1. The Literature
Dr Charlie Hindmarch

2. Who is Charlie Hindmarch?
Extended Science foundation
BSc Marine Biology and Coastal Ecology
MSc Biochemical Pharmacology
PhD Neuroscience and Endocrinology
Physiology, Transcriptomics, Genomics
Bristol, UWE, Universiti Malaya, Fed Rural Uni of Rio de Janeiro
26 peer reviewed papers
Expert reviewer –
J.Neurosci, Neuroendocrinology, Jumec, Endocrinology
Editor of Microarrays Journal
SCIENCE GEEK!

3. Learning objectives
Recognize that ‘The literature’ means different things to different people.
Recognize that ‘The literature’ is accountable and follows a defined pathway that gives you confidence
Recognize that not all literature is equal
Know where to find scientific literature
Know how to use it to make your case

4. Lesson plan What is the scientific literature? What isn’t?
What does scientific literature do?
Are all scientific papers equal?
Who can read my scientific papers?
Peer review process
How do I look for literature?
How do I use the literature?
How do I contribute to the literature?

5. What is the scientific literature? (and what isn’t?)

7. What is the scientific literature? (and what isn’t?)

8. What is the scientific literature? (and what isn’t?)

9. What is the scientific literature? (and what isn’t?)
These various publications cannot be considered part of the scientific literature because they are not accountable for what they publish.
Scientific literature can be defined as the objective reporting of original work in natural and social sciences

10. What is the scientific literature? (and what isn’t?)

11. What is the scientific literature? (and what isn’t?)

13. What is the scientific literature? (and what isn’t?)
Original Scientific Work
Peer reviewed
Scientific Textbooks/Thesis
Highly moderated (independent Ed or Examiner)
CONFIDENCE
Scientific Journalism/blogs
Low moderation (community feedback from geeks)
Scientific Reporting/News
public moderation – low integrity – tomorrows fish-wrapper

14. What is the scientific literature? (and what isn’t?)
Original Scientific Work
Peer reviewed
Original work
Scientists the publish the results and method together with an introduction and discussion of their research activities
Review article
Narrative review
Scientists review a subset of the literature which the author knows to be important for a particular topic
Systematic review
Scientists review all available data on a particular topic – usually involves a meta-analysis (stats) to weight the consensus

15. What does scientific literature do?
Nanos gigantum humeris insidentes
Bernard of Chartres used to compare us to [puny] dwarfs perched on the shoulders of giants. He pointed out that we see more and farther than our predecessors, not because we have keener vision or greater height, but because we are lifted up and borne aloft on their gigantic stature – John of Salisbury 13C
Standing on the shoulders of giants

16. What does scientific literature do?
Accountability
&
Confidence

17. Are all scientific papers equal?

19. Are all scientific papers equal?

20. Are all scientific papers equal?

21. Are all scientific papers equal?

22. Who can read my scientific papers
Free!
Immediate
Online
RCUK FUNDING HAS SPECIFIC POLICIES RELATING TO OPEN ACCESS PUBLISHING

23. Peer review process Rejected Author submits paper Editorial triage

24. Peer Review Up to 3 independent experts in their field
Experts are selected by editors based on their previous publication record
Peer reviewers have to self declare conflicts of interest – current collaborations/grant funding or research conflict
Reviewers have anonymity!!! (Free to criticise)

25. Peer review process Rejected Author submits paper Editorial triage
Editorial decision

26. Peer review process Rejected Author submits paper Editorial triage
Editorial decision
Author revision

27. Peer review process Rejected Author submits paper Editorial triage
Editorial decision
Author revision
Accepted

29. Flaws in peer review process!
Reproducibility
Plagarism
Duplication
MISCONDUCT

30. Dr Haruko Obokata

31. How do I look for literature?

32. How do I look for literature?

33. How do I look for literature?

34. How do I look for literature?

35. How do I look for literature?

36. Title and authors
Citation manager
Abstract format
Downloads
Digital Output Identifier
Keywords
Citations
Associated data

38. How do I look for literature?

39. How do I use the literature?
There is overwhelming evidence that expression of a transcript can differ from cell to cell but until recently it has been technically challenging to determine the entire transcriptome from a cell.
Hindmarch & Ferguson 2015

40. How do I use the literature?
There is overwhelming evidence that expression of a transcript can differ from cell to cell but until recently it has been technically challenging to determine the entire transcriptome from a cell.
There is overwhelming evidence that expression of a transcript can differ from cell to cell (Yamashita et al 2002) but until recently it has been technically challenging to determine the entire transcriptome from a cell.
There is overwhelming evidence that expression of a transcript can differ from cell to cell (Xi et al 1999, Yamashita et al 2002, Fry et al 2006, Hoyda et al 2007) but until recently it has been technically challenging to determine the entire transcriptome from a cell.
Hindmarch & Ferguson 2015

41. How do I use the literature?
The SON experiences a function related remodelling that is necessary for the optimal facilitation of hormone production and delivery (20, 50, 54).
These morphological changes are accompanied by biochemical events such as a strong activation of the cAMP pathway (10) and transcriptional events that extend beyond simple AVP and OXT biogenesis (32, 46).
We have previously shown that WD in both male and female rats is capable of modulating gene expression in the SON (23, 45) and that this modulation is a global transcriptome response (24).
We have also recently demonstrated that many of the genes that are regulated in the SON in response to WD are also altered by lactation (45).

42. How do I use the literature?
The SON experiences a function related remodelling that is necessary for the optimal facilitation of hormone production and delivery (20, 50, 54). These morphological changes are accompanied by biochemical events such as a strong activation of the cAMP pathway (10) and transcriptional events that extend beyond simple AVP and OXT biogenesis (32, 46). We have previously shown that WD in both male and female rats is capable of modulating gene expression in the SON (23, 45) and that this modulation is a global transcriptome response (24). We have also recently demonstrated that many of the genes that are regulated in the SON in response to WD are also altered by lactation (45).

43. Learning objectives
Recognize that ‘The literature’ means different things to different people.
Recognize that ‘The literature’ is accountable and follows a defined pathway that gives you confidence
Recognize that not all literature is equal
Know where to find scientific literature
Know how to use it to make your case
YOU’RE A SCIENTIST
PEER REVIEW
IMPACT F
PUBMED
CITATION

44. &
Accountability
Confidence

45. SCIENTIFIC WRITING – WEEK 16