MBBS 3 PubMed and Harvard Citation Style

Last update April 2013
By Mick Draper

Table of Contents

Our topic for today
Adult stem cells and repair of heart muscle necrosis.

PubMed Introduction
PubMed is a free database of more than 22 million journal articles.
Included are articles on life sciences, medicine, dentistry, & allied health.
Most PubMed citations have subject headings added to help you find articles that include the topics you want.

PubMed goes back to the mid 1940's.

Access to PubMed
The quickest way to get access to the Library's customised version of PubMed is to find it under Quick Links on the Library's home.
This customised version of PubMed has links to the Library's online journal subscriptions. This will allow you to access the full text of articles that are available online, as long as the Library has a subscription to the journal, or the article is free.

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.
Right click on the link, then click on Open in new window, or open in new tab.

Customised PubMed

From outside the university network you will be challenged to enter your username, and password.

Medical Subject Headings (MeSH)
We'll try a very simple search in PubMed using the term vasodilation.

Notice that some citations to journal articles are PubMed - as supplied by publisher,
and others are PubMed - in process.

Neither as supplied by publisher nor in process articles have subject headings added to the PubMed citation.
For most new citations, subject headings are added over the few weeks following their addition to the database.

Looking at older citations you can see these are usually - indexed for MEDLINE.

Citations that are indexed for MEDLINE have subject headings added.
These Medical Subject Headings are usually called MeSH.

Click on the title of an article and then on the MeSH Terms link to find these subject headings.

Logic Grids
I recommend that you use a logic grid to help find the right language and establish the correct logic to organise a systematic search of your topic.
Your logic grid could be on the back of an envelope, but it's better to use a bit of software that allows you to set up a table (e.g. Word)
I use a single cell for each of the concepts in the search.
There isn't any limit to the number of concepts, but remember if you make a search very specific you might not find any article citations.

What is the MeSH for our term adult stem cells?

MeSH Database
Use the drop down menu on PubMed to change the search database to MeSH.

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.
Click on Search or press the Enter key.

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.
You will also find all the citations that have the more specific MeSH Induced Pluripotent Stem Cells!

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.
This process is called explosion and I mention it just in case you come across it in the medical literature.

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.
For now I'll add [mh] to the term in the logic grid.

Not all citations have MeSH, as we saw in our search of PubMed for the term vasodilation.
The most recent citations in PubMed usually don't have MeSH added as it can take several weeks or in some cases quite a few months before the MeSH are added.

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.
What terms are authors who are writing about adult stem cells likely to use in their titles and abstracts to convey the topical contents of their articles?

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]
The * is the truncation symbol in PubMed and so this will find both the singular and plural forms of this phrase.

Notice too, that I've added OR to the end of the first search term in the logic grid.
In fact I've added a space, OR and another space.
This is because when the search is actually put into the PubMed search engine, we want to find citation that have adult stem cells as a MeSH, or adult stem cell or adult stem cells in the title or abstract.

Let's now look at the more specific subject heading Induced Pluripotent Stem Cells in the MeSH Database.
Click on the link 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.
The OR must be in upper case.

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.
Enter this term in the MeSH database.

This search fails to produce any subject headings.
We could try to think of another term, but I usually enter my preferred term into the PubMed database and ask PubMed to search only in the titles of articles.
To do this enter I'll enter the term and add [ti] to the end.

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.
These citations will have MeSH added.
We can then look for an appropriate MeSH.

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.
This is the value of using a logic grid because we can now use 3 simple rules.

There are two ways to get your search in PubMed.

Searching PubMed

Method 1
Paste the terms from the first column into PubMed
(Not into the MeSH Database but into the PubMed database)

adult stem cells[mh] OR adult stem cell*[tiab] OR ips cell*[tiab] OR induced pluripotent stem cell*[tiab]

Click on Search.

To easily remove the first search click on the X near the Search button.

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]

Click on Search.

Now click on Advanced.

All the searches you have done today are displayed.
Don't worry if the search numbers are a bit weird.

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.

Method 2
Logic Rules
Rule 1
Use OR logic to combine all the terms in a single column. Do this for each column of the grid.

Rule 2
Enclose all the terms that you OR together in round brackets.

(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])

Rule 3
Use AND logic to combine the searches from the different columns.

(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])

Enter this search into the PubMed database [not the MeSH database]

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.

Viewing Abstracts and Access to Fulltext
It will be easier to decide which articles you want to pursue if you view the abstracts.
Click on the Display Settings link.

Click in the radio button to the left of Abstract, not Abstract (text)
Click on the Apply button.

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
The Library can (usually) provide you with full text of articles even if there isn't a link to the full text in PubMed.
There is a Document Delivery Request Form at

https://library.adelaide.edu.au/cgi-bin/ddreq

Alternatively you can find this form by clicking on Library A to Z on the Library Home.

Scroll down to Document Delivery.
Click on Request form.

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.
Usually you'll want a journal article by Inter-Library Request, but you can ask for book loans.

The following screen will ask for details of the article.
Don't ask for Rush Delivery, but do give a date when the article is no longer of use to you.
Don't fill in the section on providing an account number, this service is free.
You can expect to wait up to two weeks for the article to arrive in electronic format attached to an email.

Now back to PubMed.

Filtering Results
While there are several ways of limiting search results, you must always be aware that these may lead to missing important articles.
When searching for articles in a new area of investigation it's useful to look at review articles.
These should highlight the most important articles in the field, but be aware that reviews are not appropriate for evidence based practice.
We can limit to review articles by clicking on the link in the top right of the results screen for 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
Click on 5 years or 10 years under the Publication Dates heading to limit your results to the last five years, or ten years respectively.
If you want a different date limit click on custom range and type in the dates that suit you.

Many of the other filters available are MeSH.
This means that if you select these you will lose access to the in process and as supplied by publisher citations because these don't have any MeSH.

The limits will remain in force until you change or remove them.

Selecting Citations and Output
You can select the citations that are of interest by clicking in the boxes to the left of the article titles.

When you have selected all the citations you want, click on the Send to: link.
Click in the radio button to the left of Clipboard.

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.

Related citations
PubMed runs its own searches using words from article titles, abstracts and MeSH to find similar citations.
All you have to do to find these citations is click on the Related citations link under a citation of interest.

This will usually find about 100 other citations that are reasonably similar to the parent record.
The citations are sorted by how similar they are 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.
Click on Send to:
Click in the button to the left of Clipboard.
Click on the Send to Clipboard button.

You can click on the link to Clipboard when you have finished collecting citations.

Save, Email, etc
If you'd like to email these citations to yourself, or save them as a file click on the Send to: link.

Click in the radio button for the option you'd like to use.
Select appropriate format, and sort options and continue.

Later someone else will show you how to save PubMed citations to the EndNote software.
This will allow you to add citations to Word documents, and automatically format bibliographies for your assignments.

Library's EndNote LibGuide includes a section on transferring citations from PubMed to EndNote.

Other PubMed Tutorials
Mick's (more advanced) PubMed tutorial with dental examples

Official PubMed tutorial
It's very long, but you can look at just the parts you want

Tutorials on using particular bits of PubMed including how to save PubMed searches and set up email alerts.

Uni of Adelaide Harvard Citation Style

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!

Here is the Uni of Adelaide Harvard Referencing Guide
Developed by The University of Adelaide Writing Centre

Journal articles
Leistner, DM, Zeiher, AM, 2012 Novel Avenues for Cell Therapy in Acute Myocardial Infarction Circulation Research 110(2) 195-197.
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

Book chapter
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.

Book
Leri, A., Aversa, P. & Frishman, W. 2007. Cardiovascular regeneration and stem cell therapy. Malden, Mass. : Blackwell

My text

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.

My bibliography

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.
Viewed 29th February 2013,
<http://www.expert-reviews.com/loi/erc>

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.
Viewed 1st May 2013,
<circres.ahajournals.org/>

Leri, A., Aversa, P. & Frishman, W. 2007, Cardiovascular regeneration and stem cell therapy, Malden, Mass. : Blackwell