April 17, 2008


On Today programme (Radio 4) this morning, piece about http://www.darwin-online.org.uk/, Charles Darwin's papers. Coincidentally, was on http://www.darwinproject.ac.uk/, yesterday, which is his letters. I think it might be all of them, although they are being published in a series of books as well (vol. 16 due later this year).

Bit in Guardian too - http://www.guardian.co.uk/science/2008/apr/17/darwinbicentenary.evolution

2009 is 200th anniversary of birth of Darwin, and there do seem to be a lot of books about him appearing.

Wednesday, April 16, 2008

Les oiseaux du jour

In park:

wrens, several, including one really quite cross sounding one (on a branch very close to river);
blackbird bathing in river;
moorhen looking for things in weeds around piece of detritus in river (actually a signpost from the national cycle network...).

Thought last night on way home that there are more blackbirds around in the evening.

And, on late-ish drive from Foxton Locks to home, an owl.

Tuesday, April 15, 2008

Harry Potter and the Copyright Court Case

Lots of coverage of this in the press today - JK Rowling in court in New York to try to stop the publication of an unofficial Encyclopaedia about the books. I'm interested in the fact that the material is already available on a website, and that according to BBC Newsround, Rowling has used the site and found it useful - it appears to have an endorsement from her on the home page. Interesting that the website is not viewed as a threat, or breach of copyright, but that the book is.

One place in the press is here: http://books.guardian.co.uk/news/articles/0,,2273675,00.html

Les oiseaux du jour

Yesterday (didn't manage to post yesterday), a robin, sitting on a post, singing very near me. Today, in park, a pied wagtail, as well as usual - ducks, moorhens, wrens, robins.

Sunday, in garden, a large number (well, 15-20?) sparrows, including two attempting to mate, in the tree which houses the bird feeder. We are trying to encourage the sparrows, endangered as they are, so this is very good!

Friday, April 11, 2008


If you were watching Skins last night (and I should tell you that the programme website is labelled "over 18 only", which I am, but you may not be) and wondered about congenital subarachnoid haemorrhages, which Chris had, here are some sites:

BBC Health - http://www.bbc.co.uk/health/conditions/subarachnoid2.shtml

Patient UK - http://www.patient.co.uk/showdoc/40000757/

MedlinePlus - http://www.nlm.nih.gov/medlineplus/ency/article/000701.htm

Low copy DNA

The forensic science regulator has ruled that this technique is sound, although with recommendations about how samples should be handled to prevent contamination. Low copy DNA is a technique used to get a DNA profile from a small number of cells, recently criticised in the case of the man on trial for the Omagh bomb.

The story is covered in the Guardian and on the BBC.

A Forensic Science Service factsheet about the technique is available from here: http://www.forensic.gov.uk/forensic_t/inside/news/fact_sheets.htm

I can't currently find the forensic science regulator report.

Les oiseaux du jour

In the garden first thing - sparrows, three woodpigeons. We put up some nesting material (in a ceramic apple, which I hung in one of the small trees in the garden) and it is certainly being taken.

In the park this morning - something flying along the riverbank, but probably not a kingfisher. Otherwise, the usual. On Wednesday night, son and I saw a fox, in the playing field that adjoins the park.

In the park on the way home this evening, what I am fairly sure was a blackcap - audio recording (on rather old BBC Bristol webpage) here.

In the garden after tea (or is that supper?) this evening - a lot of starlings. Lots of blackbirds on the verges of the road, too.

Thursday, April 10, 2008

Nursing in the Third Reich

Interesting piece in the Guardian about nurses' role in the human experimentation carried out in the Third Reich, and present day research and reactions into that. http://education.guardian.co.uk/higher/news/story/0,,2271638,00.html

Induced pluripotent stem cells

Discussion of five questions - anyone can do it, everyone can have their own custom-tailored cells, the cures are on their way, embryonic stem cells are the same as iPS cells, and, iPS cells have no ethical issues - in Nature, at http://www.nature.com/news/2008/080326/full/452406a.html.

iPS are created from adult cells.

Bacterial archive destroyed

An archive of infectious bacteria, held at the Pittsburgh Veterans Affairs Medical Center in Pennsylvania, has apparently been destroyed, according to Nature. It looks like this might have happened a little while ago.

There is a piece in Clinical Infectious Diseases, referred to in Nature, which is here: http://www.journals.uchicago.edu/doi/full/10.1086/528853. It includes a petition signed by 240 or so people, asking for an enquiry into how this happened.

Quake Catcher Network

Interesting piece in Nature (from a week or two ago - only just had alert of it via Zetoc). Quake Catcher Network is a scheme using the accelerometers in laptops to sense earthquakes, and then relay that information to Stanford University. The central server can then alert other people in the area, but the scheme is really to track quakes. The scheme itself has a homepage at http://qcn.stanford.edu/

Il n'y a pas des oiseaux

Apologies for any creaky French grammar. I drove the car to work.

Wednesday, April 09, 2008

Les oiseaux du jour

Pretentious, moi? Not really, I hope. It did occur to me that "bird of the day" might be open to misinterpretation. (Sorry if you are reading this because you found this phrase, and are now disappointed!).

Today, two robins, on a fence either side of the path in the park. One sat within feet of me and sang, for a little bit. I told it my news, as my father always does when robins come to watch him gardening. Is that a Norfolk habit, I wonder?

Also, two very soggy pigeons sitting in a puddle, and what seem to be the usual wrens and thrushes.

Ovid Medline and EndNote

Problem solved! I posted to Thomson's email discussion list, and John East of the University of Queensland Library replied with a solution. There are tags within the filter that EndNote uses to decide which filter to choose to import the references. There was another filter with the same settings for those tags, and EndNote was using that filter instead. That filter (the one for Ovid AutoAlerts) was set to import AU and FA both into the Author field.

I would never have thought of this in a long time! Most grateful to John for his help.

Tuesday, April 08, 2008

Les oiseaux du jour

Nothing out of the ordinary today, but two wrens, both just making chirruping sounds, rather than singing. Probably significant? Last night, two feral pigeons having a disagreement on next door's roof. This morning, plenty of sparrows - some may be nesting in next door's gutter or eaves. I think we have some too, but they resolutely refuse to go in and out of the gutters while I am watching them.

Monday, April 07, 2008

Les oiseaux du jour

Sparrows (trying to encourage them to nest by putting nesting material in garden), starlings (nesting in gutters of next door's house), and, in park, robin, dunnocks (I think), thrush, duck, moorhen, blackbird. Keeping eye out for kingfisher but not spotted yet this year.

Friday, April 04, 2008

Google Custom Search

There is a custom search on the influenza home page, put there kindly by my colleague Janet Guinea. It works, but needs tuning - I have included six or sites, mostly specifically on flu, but two (ProMed-Mail and Nathnac) are not flu-specific. This means that if you search for words like "outbreak", you get outbreaks of other things. I'm reluctant to add search words to the search, as they won't be needed for the other sites and I'd worry that I would lose relevant results.

Updating influenza pages

Just updated the links in our avian and pandemic flu pages. Have not done this for some time, so a few to change. Can't get the PubMed RSS feed to work. Also discovered that if I edit the page generated by MyIntute, using Contribute, and then try to publish it, it has terrible trouble. I ended up creating all sorts of rubbish with variant filenames. Fortunately, none of this junk actually seems to have been published. Have made mental note not to edit that page again!

From Word 2007 (added title within Blogger)

This is a posting written in Word 2007 (which I have installed in an effort to fulfil the requirements of an "expert user" at the University). I noticed you could create a blog posting if you make a new document. Turns out that you are asked to register your blog, and away you go, hopefully. Don't know what happens if you have more than one (as I haven't).

Realised when viewing this that it had no title - have just added one in Blogger. Don't yet know how to do it from Word.

Scopus and RefWorks

And another current problem is this: if you follow a link from Scopus to our link resolver, then save the reference from there to RefWorks, it only imports the first author.

Local link resolver expert, RefWorks on case so far. RefWorks indicate it is an issue with Scopus, so I will go there next.

Update: Scopus report that Scopus sends only the first author's name to the link resolver, so that is why there is only one name to export into RefWorks. Better then not to export from link resolver to RefWorks, I say.

EndNote and Ovid Medline

One of my current problems is this: if I save the Medline (Ovid) filter on my network space, it will work perfectly when used to "direct export" from Medline to Ovid. When I save it to the shared folder, where EndNote looks for these things, it doesn't work. It then disobeys its own set up and imports both sets of author names (FA and AU) to the same EndNote field.

Our local IT services, EndNote and Ovid have all been pestered, to no avail.

Les oiseaux du jour

On the way to the station - starlings and sparrows outside my house, geese flying nearby, in the park: thrush, wren, long tailed tit (duck and moorhen). At station, magpies.

Friday, January 04, 2008

Where have I been - what's in the journals today

I notice it is August since I posted something on this blog, which makes rather a joke of it being a current awareness tool!

Perhaps I will do better this year.

Anyway, in the weekly journals this week, I spotted these things:

The Lancet, 371(9606), 5-11 January, contains an editorial on the death penalty, which the Lancet opposes. The UN has voted to abolish it, in a largely symbolic vote, but the editorial gives a useful summary of the present state of the death penalty in the USA, where New Jersey has abolished it, and several states have a moratorium.

Science, 319(5859), 4 January, has pieces on the science policies of all the candidates in the primaries in the United States.

BMJ, 336(7634), 5 January, reports Medecins sans Frontieres top 10 list of forgotten crises.

University of Leicester members can use Leicester e-link to access these titles.