Tuesday, 8 January 2019

Multiple highlighting using Chrome extensions

Anyone who does literature searching will know it can be a tedious job scanning through potentially hundreds of abstracts to pick out relevant results. When recently going through HDAS results, I thought it would be useful to be able to highlight multiple words at once (more than the one allowed by CTRL + F!) – it would make the whole process much quicker and effective! A short Google later and I found two Chrome extensions that do just that. Both are available for free from the Google Chrome Web Store (links through the titles). So, here are my thoughts on the two, and how I have found them useful:

Overview


The first extension I found, this is very simple to use. To do so, you simply click the icon in the top right of the toolbar, and type the words you wish to find into the box, separated by a space:



Once activated using the on/off switch, it will highlight those words on every page you visit unless you turn it off. However, just be careful because it starts recycling colours after 6 words!


Tips

  1. You can use the colour recycling to your advantage, by distributing any synonyms to every 6 words.
  2. The third word highlights in red, so I find it useful to put a word indicating irrelevance here.


Pros

  • Really quick and intuitive to use!
  • Saves the words until you manually delete them.
  • Not case-sensitive.

Cons

  • Doesn’t support phrase searching, truncation or wildcards.
  • Recycles colours.
  • Doesn’t search within words, so you need to specify each variation e.g. ascit wouldn’t bring back ascites or ascitic – you need to put both.
  • Doesn’t work with pdfs.

Highlight This

(Or, to give it’s full name - Highlight This: finds and marks words in text)

Overview


I actually found this after increasing frustrations with Multi-highlight led me to look elsewhere. It’s not immediately obvious from its page on the Web Store, but this little extension has a lot of functionality and does address many of Multi-highlight’s flaws.

A little more complex to use, you assign words to lists which have a specified colour. However, this means that you can choose the colours you want to assign. To do so, you can either choose from their selection, or be more specific using a HTML colour code.  I use this site https://www.rapidtables.com/web/color/html-color-codes.html to find and copy over the codes. Truncation and wildcards are also supported, as is phrase searching as new words are indicated by a line break, not a space.


Tips



  1. You can highlight synonyms in the same colour, by assigning them to the same list. I’ve found it useful to have an “off-topic” list which highlights in red so I can see irrelevant results more easily.
  2. You can add words to a list simply by highlighting with your mouse and right clicking:

Pros


  • More choice of highlighting colours.
  • Synonyms can be easily highlighted in the same colour.
  • Truncation and wildcards are supported (although it also automatically searches within words – this can be turned off though!).
  • Phrases can be highlighted.
  • Individual lists can be paused, or the whole extension turned off.
  • You don’t have to go into the app to add new words to lists.
  • You can specify which sites it can highlight on.
  • Saves the words until you manually delete them.
  • Not case-sensitive.

Cons


  • Bit trickier, less intuitive and more time consuming to set up (the help page is really useful though).
  • Doesn’t work with pdfs.


All-in-all, I think it’s clear my favourite is Highlight This! However, if you’re after a quick and simple way to highlight only a couple of words, Multi-highlight may still be best for you. They have certainly both helped my results-scanning efficiency.

Have you tried either of these extensions, or maybe some similar ones? Let us know your favourites and any tips and tricks!

Friday, 14 September 2018

Our new Clinical Librarian has started!


Last month we were delighted to welcome Coral Andrews to our team.

Coral joined us as she was completing her MA in Librarianship at University of Sheffield, and has a background in Nursing.

Coral will be working with a number of clinical teams including Cardiology, Cardiac Surgery, Cancer & Haematology, Genetics, Vascular, Transplant and Renal & Urology.

Any useful tips for Coral or any new Clinical Librarians coming into post?




Friday, 19 January 2018

Influenza

This updates an earlier post about "Australian" flu.

This Guardian story has some statistics in it and reports that the present outbreak is not just of the H3N2 "Australian" variant.

Here are some places to find out more about what is happening:

North West Ambulance Service NHS Trust Library and Knowledge Service has produced this guide to sources.

Public Health England has a page about seasonal flu, with links to information from the four nations of the UK, Europe generally and the WHO

Health Protection Scotland, in addition to the link from PHE, has a page about seasonal influenza for this season

Public Health England produce Weekly national flu reports, which include information on hospitalisations, vaccinations and include data from other nations of the UK.


For surveillance data, try PROMED-Mail or the WHO's FluNet.    PROMED-Mail covers all infectious diseases, including outbreaks affecting animals and plants, and FluNet, as the name suggests, covers just influenza.  

CIDRAP, from the University of Minnesota, is useful for information on outbreaks of influenza in the USA.   It also has a more global list of literature.




Friday, 22 December 2017

Finding case reports

I searched PubMed for a rare topic and found 361 references.

Filtering to “case reports" left 197.

Of the 164 not tagged in this way, some do appear to be case reports, with titles involving phrases like “two cases”, “a rare case”.  (See below for a discussion about whether reports of more than one case are a “case report”!).

Why are these 164 not tagged?   A glance at the titles suggests some are case reports.  Some of these will be PubMed Central and some very new, so therefore not indexed.   What about the rest?  The publication type "Case Report" was first used in 2008, but then applied retrospectively back to 1966, although I wonder how consistently it was applied to older material.  

Of the 361, 73 have the word "case" in the title and 20 have “cases”.   Some of those are general articles (“associated malformations… in cases of…”) but some are definitely reporting actual cases.   76 have “cases” in the title or abstract, and some of those are definitely reporting actual cases, without mentioning that in the title.

43 have “case” or “cases” in the title, but are not indexed as Case Reports.  

Some of the items mentioning “case(s)” in the title or abstract could be case control or case series, rather than a case report.   A case series is “A group or series of case reports involving patients who were given similar treatment. Reports of case series usually contain detailed information about the individual patients. This includes demographic information (for example, age, gender, ethnic origin) and information on diagnosis, treatment, response to treatment, and follow-up after treatment.”  (NCI Dictionary of Cancer Terms).   There is a discussion of how this differs from a cohort study in this Annals of Internal Medicine article (subscription needed).   A case control study involves a control group.

I couldn’t find a search filter for case reports (if you know of one, please let me know!).   For HDAS,  
(case or cases).ti,ab may be enough, although that will also find case series and case control studies, as well as things which are nothing to do with specific cases.      

To be more specific, you could try my filter suggested below, although that will miss titles like “two cases”, “a new case”, “a case of”.

Does a case report have to be a single case?   BMJ Case Reports require prospective authors to contact the office if there are more than three cases. Oxford Medical Case Reports and European Heart Journal Case Reports don’t specify, but the latter uses the CARE reporting guideline, which seems to imply a “case report” is one single case.   And certainly cases presented to our Cardiology Education Meeting are single cases.

MeSH defines “Case Reports” as “Clinical presentations that may be followed by evaluative studies that eventually lead to a diagnosis”, which could mean one case or more.

If you don’t want to use just the word case(s), here is my possible filter, for HDAS Medline, with my search topic:

1          ("ectopia cordis").ti,ab            (340)
2          "ECTOPIA CORDIS"/    (108)
3          (1 OR 2)           (355)
4          ((case OR cases) ADJ2 (report OR review)).ti,ab       (533,996)
5          ("Case Reports").pt     (1,857,467)
6          (4 OR 5)           (2,020,257)
 7         (3 AND 6)        (229)
 8         (3 AND 5)        (197)


Changing set 4 to (case or cases).ti,ab makes set 4 3,015,101 but set 7 275.

Why that topic?   Read more about Vanellope Hope Wilkins in the Leicester Mercury (she and her parents have featured in many other media outlets too).    

The HDAS search was run on 22nd December 2017 and all the links worked on that date.

Thursday, 14 December 2017

NOACs and DOACs - a search strategy

Newer anticoagulant drugs, alternatives to warfarin, are a frequent talking point at Cardiology meetings, and I am making links with our Anticoagulation Service, which also needs to know about them.

These drugs are referred to as "novel (or new) oral anticoagulants" or NOACs, or "direct (or direct acting) oral anticoagulants", or DOACs.  They are, as I have heard pointed out, not so "new", now.

But how to find literature about them?   Some literature will of course use these phrases, but some will refer to specific drugs.    I have come up with:


MEDLINE

1.  doac* OR noac*).ti,ab 
2. DABIGATRAN/ OR "FACTOR XA INHIBITORS"/ OR ANTITHROMBINS/      
3. ((direct OR novel) ADJ2 "oral anticoagulant*").ti,ab
4.  “Direct thrombin inhibitor*”
5.  “factor xa inhibitor*” or “fxa inhibitor*”
6.  (dabigatran OR rivaroxaban OR apixaban OR edoxaban OR ximelagatran OR “fondaparinux sodium” OR bivalirudin OR argatroban OR angiox OR pradaxa OR xarelto OR eliquis OR Arixtra OR exembol).ti,ab             
7.  1 OR 2 OR 3 OR 4 OR 5 OR 6)     

EMBASE
1.  (doac* OR noac*).ti,ab 
2.  exp "BLOOD CLOTTING FACTOR 10A INHIBITOR"/ OR exp "THROMBIN INHIBITOR"/
3.  ((direct OR novel) ADJ2 "oral anticoagulant*").ti,ab
4.  “Direct thrombin inhibitor*”
5.  “factor xa inhibitor*” or “fxa inhibitor*”
6.  (dabigatran OR rivaroxaban OR apixaban OR edoxaban OR ximelagatran OR “fondaparinux sodium” OR bivalirudin OR argatroban OR angiox OR pradaxa OR xarelto OR eliquis OR Arixtra OR exembol).ti,ab             
7.  (1 OR 2 OR 3 OR 4 OR 5 OR 6)      

A PowerPoint from Imperial College Healthcare NHS Trust, called To DOAC or not to DOAC (Googling the title finds it!), provided three names (dabigatran, rivaroxaban, apixaban).  I added more names from the BNF.    Embase's indexing is extremely thorough, with a lot more individual drug names which I have not included in the free text search.

This post from Life in the Fast Lane explains some things about the names (as well as looking at the agents from a critical care perspective).

And this article from the Journal of Thrombosis and Haemostasis (subscription required) discusses recommendations for nomenclature.

Wednesday, 6 December 2017

East Midlands Congenital Heart Centre - adding research to a campaign

Our Congenital Heart Centre, at Glenfield Hospital, was scheduled to close, following a proposal from NHS England to decommission services.  Other centres in England were affected by the proposals too.

Following a big local campaign, a synergy of Trust board, communications staff, doctors and nurses, patients, support groups, local MPs, the press and the local community, the Trust presented alternative proposals to NHS England, and last week at a board meeting, NHS England announced that EMCHC would remain open.   

Some agenda items got a lot of national publicity, so many watched the live feed for those.  But we, and colleagues elsewhere too were watching it for this particular item. 

What has this to do with Clinical Librarians?

Well, I set up a weekly Medline alert to look for research articles discussing complications of, and mortality following, congenital heart surgery, and looking for articles using audit or registry data.  I wanted to make sure colleagues knew of any new research that might be useful to our alternative proposals.   The alert went straight to senior clinicians and the project manager, but also to me so I could check the search was finding what I had in mind, and so I could check for things I thought would be worth reading in full.   

UHL's press release about the announcement.

More about the Centre, including press releases and information from the campaign.