Monday, April 27, 2015

More about abstracts that make it no further

Or do they?  This carries on from an earlier post.

I searched Conference Proceedings Citation Index (Web of Science) for the phrase "antibiotic resistance" in titles, published in 2007.  Many of the results were not abstracts, but papers presented at conferences, something useful to remember.   Refining to meeting abstracts left 34 items.

I searched Science Citation Index and Conference Proceedings Citation Index, for all years, to see if I could find a full paper presenting the same results.  Of course, in CPCI there are no abstracts of abstracts, so without checking the abstract, all I had to compare was the authors and title.   I searched for the first author, using their first initial and truncation, and a word or phrase that seemed significant out of the title.  I was assuming, of course, that the first author was involved in any full paper, which might not be true.  It might be better to use all the authors, combined with OR.  Some of them would be the same.   I am also assuming that the full paper would have a similar title to the conference abstract.

For three of the abstracts, there were no other results.

For one, there was one possible match, involving all four authors (but not listed in the same order), but the full paper had a more specific title, although one that could fit the abstract.  The abstract was titled "Antibiotic resistance and penicillin tolerance in clinical isolates of group B streptococcl", and the paper (published two years later) "Antibiotic resistance and penicillin tolerance in ano-vaginal group B streptococci".  The two were not in the same journal.

Interestingly, although a bit of an aside, that abstract title does really say "streptococcl" with an L.  If you search for titles containing that word, you find one other, and WoS suggests that you meant "streptococcAl", with a link to 9000+ results.   I shall report both streptococcl titles!  You would find the paper with other search terms, as correct spellings would appear in the abstract and keywords, but possibly a different story with the meeting abstract.

For one other of the five I searched, I am fairly confident I found a match, different journal, published in 2013, same two authors in the same order, and an abstract that indicates that the data was collected in 2005-2006.

So tiny sample, and problems with methodology, but 1/5 of the abstracts made it to a full paper (and therefore a presentation of the full data), and another 1/5 might have done but we would need to check both items in full to be sure.   The other 3 (methodological problems excepted) went no further. 

Another thought about contacting the authors - I was wondering what exactly the students had said, or asked.   Would it make a difference how specific they were when asking for data, or what language they used?

Practice based learning

Was at the optometrist, at the hospital.   With the optometrist was a doctor, a Specialist Registrar, undertaking ophthalmological training.  They were introduced as an observer, but in fact the optometrist asked several questions as the various tests were done.   What did they notice about what just happened (eye movement, for example)?   Did they notice a particular phenomenon?  What did that phenomenon mean?   And there were explanations, although some longer ones were obviously being saved for later, after I had left.

It is a side effect of being a medical librarian that visits to hospitals are fascinating.   Thank goodness that those visits have not been for me life threatening or life changing.  (Although a visit last year after a fight with a tramline was possibly more potentially life changing than I realised at the time, and it was still fascinating because I had no real idea while I was there what had happened and how I had got there, and no real thought at the time about how much more serious it could have been.  That thought has only come later).

But this one was fascinating for another reason.  It was interesting observing the observer, and observing the teaching (or facilitation of learning, if you would rather).

Would that method work for medical librarians?   The observer did not administer any of the tests, but they did observe and have to understand enough to answer the questions.  What did just happen?   What does it mean?    Could we just demonstrate searching techniques, say, and then ask about it?   Maybe it is preferable to get people doing active things, but if you have to teach a session using a search demonstration (because you are in a seminar room, for example), there are lessons here.  Perhaps later in the day, the observer got to administer the tests, of course that I will never know,

Two thoughts to end.  Interesting that -
- the one asking the questions and the one answering were not from the same professional group, and perhaps interesting that the one answering was a doctor and the one asking was an allied health professional (this may just show how out of date I am, although it is an example of interprofessional learning);

- the observer was not there to comment on the behaviour and technique of the other, as would happen if you went to the GP and a medical student was examining you.

Wednesday, April 22, 2015

Abstracts that make it no further

I recently ran a literature searching tutorial for MSc students undertaking a systematic review as a piece of course work.  I'd seen many of them individually, as had colleagues, and so offered the tutorial to make sure we had not missed anyone.  Of course, those who turned up had already been to see us individually!   The keen ones take up all the offers and the challenge is to reach those who are not so keen, don't feel they can ask for help, or think they are ok.  

I had it mind to talk about general things, but began by asking if they had any specific questions.  This was one: if you find a conference abstract, and you want to use the data in your analysis, and the data in the abstract is not detailed enough, where do you go to get the detailed data?  

I said that you would have to look for an article about the same study.   But how easy is this article to find?   Presumably it has the same authors and title, but maybe not.   If the abstract is of a trial, and the trial is recorded in a registry, the registry entry may well record the article.   

The students also had an example of the same trial being written up in two articles.  Ben Goldacre's work records that many trials never make it into any sort of article.   Both these things are, it seems to me, rather naughty.  Perhaps it is more difficult to find the associated article than I think.  

I had a quick look in Web of Science Core Collection for conference abstracts from 2007 about antimicrobial resistance.   I chose three (which I know is a tiny and unrepresentative sample).   I then looked in PubMed (a proper look would have course been in WoSCC as well, which I shall endeavour to do before too long) for the first two authors, or authors and a title word if that found too many.   One found something very similar which on closer inspection was from 2005!   The other two did not seem to appear.   Perhaps they were never written up in full articles.  If not, why not?   Some subject areas in non biomedical science assign great importance to abstracts and maybe things get no further.  Is antimicrobial resistance an area like that within biomedical science and was there no need to write it up?    If so, then this means it really is important to search for abstracts and not just articles.  Or were the studies not quite up to it?

Of course, a fuller and more systematic investigation is needed!  There is a bit more elsewhere in another post.

If you can't find an article that has the detail you need, and there is not enough detail in the conference abstract, what then?   Is this one of those situations where you contact the authors for more information, as the textbooks about systematic reviewing say?    Interestingly, the students had tried this (not sure if it was for data from a study that had only appeared as an abstract, or not) and had received the reply that the author(s) was/were too busy to help.   Perhaps if you are not a student, but a postdoctoral researcher, you have more luck.

Another quick look in WoSCC turned up two papers by the same team, Yunal Dundar and colleagues from the University of Liverpool, from 2006, one about searching for abstracts and the other comparing data from abstracts and subsequent full articles .  (The links are via DOI and you will need a subscription to read them). 

Both are in the context of health technology assessments and I need to read both before I meet people in the same situation as my MSc students!

Learning patient safety from the airlines

I was already aware of links between patient safety and techniques employed in airlines to ensure safety of aircraft and passengers.   I heard a story of a junior doctor or medical student (can't remember which, but it doesn't matter) who spotted that an x-ray was being displayed the wrong way round.  No one else seemed to notice.  But they did not feel it was their place to say anything.  The possible consequence was that the wrong bit of the patient would be operated on.

So, I was interested to catch on BBC television a piece on training junior doctors to be assertive and challenge their senior colleagues if they were concerned with what those senior colleagues were asking them to do.  Here is the piece on the BBC website.   The training session that was televised involved very sophisticated mannikins, like the sort you learn first aid on only much more lifelike.  The mannikin was a patient with heart problems, the senior doctor was insistent on one course of action, but the junior was sure that the signs and evidence pointed to a different course of action.   They could have given in to authority, but were learning ways to be assertive and make it clear that they were unhappy with the senior's wishes.

Where do airlines fit into this?   In this televised training session was an experienced pilot, and the techniques being taught to the juniors were the sort of thing that pilots are trained to do, the repetition of certain phrases to put across feelings, and general protocols regarding communication, for example. 

A quick web search turns up these two items, both from 2006:

This article in very similar vein from the New York Times

This report from the (US) Agency for Healthcare Research and Quality

My original search also turned up several things which proved to be about pilot projects, not pilots, so I tried the same keywords as the PubMed search (below), which was better, and turned up this counter opinion

A PubMed search for patient safety AND aviation finds 400+ items, which will help to fill in the many gaps in this post.  

Monday, April 20, 2015

What is this? Mystery illness kills 18 in Nigeria

Saw this first in De Volkskrant.  A mystery illness kills 18 in Ondo, Nigeria.   It is not Ebola.   The Volkskrant piece (in Dutch) links to a BBC item, reporting blurred vision, headache and loss of consciousness and that lab tests have ruled out any virus.

So, what is it?   How would you tell?

I checked ProMED-Mail, a useful source of information about infectious disease outbreaks.  A search for Nigeria in the subject finds reports of "undiagnosed illness", with an item from 19th April reporting that it is not Ebola.   An item from 18th April (archive number 20150418.3306299) has the suggestion that it is methanol poisoning.

I also checked Healthmap, and a search for Nigeria as location finds it, and leads to this item from the Guardian  in which the WHO are reporting that the likely cause was weedkiller.  Not the usual Guardian that I cite, but one based in Nigeria.

I suppose it reflects anxiety, and the recent and ongoing Ebola outbreak in neighbouring countries that Ebola or infections were the first thought.  And the symptoms are quite general, in the sense that many illnesses have this sort of symptom.

I shall try to return to this for updates.

Saturday, April 18, 2015

Medline, PubMed, or both?

A question raised in a recent teaching session with MSc students undertaking systematic reviews.  Should I search Medline and PubMed?

Actually, people don't usually ask the question, but instead tell you that they have searched both, or that someone has recommended they do so, or that they have read a review where the reviewers have searched both.

I always say I am not convinced you need to search both.  But am I right?

I know PubMed includes things that Medline does not:

1. Medline indexes some journals (like Science and Nature) selectively, and will not include non biomedical / life science articles.  PubMed, however, does include them.  

I don't think this would matter to a systematic reviewer in healthcare.  

2. Issues of a newly accepted journal that predate the date when it was accepted for indexing in Medline will be included in PubMed.  This might matter, but I have never been convinced that it matters enough to search both databases.

3.  References sent from the publisher, but not yet indexed for Medline.  This of course, might matter, but we have access to what used to be called "PreMedline", and what is now called "Medline In Process", which is these references.  So, if your search includes freetext, you ought to find it without using PubMed.

But what about the fact that PubMed and Medline have interfaces that work in different ways?   Is it possible to find material in one that you did not find in the other, just because of the way the search works?   Surely if you search PubMed using the MeSH browser, and select the same MeSH terms as you did in Medline, you would find the same material.   I have to say, that when I have been doing detailed searching for research projects (and this is not something I do a lot of, I do spend much more time teaching others to do it), I have never used PubMed, and always used Ovid Medline.

Here is a search that I did in Ovid Medline and PubMed.  The syntax is Ovid's, and I used the MeSH browser and Advanced Search in PubMed to replicate it.  The unexploded MeSH heading was not used in the results set, but I just wanted to check that PubMed had exploded the heading in set 1.

Searches run 2230 BST 18.4.15

Ovid Medline
Exp Diabetes Mellitus, Type 2/
Diabetes Mellitus, Type 2/
Type 2 diabetes.ti,ab.
Insulin glargine.ti,ab.

(1 or 3) and 4

(1 or 3)

1542 references in total.  Using RefWorks to remove close duplicates leaves 795. Because author names are not formatted the same, and journal titles in one database are abbreviated and in the other not, finding exact duplicates did not identify many.  However, the first pair of references (that is, a pair that RefWorks thought were duplicates) were not, which makes me wonder if I deleted items that were not duplicates.  

So, there are a few references in PubMed that are not in Ovid Medline, and vice versa.  I need to look in more detail at this to see why.

Removing large numbers of duplicates in RefWorks (I tell my students they can use RefWorks to manage duplicates when working on a systematic review) was interesting!  I changed the default number of references per page to 500, or I would have had 50+ pages to deduplicate.  I also looked at using EndNote Online to do this but it only seems to remove duplicates across the whole library, not a single folder, and as I had been using it for a real project, I decided not to do that.