Wednesday, February 11, 2015

Searching PROSPERO

Prospero is an international database of systematic reviews.  Reviewers can register review protocols in it, and link to publications once they appear.   Prospero is hosted by the Centre for Reviews and Dissemination at the University of York.  There is information about registration and the data that is required here.

Searching Prospero before you start a review could stop you duplicating work that is already in progress.  

As part of an enquiry at work, I was searching Prospero for reviews to include in a review of reviews (an "umbrella review").   Searching Prospero would locate reviews in progress, and would identify published reviews (alongside those identified using Medline and other databases). 

I have not found any search help specific to Prospero.  I am fairly sure the search help at http://www.crd.york.ac.uk/crdweb/GuideToSearching.asp applies to the other CRD databases.  

The References and Resources section contains a lot of useful information, including reviews of progress, and there are some interesting articles about Prospero under "Registering a systematic review", but the main emphasis of all the material seems to be about registration, not searching.  So, I thought it might be useful to "publish" my notes about searching Prospero.



Complex search strategies are difficult.  You can't see a search history, and so can only submit one query at a time.  If you use one search box, you can't use Boolean operators, although you can use * to truncate.  You can't enter phrases in inverted commas, but I wonder if phrase searching is the default.  Using more than one search box does give you a way to search using Boolean in one field (change the drop down box at the top) or across fields, but you have to have just AND or OR.  
You can't export results, only view them, so reviewing results for items to include in your research would need to be done on screen, and I am not sure how you would then put those items into reference management software for retention.

The Participants/Population field records details about the group(s) being studied in the review.  My enquiry involved finding material relating to older people.  Searching for aged did not work, as this found phrases like "patients aged 10 or above".  Older worked better, although that still found phrases like "30 years and older".  Elderly and geriatric worked as well.  There is no standardisation in this field, and no equivalent of Medline's age limits.

You can display all published records, and doing so shows that at the moment there are 5739 records, so the dataset is a lot smaller than something like Medline, and this combined with the fact that searching Prospero would be to augment more systematic searches done elsewhere, means that broader searches are still practical.

Saturday, February 07, 2015

A host of golden daffodils

Beside the lake, beneath the trees, fluttering and dancing in the breeze.  But not near the food in supermarkets.  According to this report in the Guardian, Public Health England have issued guidance that says daffodils should not be displayed in shops near the food as daffodil bulbs are easily mistaken for onions, and daffodil stems look like a "type of vegetable popular in China".  There seems to be no sign of this announcement on the Public Health England website, but however.  

So, where is the evidence?

The Guardian quotes the British Columbia Drug and Poison Information Centre, a reputable looking site that also happens to be quite near the top of Google search results for daffodil poisoning.  Slightly lower down the results is The Poison Garden, which has a lot of detail (the site is run by someone who volunteered at the Poison Garden at Alnwick Castle, but is not connected with it).  There are plenty of stories of poisoning in this site, but as it points out, it is poisoning that usually does not require hospital treatment and so does not end up in statistics.

It seems not to end up in the medical literature either, for, I imagine, the same reason.   A search of NICE Evidence Search for daffodil poisoning finds three things, one of which is a red herring.  The first is about plant enquiries made to New Zealand's National Poisons Centre, reporting that the daffodil was the tenth most commonly reported plant.  The third is from the Pharmaceutical Journal, providing historical stories about bulb poisoning.     If you search NICE Evidence Search for just daffodils, you find items about contact dermatitis caused by daffodils, and galantamine, a drug used for treatment of cognitive impairment and Alzheimer's disease (and one of the compounds mentioned by The Poison Garden as causing problems if you eat the bulbs).  

Searching Google for daffodil poisoning site:nhs.uk finds information from NHS Choices, covering plant dangers in the garden and countryside and making a tiny but significant mention of daffodils.  
 Looking in PubMed turns this up, an article about poisoning caused by eating the stalks.  Although the study was published in an American journal, the incident involved the Chinese community in Bristol.  The daffs were indeed next to the veg.  This incident is mentioned in The Poison Garden. 

So, where's the evidence and what is it?   Not much in the peer reviewed literature, but some sites that advise of the problem and record the stories of individuals. 

Thursday, February 05, 2015

Statistical literacy

Ben Goldacre (of Bad Science and Bad Pharma fame) was on BBC's Newsnight last night (Wednesday 4th) advocating severe punishments for politicians who misuse or abuse statistics.   I am not sure I would go that far, but I think the point about misuse of statistics is a good one.

One possible response to statistical misbehaviour is people being more statistically literate, so they can spot the misbehaviour.  There is a discussion of the problem in Wikipedia.

How much knowledge would we need to be statistically literate?   If we are a healthcare practitioner trying to apply the results of a piece of research to our own practice, then I suspect quite a lot, and the sort of thing that is covered in health education courses.  But someone looking at government statistics about, say, unemployment, or waiting times might just need to be able to identify things like graphs whose vertical axis doesn't start at zero, using different time periods or starting points, and the different sorts of "average".

So, what would help?  There are books, like How to lie with statistics, and The tiger that isn't.  There are revision guides on the web, for GCSE, for example, but they rather assume you know what statistical technique you need.    There is the BBC programme "More or Less", which has pages that discuss various things in the news, as well as clips and episodes.   The Open University, a partner in the programme, have a site with resources.

Making sense of statistics, from Sense about Science and Straight Statistics , looks rather useful.  It covers percentages and certainty, among other things.   

The work of Straight Statistics is now carried on by Full Facts, a fact checking organisation, whose site looks at statistics in all sorts of areas including health.  


Tuesday, February 03, 2015

English sweat

In the current BBC adaptation of Hilary Mantel's "Wolf Hall", Thomas Cromwell loses his wife and two daughters to a mysterious and very sudden illness.  All we see is that they all go to bed as usual, and then cannot be woken in the morning.  There is a suggestion that there were symptoms, but we don't see them.  The disease is described as "English sweating sickness", either in the programme or in something I read about it (bad note taking, can't remember my source).

What was it?   A search of PubMed for English sweating sickness brings up this very new article proposing that the guilty agent was hantavirus.  Related citations displayed include this older one from the New England Journal of Medicine, and this from Medical History.  The new one and the Medical History are free to read, the NEJM one may need a subscription.

Searching English sweating sickness with inverted commas "English sweating sickness" helps, as you then don't get things about other things, and searching for just English sweat is also useful (spotted from the Medical History reference).  There is also a MeSH term Sweating sickness/ and one for Hantavirus and another for Hantavirus infections, so plenty of other avenues for exploration.  


CDC advice suggests hantavirus infection is still a real possibility in the USA and a good reason for not having mice or rats in your house.  There is UK government advice too, which suggests it's much rarer in the UK, but is indeed a real issue elsewhere.  Finally, the Health and Safety Executive's page about zoonoses has general advice on zoonoses (infections transmitted from animals to humans) in agriculture, and a link to an information sheet.

 Have a read if this post has made you worried.


Monday, February 02, 2015

PEDro - evidence for physiotherapy practice

I knew about PEDro, the physiotherapy evidence database, but have actually been using it to find material about head injuries (my obsession with this is explained elsewhere!).

PEDro is a freely accessible database of RCTs, systematic reviews and practice guidelines in physiotherapy.  It gives you bibliographic details and (if permitted by the publisher) an abstract, with links to full text. These links include publisher links, which will work if you or your institution subscribe that way (and you are on campus, in the institutional case), links via DOI, and sites like PubMed Central, and links to PubMed.

Something it offers that Medline does not is an independent assessment of quality, giving a score out of 10.  The reason for the score is transparent, and when you read the record you will see how the item scored with regard to things like blinding, allocation, and intention to treat. 

On the advanced search screen you can use the drop down boxes to select therapy, problem, body part and topic.  Method is RCT/SR/practice guideline.

So, to find things about work with people who have had a head injury, you could select Body Part = Head and Neck and Topic = Neurotrauma.  This finds guidelines from NICE and SIGN and one from Australia (PEDro is Australian), three systematic reviews and a dozen or so trials.  The guidelines are not in Medline, for sure, and some of the other material might not be.

You have to move from result to the next by going back to the results screen and choosing the next one, but if you click the select link on that results page, you can then display full records of those you have selected, on one screen.   From that screen of selected records you can export to EndNote or RefWorks.

Import to EndNote involves emailing the results and saving the email as a text file. I can't work out how to do this in Gmail, but I did copy the text from the email to a plain text file and managed to import that, following PEDro's instructions.

Import to RefWorks involves copying the results, then importing using the "Import as Text" option under References > Import.  For this, you paste those copied results into a box in RefWorks.  This worked although PEDro only includes authors and title, and does not seem to include guideline number.  

PEDro is a good way to find evidence for practice in physiotherapy and perhaps beyond, and its quality assessment information is not to my knowledge matched by anything elsewhere.

Sunday, February 01, 2015

Information about head injuries and seizures

Or brain injuries and epilepsy (see an earlier post).

Here are some sources of patient information about head injuries, seizures, or both:

NHS Choices - Epilepsy - Causes

NHS Choices - Severe head injury
A head injury is "severe" if it involves unconsciousness or a low score on the Glasgow Coma Scale.

Neither of these is, as they themselves will tell you, a substitute for a doctor.

Cookbook medicine



This was a criticism levelled at evidence based medicine, when it became a way of thinking some years ago.  The criticism was that your doctor would diagnose you, and then look up what to do and do just that.  There was no place for expertise or experience.   

Present day diagrams of evidence based medicine include, of course, professional expertise and patient experience, as well as the research evidence. 

I don't think that was ever a fair criticism, but having had a head injury in September (I fell off my bike), and been in receipt of doctors' advice, I think it misses the point. 

The diagnosis may not be easy.  And the evidence may be difficult to find, and when you have found more than one piece of evidence, you may have more than one recommendation.  

Following my accident, the DVLA told me I must stop driving.  I had reported the accident in late September, and they told me this in mid January.  This was because I am at an increased risk of a seizure, as a consequence of the head injury.  This is the guidance of their medical panel.

However, after I was declared fit for work, and while I was waiting to hear from the DVLA, I asked my GP for advice (the DVLA recommend this, while you are waiting).  They felt I was ok to drive.  They examined me, read my notes, and talked to me (the DVLA had only been able to do the second of those), and they knew what the DVLA would be worrying about and felt I was at low enough risk.   

Why the difference?   Was someone not applying the evidence alongside the patient experience and their own expertise?  Was someone living by the cookbook method and the other one not?  Was there something wrong with the cookbook?

What does a medical librarian do when faced with a health problem?  That's right, they do a literature search. 

Guidelines do seem to agree that having a head injury makes you more at risk of a seizure.  They don't, however, quantify the risk, and they don't seem to talk about any other factors that might increase the risk.   So I searched Medline.

And that is what made me think of the second and third of my reasons.

Was it a head injury, or a brain injury?   The MeSH term Craniocerebral trauma/ covers them all, but is that too broad?  And are we talking about Epilepsy as the complication, or Seizures?   Several articles I found did indeed say that head trauma (another possible search term!) did leave you at increased risk of epilepsy, but maybe for a year, not six months, and maybe much longer.  It does not seem to be clear cut.

A textbook I found said that a seizure at the scene might actually not count as epilepsy, and that there is also an issue with who observed it.  If it was someone who had come to help, they might think it was a seizure when it was not.  I wouldn't know the difference, I am sure, and would probably tell the paramedics that I had seen a seizure.  But what if your helpers were health professionals and actually knew?

And was it a mild head injury or a serious one?   This might depend on the definitions in the paper you are reading, but is there an agreed set of definitions?


So, no cookbook medicine.

Even if the diagnosis was straightforward (seizure or not, mild or serious injury...?), finding the evidence is not, and reconciling it with other evidence is not either (is "post traumatic epilepsy" the same as a post traumatic seizure, why do different studies report different risks...?).   There is a need for the expertise of the professional alongside the evidence and knowledge of the experience of the patient.


Patient information

Simon Stevens' Five year forward plan for the NHS mentions people making more use of web based health information as an alternative to a visit to the GP or A and E ("Build the public’s understanding that pharmacies and on-line resources can help them deal with coughs, colds and other minor ailments without the need for a GP appointment or A&E visit." - http://www.england.nhs.uk/ourwork/futurenhs/5yfv-ch3/, Box 3.1).

This could help some people avoid having to use hospitals, unless they need to hear something from a health professional rather than read it.  But perhaps if people knew how to find and appraise web based information, they would feel more confident in their own discoveries and more confident in the advice they have read, and not want to get professional input.  And they could look for information to add to information they have received from a health professional.

There's an interesting potential role for health information professionals in this task of building understanding that online resources are an alternative to securing and sitting waiting for an appointment, or waiting in A and E.  Could we work with the NHS or with patient organisations to help people to realise that online resources are useful, and how to find material you can trust?  

On Facebook recently, two people I know have reported family health problems, both with children.  Should I have offered some information?  Or is that presumptuous, as I don't really know the whole story.   In fact, in one case, I did, as it was something we had encountered in our family and there was information we had looked at.  I had known that information was reliable (it was from NHS Choices) and we had found it useful. The other case was nothing we had encountered, and so I did not offer anything.   You cannot possibly get the whole story on Facebook, although maybe I assumed in the first case that because we knew about the condition, we did have the full story.

And is there a potential role for health information professionals in "training" people in general, perhaps patient groups (who might be receptive to the idea of web based information, and already be doing it), or community groups?   I imagine those groups themselves are already offering support in finding information, or actually providing trustworthy information, and some have health information professionals working for them, but perhaps others of us can offer our skills.

NHS Choices Information Prescriptions is an interesting service for all sorts of conditions - enter a condition and a postcode and receive information about the condition and local services.

Wednesday, January 21, 2015

Classroom observation


I get to take my younger son to school three mornings a week, not something every parent gets to do.  On the way home recently I found myself thinking about levels of understanding and evidence based practice.    As you do.

The children enter the classroom ten minutes before registration.  On the whiteboard (electronic) is a piece of work.  They do that work on individual whiteboards (the sort that need pens).   It might be writing down the nouns they can see in a picture, or adding adjectives to a sentence.  When ten minutes is up, the bell goes, and grown ups, who are allowed to stay and help with this work, have to go.

For some grown ups, "help" is writing the questions on the whiteboard for their child (the teacher would rather they didn't), for others (including me, sometimes), it is frustration when their child does not engage with the task.

Sometimes the whiteboard work is numbers, and recently it was partitioning numbers - 25 is 2 tens and 5 units, 123 is 1 hundred, 2 tens and 3 units, for example.

My son could not remember what to do.  He had done the work before, and at the time had understood it well enough to explain it to me.  On this occasion, everyone else on his table had made columns, one for hundreds, one for tens and one for units, and then filled them in.  Reading the question on the class whiteboard made me think this was a possible way to do it, but I could not remember how he had done it before.

I suggested he try the table and columns method.  Just before I left for home, though, the teacher mentioned to me that the column way of doing it was what one parent had done, and then everyone on that table had copied it.  I am not sure who copied it - parents or children - but it was not the method they had been shown in class.  That might explain why my lad was reluctant to do it that way, even though he could not remember how he had done it in class.  I wonder where the parent had come across the method?

The child next to him offered to help, but his help was to allow my lad to copy his table of columns.  My lad obviously did not understand what he was seeing but copied it anyway.

Several things occurred to me on the way home.

First, my lad had understood partitioning when he did it the first time, and had explained it to me.  When they had partitioning to do on whiteboards at that time, he had been able to do it.  And now not.  Why not?   Had he forgotten?   Lack of practice since?  What form did his understanding at the time take? The fact that I could not remember what he had explained to me is telling, too!

Then, he did not feel able to use the method that those around him were using.  I could see it made sense, but did he remember that it was not the method they had used before, even though he could not remember that method?

Then, what did the parents see as "help"?  Completion of the task?  Doing it for their child?   However, I am not sure I saw that - even if a parent writes down the questions, they don't write the answer.   Even if it was a parent who thought of the table and columns method of partitioning, it was the child who was filling in the numbers.

As someone involved in higher education, I then started to think about medical students.   They have learnt to do something in a particular way, and they might remember that way.  For example, they have learnt to search Medline in a particular way and might remember it for an exam.  But do they remember why that way is the "best" way, or a good way, at least?  Have I covered that in my teaching?  Can they apply those skills in another context?  They learn to search to complete an exercise, and again to pass an exam, but can they use it to find information for assignments or even, in due course, for patient care?   Do they see that those skills apply in those other contexts?   Can they remember those skills for long enough to use them in another context?  Or if they can't remember those skills, do they at least remember they need them, and go and learn them again?

What do they see as the aim of learning a particular thing?  Just to pass a test or click a box?  What application does it have?  And what happens when they have spent time learning other things, do they still remember it?

Then there is the "see one, do one, teach one" model - that is copying what you have seen.  Can you teach it if you don't understand it?   If you keep up to date and find out about a new way to do it, then do you need to understand what you did before in order to be able to change your practice? 

And having thought of all that, I got home.

Saturday, January 17, 2015

Finding your way

Driving somewhere?  Satnav or map reading, that is the question.

Satnav, pluses and minuses:
  • - Risk that you will just follow instructions (copy what you are told);
  • - You may have no idea how the route is generated;
  • - You may not not know where you are in relation to your destination;
  • + You don't need to make a choice over route;
  • + If you go wrong, the satnav will work out what to do;
  • + You can drive solo with a satnav;
  • + It is easy to get started with a satnav;
  •  - But better if you take time to work out how it functions.

Maps, pluses and minuses:
  • + You know where you are in relation to your destination;
  •  +/- You have to work out how to get there
  • +/- You need to decide which route, if there is a choice to be made;
  • - The map won't tell you where the potential bottlenecks are, although it will tell you which is the most major road if you know the symbol;
  • - You can't read a map and drive at the same time;
  • - If you go wrong, you need to work out yourself what to do.

Our family car recently gained a satnav, a birthday present for one of its drivers.  We have named it Sally Satnav, as it has a female voice. It (she?) has navigated one or other of us around areas we did not know, and worried for us about the correct junction to take off the motorway and what to do next.  And when we missed a turning, Sally recalculated for us.  Our youngest is amused when Sally does not know the name of a road and tells us to "turn left on road", rather than something like "turn left on Leppings Lane".  And we know what time we are likely to arrive.

I remember testing Sally Satnav on a familiar route in the town where we lived at the time.  She wanted to go a different way to the way I had always gone.  It would have worked.

We have had to learn about how Sally works in order to get the most benefit.  How much notice do you get of junctions?  How do you know if that side road is the one?  Can she tell you what lane to be in at large junctions?  Does she know about roadworks or traffic jams?

But, we have had left turns that are almost too sharp to get round, and more than one road that is only just wider than the car.  And cases where the lane markings and the signs at a roundabout say to go one way, and Sally says to go a different way.  Was it a shortcut?   These things, I imagine, are because of the way Sally calculates your route. 

I am much happier with a route if I have done it before, and not that confident at map reading, so a satnav seems ideal for me.  But to find my way around Sheffield, I have decided I prefer maps.  I want to know where I am in the city (north, south, east or west) and if I am near an area I know, and those things are easier with a map.  I begin to build up a picture of the city in my head.   And on longer trips to unfamiliar places with the satnav, I have not enjoyed the feeling of not knowing where I am on a map, not knowing where I am in relation to where I want to be.

Recently, an academic colleague used the image of satnav and map in discussions about levels of understanding of our medical students.   I have been unpacking the image since.

They learn something and can repeat it in an exam, and perhaps explain it to someone, but if they have to apply that thing in a new context, they are less sure.

With a satnav, I know when I have arrived, but don't always understand how I got there.  I am just copying what Sally Satnav is telling me to do.  Some parts of the route might have been difficult (narrow, sharp turns) and I may not know why.   If I go wrong, I can follow new directions, but I don't have to work them out. With a map, I understand how I got there, and where I went on the way, and I also know how near I am to the destination. If I go wrong, it is easier to see where and how it happened, and I have to work out what to do about it.  Both satnav and map require learning - how does Sally Satnav choose a route? - but you can use a satnav without needing to know that sort of thing, whereas maps are not a lot of good if you don't know how to read them and don't study them in advance.

So, I can follow the images in Netanatomy and know the anatomy of the collarbone.  I can answer a question about the anatomy of the collarbone, and tell you about the anatomy of the collarbone. But faced with a patient who has broken their collarbone, how am I going to use that knowledge to help it mend?   I might learn about the mechanism of fracture healing from a YouTube video, but can I use that basic science to advise the patient what they can do while the bone is mending?   And what if it doesn't mend, or they decide to ignore my advice?   How does the science help me decide what to do next?

Final thought in this ramble.  If I know the route, or have done it before, how about using the satnav as a way to follow it?  If I know I apply that basic science, watching the video or looking at the image may enable me to check my basic knowledge before proceeding.

H1N1 influenza in Aosta, Italy


I am off to Italy for a short break later this year, lucky me, so am trying to resuscitate my holiday Italian.   And so I have downloaded the Android app for La Stampa (I tried two others but the full text wasn't free to read - cheapskate!).  And I spotted this piece about cases of H1N1 influenza in Aosta, northern Italy.

Other Italian sources (like ANSA) are reporting the same, and today (18th January) I have found this in FluTrackers, linking to a local site.

It seems that one man has died, although he may have been in hospital with other conditions (the sentence in ANSA with "pluripatologie", but not sure), and a woman is ill.

FluTrackers also lists other cases in Italy here, some of them also this year.

I hope that's right - or I have just caused panic!   If you know it isn't right, or spot something in English, please add a comment! 

Thursday, January 15, 2015

A and E crisis - amended 20th January

Much in the media in recent weeks about the crisis in Accident and Emergency, with articles comparing A and E unfavourably to military hospitals in the Iraq War, and about the longer and longer wait until you are seen.  Here are some things I have come across in the last few days:

Surviving a night in A and E: a doctor's story - an anonymous diary of one doctor's night duty in A and E, giving an insight into the patients and the staff.  Several patients who ought to be somewhere else, some who are there because they are drunk, and some who are in the right place.

A & E crisis: understanding health at a systems level could drive a better NHS - by Terry Young, Professor of Healthcare Systems at Brunel University, arguing that it is the complexity of the system that needs to be tackled, and arguing that it is time to use the tools that have been developed in other complex areas of life, referring to Atul Gawande's recent Reith Lectures.  This article is part of a series - go to the end of this page to see links to others.

A report in the BMJ about a recent report from the Health Foundation and the Nuffield Trust, which finds that most reasons for the problems do not explain the whole story.  You will need a subscription to read this article.

Rather older, dating from July 2013, a Lancet article by John House (I know, I thought that, but not him!), asking experts about the causes of the crisis.  You will need a subscription to read this too.


An Observer article about operations being cancelled because of the crisis.

The work of the King's Fund on urgent and emergency care. This site includes statistics, publications, and an "alternative guide" which examines the myths.

A new "finally", added 20th January - the BBC's A and E Tracker, which indicates how many patients in the four home nations were seen within 4 hours (England is hiding under "How is your local hospital doing?", at least for me, in England).   You can search by postcode to see how your local hospital is faring.

Saturday, January 10, 2015

Search filters

I have been invited to do the literature searching for a research project looking at care of older people in hospital.  The first part of the project is a literature review.  It's fascinating, and very instructive - I have spent a lot of time working to support others who are doing this, and it is quite eye opening to do it for myself!

The literature review is of systematic reviews (SRs) and meta analyses.  I first of all had to devise the strategy, and that was very interesting.  And then decide how to locate the SRs.  And so is that ...

I could:

1.  Use the standard Medline search limits.  There never used to be a limit for systematic reviews, and meta analysis was the nearest fit, although it is not the same thing.  Publication type limits in Medline are not without issue.  There may be references indexed as meta analyses which are not (but which say they are), and there may be things that are meta analyses, but which are not so indexed.  Now there is a SR limit, but in PubMed anyway it is a filter, not a straightforward limit.  Certainly a search in Medline for systematic review.pt. finds zero.

2.  This leads us to the second possibility.  As a way to address the shortcomings of the standard limits, and as a way to get reproducible searches, there are search filters, not part of Medline, strategies which can be bolted on to your subject search.  But there are several SR filters.  Which one to choose?   Some have high sensitivity ("the number of relevant reports identified divided by the total number of relevant reports in existence") and others have high precision ("the number of relevant reports identified divided by the total number of reports identified" - this, and the definition of sensitivity are taken from the Cochrane Handbook). 

 The ISSG Search Filters Resource lists many filters, and evaluates many of them.  I wanted it to recommend one, but of course because it depends what you are aiming for in terms of sensitivity and precision, no one can say "this one is the best".

3.  The third option is not to use a filter or limit at all, but include or exclude things yourself.   If you do this, you know exactly what you have kept.  But, there is a practical consideration, which is that if you get 2000 results, do you have time to scan them all?  This is interesting, as I have certainly said to students I have been helping that they may end up with this sort of number of results!

So, what to do.  I think I will be running all the filters (and the "limit") separately, and merging the results.  I suspect, but don't know, that these separate result sets will overlap but that none will completely include any of the others.  We shall see.  I then plan to remove this merged set from the unlimited/unfiltered results, and then we can sample the remainder and see if any of the sample are an SR or a meta analysis.

I put out a request for experience and expertise on two Jiscmail lists, and the results (I shall summarise for the lists) have informed the above.

Friday, January 09, 2015

(Auto)biography as health literature

When I started out in health librarianship, I am sure there was a book called "At the end of all our work is a patient".  I can't find it at the moment, but I can find an article by Shane Godbolt with that title (1).  And as she was my first boss, that is an excellent thing to find, and perhaps that is what I was thinking of.   That fact attracted me to this field of work, and still does. 

Watching the excellent History Boys recently (excellent, and to some extent familiar, as I was at school then, though not in Sheffield and not looking to go to Oxbridge or do history), I was reminded of Alan Bennett's memoir Untold stories (included in a volume with the same name) (2).  In it he writes about his mother's experience of mental health problems, and his discovery that his grandfather had also had them and had in fact committed suicide.

Perhaps there is material in that memoir that didn't make it into textbooks or research papers, perhaps, I am tempted to say, particularly at the time.  And so this sort of literature adds something to the evidence that informs practice and research.

I was recently in hospital for a week following an accident.  I remember what I was doing in the moments before but not what actually happened at the moment of the accident, as I had a head injury.  I don't remember anything till the end of the following day, when some family members came to visit me.  I remember them being there, but not what we talked about - apparently I repeated myself and was not able to sustain any sort of conversation.  I remember my wife coming back to visit me the following day with a friend, and remember realising that this was not a dream, but again I don't remember what we talked about.  On one visit, family members brought a photo album and apparently I couldn't remember the holiday (in one of my favourite places).  I actually don't remember the photo album being brought, either.  My younger son remembers me talking to him on the phone, but I don't.

My experience as a patient is surely valuable to practitioners, although I cannot know if it is typical (surely it is not as we are all individuals), so therefore the experience of other patients is valuable too.   But so is the experience of families and loved ones.  My family remember things about the visits that I don't, and of course my wife had the dreaded phone call from the paramedics to say what had happened, and would she get there as soon as she could.  They have feelings about the whole thing that I do not, and could not have.  I don't remember ever wondering how I ended up in hospital, or whether I would be ok, although I know my wife wondered that last thing, particularly after that phone call.  Also, I came to realise that it could have been so very much worse. 
 
So, do I as a health librarian buy (or buy access to) biography and autobiography? I read Untold stories while off work recovering.  And fiction, like Ian McEwan's Enduring Love (3), which I read then too (elder son doing it at A level) - plenty of mental health related issues in there.  Do you as a health practitioner or student read (auto)biography and fiction to inform your work or studies?   What can we do with this sort of material as evidence?   Does it end up in reviews?  Patient experience of head injury as related in biography and fiction, that sort of thing.

Let me say that I had the most excellent care at the Northern General Hospital, Sheffield.  And very good follow up care - for an accident that took minutes, I have had a week as an inpatient, and five outpatient visits (two for physiotherapy, two to the fracture clinic and one to the maxillofacial clinic), and one more outpatient visit (to the head injury rehabilitation clinic) to come.  And two GP visits (I chose to have those, although one was for symptoms).   What a lot of health service time for one short accident, and I am grateful it is there. 

References (well, I am a librarian)

(1) Godbolt S. At the end of all our work is a patient.  LA Record, 79(2): 86-9, quoted in Carmel M. (1986). Impact and image: improving the library's contribution. Health Libraries Review, 3: 94-10.  Available from http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2532.1986.320094.x/pdf  (Accessed 9th January 2015).
(2) Bennett, A. (2005). Untold stories, in Untold stories.  London: Profile Books, p.1-125
(3) McEwan, I. (1998). Enduring love. London: Vintage.


Wednesday, December 17, 2014

Updates

A long time has passed since the last post, longer than ought to happen on a blog, but here goes...

Translators without Borders has funding to extend a project to produce Ebola information in local languages, to more west African languages.  Thanks to the excellent HIFA2015 list for this information.

Avian influenza in the Netherlands - De Volkskrant reported yesterday cases in Niedersachsen, Germany, which borders the Netherlands.  It is H5N8.   The Dutch government is maintaining its English language page, which seems not to have any new cases in the country, but which has added information about adjusted government measures.

Wednesday, December 03, 2014

Avian influenza (Vogelgriep)

Just discovered this official Dutch government site, in (of course) Dutch, which has a complete record of the affected sites in the Netherlands,  (go to Overzicht or Inhoud, then Locaties vogelgriep), as well as news and links to official publications.  As well as sites where the virus has been found, it also lists places that have been investigated but nothing found, so not every place listed has had the virus.

I can find nothing new about avian influenza in the UK.  The UK government site about the discovery of the virus in Yorkshire was updated today (3rd December) but that seems to be relating to rules about transport of eggs.


Tuesday, December 02, 2014

Could I get Ebola?

I had already seen this Top 10 things you really need to know about Ebola from the CDC in the United States.  I was in two minds whether to blog about it, as some of the points it makes apply to the USA.  But, of course, the basic medical science applies everywhere.   And also, of course, you the reader might well be in the USA!

I mention it now because last night the BBC broadcast a television programme called "Could I get Ebola?", looking at how likely it is to spread to and  in the UK.  That programme has a similar approach to the CDC poster.  There are links from this iPlayer site to further resources from the BBC and elsewhere.  The programme presenter, Dr Chris van Tulleken, works at one of the hospitals that will receive Ebola cases and has been trained in the management of Ebola.

The basic conclusion of both is that, if you are in the UK or USA, the chances of catching Ebola are very very small and it is very very unlikely that you will catch it.  

The BBC have a regular News about Ebola slot - in addition to World Service radio programme, this also includes downloadable podcasts.

Sunday, November 30, 2014

Avian influenza in the Netherlands - new case in Zouterwoude

I get daily emails from Dutch newspaper De Volkskrant.  So De Volkskrant is the first place that I saw reports of another outbreak of avian influenza in the Netherlands.  The outbreak is in Zoeterwoude (South Holland, south of Leiden),   Exactly which strain of the virus it is is not yet known, with results expected tomorrow (Monday).

Read the article (in Dutch).

The article mentions (if my Dutch is ok!) that this is the fifth case, with five businesses affected, but names only four places  - Hekendorp, Ter Aar, Kamperveen and now Zouterwoude.  The NOS says that there were two businesses affected in Kamperveen, which makes everything add up.

There are English language reports of the Zouterwoude outbreak:  the Guardian and the Dutch government - in English here.  And the Avian Flu Diary blog also has a piece.

Added 2nd December - De Volkskrant reports that the strain found in Zouterwoede is H5N8 (introductory paragraph), something confirmed in the English language news site of the Dutch government.








Friday, November 28, 2014

Not meeting Campylobacter

Much recently in the press about campylobacter in supermarket chicken, for example, here.  That article seems to talk about just supermarket chicken, whereas this one, refers to Food Standards Agency research from a few years ago, research which looked at supermarkets and butchers.  It seems from a quick reading of that second article that there are certain points in the process which make the problem worse.   Campylobacter is present in the chicken anyway.

If that's the case, how can we reduce the risk when cooking?

Food Safety Week 2014 had advice on preparing chicken - http://www.food.gov.uk/news-updates/campaigns/campylobacter/fsw-2014/;

and this Patient.co.uk leaflet about treating infection lists the FSA's 4Cs designed to reduce the risk of food poisoning - http://www.patient.co.uk/health/campylobacter-leaflet.  Cleanliness, cooking, chilling and cross-contamination, but read the whole thing to find out exactly what!


Ebola update - two being tested in the UK

The Guardian is reporting in not a lot of detail that two children are being tested in Newcastle upon Tyne for Ebola and malaria, as a precautionary measure.  They have arrived from Africa but it is not clear where, and Public Health England are of the opinion that Ebola is very unlikely.

The Guardian is also reporting that trials of a vaccine look promising, according to the manufacturer.

Here might be a good time and place to mention the BMJ's news piece from a few weeks ago reminding NHS staff to be on the lookout for Ebola.  The news item refers to a BMJ letter from Bruce Keogh.  Access to the BMJ's content about Ebola is currently free.

Saturday, November 22, 2014

Avian influenza and Ebola update

Avian influenza has been found at a second and third location in the Netherlands:

The second is in Ter Aar - Guardian
The third is in Kamperveen, confirmed as H5N8 - De Volkskrant (in Dutch)

De Volkskrant is also reporting a new case of Ebola in Mali, and has a graphic showing the present situation.  The captions are of course in Dutch, and English language alternatives for current statistics are CDC and WHO.  The CDC site has a graphic on the right.

Friday, November 21, 2014

More resources about Ebola

The BMJ has made all its Ebola resources available free of charge, and these include guidance for healthcare workers, a clinical guide, a video guide, patient information, and all BMJ articles relating to the virus.

And via an article in International Nursing Review, I discovered the Madrid Declaration, arising from an international summit on "Nursing and the Ebola Virus".  The Declaration calls for particular action from governments, and agrees a course of action for the profession.  Those present at the meeting included the International Council of Nursing, several Spanish organisations, expert nurses in the care of Ebola patients, and Medecins Sans Frontieres.

Tuesday, November 18, 2014

More about avian influenza

The UK government has updated its advice (adding an interactive map so you can see if you are in a restriction zone - the information at the end of the page will tell you what has changed).

There is also an official news item about the incident (with a link at the end to the DEFRA announcement).

Most newspapers and news sources look to be covering the story today, but these look worth mentioning:

British Veterinary Association and British Veterinary Poultry Association
National Farmers' Union
WebMD

NHS Choices has information about avian flu (although nothing has been added yet in the light of the incident in East Yorkshire).

Note added at 1842 - the BBC is reporting that the strain found on the farm in Nafferton, East Yorkshire is H5N8, the same one found in other outbreaks in Europe.

In addition to ProMedMail and HealthMap (see yesterday's post), for news, try CIDRAP.

Monday, November 17, 2014

Avian influenza in East Yorkshire

I imagine this post will get a lot of editing!   I will put new information (added since I first posted) in bold.   Last updated at 1822 on 17th November 2014.

According to the BBC, a duck farm in East Yorkshire has had a confirmed case of bird flu.  At the time of writing, the BBC are reporting that it is not H5N1, but not what it is.  BBC World News this morning (Monday, as shown on BBC2) was reporting that there is a current outbreak in Hekendorp in the Netherlands.

The government has updated its avian influenza advice today (17th November).

This next paragraph is dependent on my Dutch being good, but Dutch newspaper De Volkskrant is reporting that H5N8 is the type involved in the Hekendorp outbreak, dangerous to people if they are in prolonged contact with infected animals.  De Volkskrant is not confirming which type has been found in Yorkshire (see http://www.volkskrant.nl/leven/ook-groot-brittannie-getroffen-door-vogelgriep~a3791972/) .  NOS is also reporting that the Dutch outbreak is H5N8.  The Dutch Ministry of Economic Affairs have a news release (entirely reasonably in Dutch) with links to further official documents.

DEFRA is reporting this strain in turkeys in Germany.  So is the Food and Agriculture Organization of the UN, with some discussion of how it arrived there, and a current outbreak in the Republic of Korea.

ProMedMail is reporting the Dutch outbreak but not yet the Yorkshire one.

HealthMap is reporting both.   Click the arrow next to the number of outbreaks for all diseases and you can choose Avian Influenza (you can also choose a specific type).


Saturday, November 15, 2014

Ebola resources

I am planning to resurrect this blog, and here is the first post for some years!

The September 2014 issue of the Health Libraries Group Newsletter contains a list of internet resources concerning the Ebola virus.  You can see the column here.

I have checked the links for the December issue (in preparation), making any changes, and added some new sites including some in French.

I will update this post when the next issue is published.

Thursday, February 18, 2010

Checklists for surgical safety

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

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

Here are some links:

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

Friday, February 05, 2010

Changes to PubMed

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

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

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

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

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

Monday, February 01, 2010

Citizen science

Added to in March 2010.

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

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

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

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

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

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

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

Monday, January 18, 2010

Haiti: health information

Revised 23 February 2010.

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

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

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

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

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

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

More things added 19th January 2010:

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

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

Refugee Health Information Network, items in Creole.

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

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

And another thing added 23 February 2010:

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

Friday, January 08, 2010

EndNote and 2010

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

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

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

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

Thursday, December 17, 2009

Another use for E. coli

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

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

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

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

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

Thursday, December 03, 2009

Trailblazing

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

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

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

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

Thursday, November 26, 2009

Google in consumer news

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

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

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

Friday, November 20, 2009

Nasal spray and Burkholderia cepacia

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

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

For more on B. cepacia, try these:

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

Wednesday, November 18, 2009

Worms in space

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

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

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

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

Tuesday, November 17, 2009

Developing countries and the media

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

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

Tuesday, November 10, 2009

Animals containing human material

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

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

Still here

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

Monday, March 23, 2009

World TB Day

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

Tuesday, March 17, 2009

Malaria resources

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

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

Malariasite – comprehensive site.

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

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

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

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

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

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

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

Malaria – MedlinePlus interactive tutorial with PDF summary.

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

Insecticide treated malaria nets: a WHO position statement]

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


Incidence and statistics

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

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

UNICEF – statistics on prevention, treatment and incidence.

Genomic information

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

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

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

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

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

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.