Tuesday, December 23, 2008
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
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
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).
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.
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 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
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
Today obviously reported this as well, as there is an audio clip here.
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
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
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
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.
Tuesday, September 30, 2008
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
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
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
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
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).
University of Leicester members can access the Lancet via ScienceDirect.
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
BMJ news item here.
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
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
Wednesday, August 27, 2008
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
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
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]
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
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
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
Wednesday, July 23, 2008
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
"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
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
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
"Manuscripts received by September 15, 2008, will have the best likelihood of being included in this theme issue".
HuGENavigator is "an integrated, searchable knowledge base of genetic associations and human genome epidemiology" - HuGENet is a CDC based project.
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
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.
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.
"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!)
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.
Monday, July 14, 2008
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
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!
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
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
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.
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
Tuesday, June 17, 2008
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)
Read the article
Thanks to the very useful Library Link of the Day for this.
Monday, June 16, 2008
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
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.
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
The website is at http://www.mbsuriname.org/index.html
Wednesday, May 14, 2008
Tuesday, May 13, 2008
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.
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
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.
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.
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
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
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
Leicester Royal Infirmary
De Montfort University
Leicester General 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
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.
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.
Friday, April 25, 2008
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.
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.
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)....
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
Tuesday, April 22, 2008
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);
Link to the paper using the DOI here.
Sunday, April 20, 2008
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.
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
Bert flew around the busy road for ages we had to leave him flying around.
We will inform the local bat group.
One tree might be an elder, the other a rowan. But I am not convinced yet.
Watch this space.
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
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
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
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
One place in the press is here: http://books.guardian.co.uk/news/articles/0,,2273675,00.html
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
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
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.
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
iPS are created from adult cells.
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.
Wednesday, April 09, 2008
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.
I would never have thought of this in a long time! Most grateful to John for his help.
Tuesday, April 08, 2008
Monday, April 07, 2008
Friday, April 04, 2008
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!
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.
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.
Our local IT services, EndNote and Ovid have all been pestered, to no avail.
Friday, January 04, 2008
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.