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MBBS 3 PubMed and Harvard Citation Style
Last update April 2013
Table of Contents
Our topic for today
PubMed goes back to the mid 1940's.
Access to PubMed
Using a search engine to find PubMed won't provide direct links to Uni of Adelaide online journals.
You can also find customised PubMed using The Uni of Adelaide Library Search.
Direct access to the customized version of PubMed by clicking on the link below.
From outside the university network you will be challenged to enter your username, and password.
Notice that some citations to journal articles are PubMed - as supplied by publisher,
Neither as supplied by publisher nor in process articles have subject headings added to the PubMed citation.
Looking at older citations you can see these are usually - indexed for MEDLINE.
Citations that are indexed for MEDLINE have subject headings added.
Click on the title of an article and then on the MeSH Terms link to find these subject headings.
What is the MeSH for our term adult stem cells?
Alternatively open a new PubMed tab/window and select MeSH Database from the More Resources column
Enter a single concept such as adult stem cells.
If your search term is a MeSH or PubMed recognises your term, then the MeSH, or a range of possible MeSH will appear.
In this case adult stem cells is the MeSH.
Note the date this MeSH was first added to PubMed citations.
Scroll down the screen to see where your term fits in a hierarchy of MeSH.
If you search Adult Stem Cells as a MeSH in PubMed then you will find all the citations that have this subject heading.
The ability of PubMed to find more specific subject headings is a powerful tool for finding many citations without necessarily having to type in lots of search terms.
To make sure PubMed will search adult stem cells as a subject heading you'll need to add [mh] to the term in your search.
Not all citations have MeSH, as we saw in our search of PubMed for the term vasodilation.
These citations to recent articles are very important though, because recent articles have the most up to date research findings.
Adding [tiab] to the end of a search term will make PubMed search for terms that are either in the title or in the abstract of an article.
The MeSH database lists synonyms of the MeSH under the heading Entry Terms.
We can add [tiab] to any of these terms in our logic grid, but authors are unlikely to use inverted terms such as stem cells, adult in a title or abstract so we can stick to
adult stem cell[tiab] as well as adult stem cells[tiab]
Notice in the logic grid I've used adult stem cell*[tiab]
Notice too, that I've added OR to the end of the first search term in the logic grid.
Let's now look at the more specific subject heading Induced Pluripotent Stem Cells in the MeSH Database.
There are several Entry Terms that might be useful to add to the logic grid.
We can add ips cell*[tiab] and induced pluripotent stem cell*[tiab] to the logic grid.
The other terms listed under Entry Terms are either inverted or contain one of these two terms.
Note that as far as search terms go you can use upper case or lower case or a mixture.
In a comprehensive search I would also investigate other cell types such as mesenchymal stem cells.
Now let's search for a MeSH for the second concept heart muscle necrosis.
This search fails to produce any subject headings.
The plan here is to find some article citations that have this term in the title, and then to find citations that are indexed for MEDLINE.
Click on a link for an appropriate citation.
Click on the link to the MeSH.
Find an appropriate MeSH for our concept and click on it.
Click on the Link to MeSH.
Click on the link to this subject heading.
Add appropriate terms to the logic grid, remembering that to search for this term as a subject heading we have to add [mh] to the end of the term.
Now we have sorted out the language of the search, the next step is to make sure we have the logic correct.
There are two ways to get your search in PubMed.
adult stem cells[mh] OR adult stem cell*[tiab] OR ips cell*[tiab] OR induced pluripotent stem cell*[tiab]
Click on Search.
Now paste the terms from the second column into PubMed.
myocardial infarction[mh] OR myocardial infarct*[tiab] OR heart muscle necros*[tiab] OR myocardial necros*[tiab]
Now click on Advanced.
All the searches you have done today are displayed.
Click on Add (under the heading Add to builder) for one of the significant searches.
Add the other significant search.
Now that both searches are added to the Search Builder, click on the Search button.
The results appear.
(adult stem cells[mh] OR adult stem cell*[tiab] OR ips cell*[tiab] OR induced pluripotent stem cell*[tiab])
(myocardial infarction[mh] OR myocardial infarct*[tiab] OR heart muscle necros*[tiab] OR myocardial necros*[tiab])
(adult stem cells[mh] OR adult stem cell*[tiab] OR ips cell*[tiab] OR induced pluripotent stem cell*[tiab]) AND (myocardial infarction[mh] OR myocardial infarct*[tiab] OR heart muscle necros*[tiab] OR myocardial necros*[tiab])
Click on Search or press the Enter key.
Compare the result above with the 'naive search' adult stem cells AND heart muscle necrosis.
Return to the systematic search.
Click in the radio button to the left of Abstract, not Abstract (text)
You can now view the abstracts and see links to the full text.
You can click on the Uni of Adelaide Online icons to view the full text.
Getting fulltext when there is no Uni of Adelaide icon
Alternatively you can find this form by clicking on Library A to Z on the Library Home.
Scroll down to Document Delivery.
On the next screen click in the box to agree to abide by the copyright act.
At the bottom of the screen enter your username and password.
The next screen confirms your identity and asks what sort of item and which request type you want.
The following screen will ask for details of the article.
Now back to PubMed.
To remove the limit to review articles click on Review again or on Clear all.
There are quite a few filters available, but for undergraduates the best limits are to articles in English and perhaps to recent articles.
To limit to article written in English first click on Show additional filters.
Click in the box to the left of Languages.
Click on the Show button.
Scroll down and click on the link to English under the Languages heading.
Now the results are limited to citations of articles published in English.
Publication Date Filter
Many of the other filters available are MeSH.
The limits will remain in force until you change or remove them.
When you have selected all the citations you want, click on the Send to: link.
Click on the Add to Clipboard button.
The Clipboard is a temporary holding area where you can collect citations of interest before emailing them, or saving them to a bibliographic database management system.
This will usually find about 100 other citations that are reasonably similar to the parent record.
As above you can select any citations you want to keep by clicking in the boxes to the left of article titles.
You can click on the link to Clipboard when you have finished collecting citations.
Click in the radio button for the option you'd like to use.
Later someone else will show you how to save PubMed citations to the EndNote software.
Other PubMed Tutorials
Official PubMed tutorial
There are many versions of the Harvard citation style. Each version has some difference. The Uni of Adelaide version is the only one that is acceptable for your assignments!
The use of adult stem cells in the repair of myocardial infarction blah blah blah (Leri, Aversa, & Frishman 2007, p. 73). Leistner and Zeiher (2012, p.195 ) state that although myocardial regeneration is modest in humans receiving stem cells, revascularisation is significantly improved. Improved cell signalling may blah blah blah (Beitenes et al 2011, p1021; Leri, Aversa & Frishman 2007, p74)
Note that in the second article listed above under Journal articles, where there are more than 3 authors of a particular work I've entered the citation as Beitenes et al. This isn't in the instructions given in the Guide, but I think it's sensible to use just the first author and et al. Surely if there are a great many authors you aren't expected to put every one of them in the text of your assignment. In the bibliography though, you should include all authors of the article.
Beitnes JO, Lunde K, Brinchmann JE, Aakhus S. 2011, 'Stem cells for cardiac repair in acute myocardial infarction', Expert Review of Cardiovascular Therapy 9(8) 1015-25.
Ellis, S.G. and Bolwell, B.J. 2007, 'Strategies for cytokine modification and stem cell mobilization for acute myocardial infarction', (In) M.S. Penn (ed) Stem cells and myocardial regeneration, Totowa, N.J.: Humana pp 295-284.
Leistner, DM, Zeiher, AM, 2012, 'Novel Avenues for Cell Therapy in Acute Myocardial Infarction', Circulation Research 110(2) 195-197.
Leri, A., Aversa, P. & Frishman, W. 2007, Cardiovascular regeneration and stem cell therapy, Malden, Mass. : Blackwell
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