PubMed 3 - Display Options - Infected Non-union of the Tibia
This is the third in a series of mini-workshops on the subject of using PubMed to
undertake orthopaedic literature searches. We will use the subject of infected non-unions
of the tibia.
Open PubMed and enter the search string infected non-union tibia and run the
search. This search produces a surprisingly small number of papers (26). As we learned in
the previous workshop the best
response to an unexpected search result is to look up Details to see how the search was
The Translation does not show any real surprises but does explain why we
didn't get a very long list. It is significant that "non-union" and
"infected" are not MeSH terms and do not get translated into MeSH terms. This
means that if the article refers to other synonyms (nonunion; osteomyelitis) it will not
be found. In a later workshop we will look at ways to find the appropriate MeSH terms to
ensure that your search is comprehensive. For the present purpose we will do what we did
in the first workshop and find
a good looking article the use the related articles link
From the list below I selected
#6 and looked at the abstract
Efficacy of microsurgical free-tissue transfer in chronic osteomyelitis of
the leg and foot: review of 22 cases. J Reconstr
Microsurg. 1999 May;15(4):239-44. Review.
PMID: 10363546 [PubMed - indexed for MEDLINE]
Circular frames in the management of infected tibial non-union: a
modification of the Papineau technique. Injury. 1996 Jan;27(1):31-3.
PMID: 8746313 [PubMed - indexed for MEDLINE]
The abstract confirms that this article is right on subject.
You may have noticed that there is a collection of pull-down menu boxes above the text. .
eg. Display In the workshop the menu boxes will display their options but are
inactive. On the site, if you select a different option in the display pull-down menu box
you will get a different display.
The treatment of infected non-union of the tibia by
compression-distraction techniques using the Ilizarov external fixator.
Department of Orthopaedic Surgery, Benha Faculty of Medicine, Tanta El Gharbia, Egypt.
Circular external fixation using the Ilizarov apparatus combined with
compression-distraction techniques was used to treat 11 patients with infected non-union
and segmental bone loss of the tibia. The series comprised 8 males and 3 females, with an
average age of 27 years (range 17-51 years). The average number of previous failed
surgical attempts at union was 2 per patient (range 1 to 4). Three infected non-unions
without shortening were treated with complete resection of the site and conversion of the
diaphysis into a segmental defect. The functional results were excellent in 5, good in 3,
fair in 2 and poor in one patient. No additional procedures were used in any of the
To see how this article was classified use the pull-down menu box to
change the display to Citation
The abstract will be displayed again but this time the subject classification is shown
below the text, as MeSH terms. We note that Fractures, Ununited is the MeSH term for
non-union and that Infection is the MeSH term, not infected. So that is why our search
string was not comprehensive. If you wish to be distracted, the most comprehensive search
string for infected non union of the tibia is infection
Click on the Related
Articles link for Hosney & Shawky 1998 This yields 237 articles and we can see
that many of them spell non-union nonunion. Although this collection is not comprehensive
on the subject of infected non-unions of the tibia it is suitable for our purposes. We are
going to see how using the display controls can make it easier to winnow out desirable
papers from a long list. For the purposes of this exercise we are going to make a reading
list of papers that about Ilizarov techniques for management of infected tibial
non-unions. To do this we need to select them out of the list produced by PubMed and
create our own list. There are several functions to help us do this including a clipboard
with a capacity of 500 citations. We are going to select out relevant articles and copy
them to the clipboard prior to displaying the full abstracts.
Open the pull down menu for "Show" and select 500. This control tells the site
how many citations you want to see on one page. It is an advantage to have all the
citations on the same page.
Open the edit menu of your browser and select "Find"
Type in "Ilizarov" and click on Find Next
The browser will advance to the first occurence of the word Ilizarov in the citation list
and highlight it.
If the article is (or might be) on infected non-union of the tibia treated by the
Ilizarov method check the checkbox beside the authors. In the example below articles 1
& 3 were selected because the title indicated they were about Ilizarov treatment of
infected non-union. Article 2 appears to be about treatment of the acute injury.
Bifocal compression-distraction in the acute treatment of grade III open
tibia fractures with bone and soft-tissue loss: a report of 24 cases. J Orthop Trauma. 2004
PMID: 15091269 [PubMed - indexed for MEDLINE]
The treatment of infected nonunions and segmental defects of the tibia by
the methods of Ilizarov. Clin Orthop
Relat Res. 1992 Jul;(280):143-52.
PMID: 1611734 [PubMed - indexed for MEDLINE]
Repeat the "Find Next" and selection steps (3 and 4) until you have gone
through the whole list. You can do this by scrolling down but this way is much faster.
When you have finished click on the "Send To" menu box which can be found at
either the top or bottom of the page. Select Clipboard
The page re-loads. You will note some lines near the top which states how many citations
were placed on the clipboard.
41 items were added to Clipboard.
Clipboard items will be lost after eight hours of inactivity.
The maximum number of Clipboard items is 500.
For the obsessive repeat steps 3-6 using the term "fixator" in case the word
Ilizarov was not used
Open the Clipboard by clicking on the clipboard tab at the top of the page
All the articles sent to the clipboard are now displayed in the default (Summary) format.
Change the display to Abstract
The complete abstract is now displayed for all the items on the clipboard (make sure the
"show" menu has been adjected to display enough articles). If you are
comfortable saving this as an html file you can do this using File/Save As on your
browser. This will have the advantage that all the links (eg to related articles) will be
and you may have to save a number of small Icons and logos for the page to load correctly.
Don't expect the page you save to behave exactly like the site.
Send to text
Save text. This text is saved on the Orthogate server as
there was not enough room to put on this message.
One further display control which you may find helpful is really a filter. If you
select the "Review" button the only articles from the current list which will be
displayed are those characterised by the librarians as reviews. In this instance this is
not a particularly helpful thing to do.
The display controls for PubMed are shown below. They are most useful when you are
trying to select out a subset of articles from a longer list. The drop down menu boxes in
this illustration are functional but they do not control PubMed functions in this
workshop. You can try them out to see what options there are but don't expect any action
The Display Control alters the way in which the article(s) are
displayed. There is a large variety of display types. The ones found most useful are
Summary - the default. This gives Authors, reference, article title, link out to full
text if available, and related article link.
Brief - Cuts down the citation to one line. The title is often truncated.
Abstract - displays the reference, title and abstract of the article(s)
Citation - same as abstract but also displays the NLM's classification of the subject
Link-Out - displays the reference with links out to full text (if available), libraries
which have the journal and free related material such as MedlinePlus (patient information)
or PubMedCentral (free full text - not often available)
Cited in PMC - this only displays articles which are in PubMedCentral and thus have full
text freely available.
Show: this controls how many articles are shown on each page
Sort by: this controls the order in which the articles are displayed.
The initial sorting is by relevance and publication date. Sorting can be done by
Publication Date, Author or Journal
Send to: this control sends the page or selected items from the page
to various destinations
Text - converts the displayed page to text, without links etc. Useful if you want to
incorporate it in a document or message
File - sends a text file to your computer with the currently displayed list. Note, even
if you only have 20 items diplayed per page you will get the whole list if you use this
Clipboard - this save all selected article to the clipboard for later retrieval
Email - I have not used this
RSS feed - or this
Order - selected articles are sent to Loansome Doc and copies can be ordered.
All button: This is the default setting. If you have previously
selected the Review filter (see below) clicking on All will return you to the full list.
The number of article in the full list is noted
Review Button: This imposes a filter on the list. If you click it the
only articles displayed are those classified as Review Articles. This could be a helpful
way to cut down the list but often is not very rewarding. The number is the number of
review articles in the list.