A&HB 3313. SKILLS FOR YOUR GROUP PROJECT: LITERACY, Pubmed , Endnote, Basic Statistics.

1. A&HB 3313.SKILLS FOR YOUR GROUP PROJECT: LITERACY, Pubmed, Endnote, Basic Statistics. Miranda Grounds and Hannah Radley

2. Searching for scientific literature. • Scientific literature is vital – text books, book chapters, journal articles or conference abstracts. • PubMed • UWA library - online access and hardcopies. • Google Scholar • Ask academic consultants – homepages, re-prints. A&HB 3313 Hannah Radley

3. PubMed http://www.ncbi.nlm.nih.gov/PubMed/ • PubMed is a search engine you can use to access scientific journal articles on-line (biological and medical). • Journal articles are not free, it is necessary to use a UWA computer the access the journals. • TASK #1 – Search for articles relevant to your project. • - Academic consultant, Miranda Grounds or me. A&HB 3313 Hannah Radley

4. EndNote http://www.endnote.com/ • EndNote is an excellent referencing programme that allows you to create a library of journal articles  inserts citations and automatically create bibliography. • All computers in G.03 have Endnote 11installed on them. Also, students are entitled to have endnote installed on their personal computers. They can download the installer by going to https://software.webservices.uwa.edu.au/Login.aspx A&HB 3313 Hannah Radley

5. How to make an EndNote library • Open EndNote  Create new library  Save • Manually insert reference OR • Tools  Connect  PubMed • 3 windows – Library, Search window, search results. • Search for article in PubMed through EndNote. • Move search result in EndNote into library  highlight article  Copy all references to. A&HB 3313 Hannah Radley

6. Endnote and Microsoft Word • Open you word document. • Open your endnote library (Office 2007 – Add Ins, Office 2003 – endnote toolbar). • Highly recommend turn off ‘Cite while you write’. • Highlight the appropriate reference in the library. • Insert citation {Radley, 2008 #library}. • When document is complete you can choose a referencing style and create the bibliography  updates citation in text and creates bibliography at end of the document. A&HB 3313 Hannah Radley

7. Endnote - TASK #2 • Practice the following: • Create a new library and import a citation • Manually insert a reference into your library. • Put a citation into a word document. • Create a bibliography in word. • Un-format and re-format your document • Examine different output styles – Author/Date or one specific to a particular journal. A&HB 3313 Hannah Radley

8. Projects - Planning • Page 16 – 21 in handbook (orange sheets). • Group project outline due by 9am on Wednesday 18th March. • Designate tasks among group members. • Plan ahead – book time in CELLCentral and with your supervisors. • Image capture and analysis can be time consuming. A&HB 3313 Hannah Radley

9. Projects – Experimental • Experimental Design: • Sample populations : age & sex matched. • N (number of animals, tissue sections). • Appropriate controls. • Fixation and preparation. • What are you testing and how will you measure it? • In the lab: • Accurate, consistent (reduce variation). • Label everything. • Write everything down as you go (methods). A&HB 3313 Hannah Radley

10. Projects – Descriptive result. TASK #3. A B Figure 1.ChAT (Choline-acetyl transferase) positive neurons in coronal sections through the basal forebrain (indicated by arrow symbol). There is an increase in both the number of positive neurons and staining intensity in B – wildtype male mice in comparison to A- hypogonadal male mice. Scale bar represents 50um for both images. Eleanor Drummond 2008.

11. Projects – Results and statistics • Descriptive statistics – mean, mode, median. • Average of ‘test’ group vs average of ‘control’ group. A&HB 3313 Hannah Radley

12. Projects – Results and statistics Data set has low variation (small standard deviation) A&HB 3313 Hannah Radley

13. Projects – Results and statistics Data set has high variation (large standard deviation) Difference between groups is less convincing. Variation within groups is very important A&HB 3313 Hannah Radley

14. Projects – Results and statistics • Are the groups significantly different (difference did not occur by chance)? • T-test = difference between the means of 2 groups (P<0.05). • Anova = compare multiple groups (assumptions, post hoc tests) • Standard deviation – How much variation there is in the sample group – the spread away from the mean. • Standard Error – SD adjusted for sample size A&HB 3313 Hannah Radley

15. Graph and caption – TASK #4. B * C * B B A A Figure 1. Final bodyweights of 24 week old male C57Bl/10 and mdx mice. There is a significant (*) increase in bodyweight of both C57Bl/10 and mdx mice after consuming a high fat diet (P<0.05). Bars represent standard error and n = 8 mice per group. A,B,C denotes significant difference between groups, groups with different letters are significantly different from each other. A&HB 3313 Hannah Radley

16. Projects – Report & seminar • Abstract (200 words – summary) • Introduction (literature review – citations in text) • Methods (including statistical method) • Results (all graphs and pics labelled appropriately) • Discussion • Conclusion • Acknowledgements • References – use EndNote A&HB 3313 Hannah Radley

17. No lecture on Monday March 30th – all covered in today’s tute. A&HB 3313 Hannah Radley