How to write a paper (1): Organization Kyushu University Warren Raye, PhD

How to write a paper (1):
Organization
Kyushu University
Warren Raye, PhD
Senior Life Sciences Editor
Edanz Group Japan
21 January 2012
A little about me…
Author
Researcher
Virology, Stem Cell Biology, Arthiritis, Immunology & Molecular Biology
Lecturer & teacher
Senior Life Sciences Editor
Edanz Group Japan | 2
Reporting your research
You are telling a story
Beginning → Middle → End
(Introduction)
(Body)
(Conclusion)
MUST be easy to read AND easy to understand
Edanz Group Japan | 3
‘Tell them three times’
3回伝える
回伝える
Introduction/Beginning
Assertion
‘tell them what you are going to tell them,’
Body/Middle
Evidence
‘tell them,’
Conclusion/End
Affirmation
‘tell them again what you told them’.
Edanz Group Japan | 4
Basic manuscript structure
論文の
論文の構造
Expanded IMRaD model
Abstract
Introduction
Assertion
Methods
Results
Evidence
and
Discussion
Affirmation
References
Edanz Group Japan | 5
Variations of IMRaD
Abstract
Introduction
Results
Discussion
Methods
References
Edanz Group Japan | 6
Sections will differ among journals
Summary
Graphical Abstract
Research Highlights
Introduction
Protocols
Results & Discussion
Conclusions
References
Supplementary Information
Edanz Group Japan | 7
And within research fields
Boehmer et al. BMC Cancer 2011, 11:400
Structured Abstract
Background
Methods
Results
Discussion
Conclusions
Kampman et al. Curr Nutr Rep 2012, DOI 10.1007/s13668011-0004-9
Unstructured Abstract
Introduction
What Do We Know?
Ongoing Challenges and Steps to Be Taken
Conclusions
Edanz Group Japan | 8
The ‘write’ order
執筆の順序
For maximum clarity and consistency, write your
manuscript in this order:
Methods
Results
Introduction
Discussion
Write during the research
Write after selecting your target
journal and analyzing results
Abstract
Title
Write last
Edanz Group Japan | 9
Abstract Summarizes your work
アブストラクトに研究内容を要約
Concise (100–300 words)
1–4 sentences – describe problem(s) addressed
1–4 sentences –objectives/hypotheses
1–2 sentences – techniques; AVOID details
1–3 sentences – most important results
Final sentence – concluding statement
Edanz Group Japan | 10
Introduction Why?
緒言に研究課題を記述
What question (problem)
was studied?
The answer to this question is contained
within your Introduction
Beginning → Middle → End
Edanz Group Japan | 11
Introduction Beginning
Sufficient background information
Puts your work into context
Start with a broad background
General
Specific
Comprehensive literature review
Cite reviews
Edanz Group Japan | 12
Introduction Middle
Rationale
The reason(s) for doing this work?
Why is it important?
Justify your work
Explain how you tried to address the problem
(1–2 sentences)
DO NOT state results from your study
Edanz Group Japan | 13
Introduction End
State the methods you plan to use
Clearly and explicitly state 1–3 specific
hypotheses or objectives of your study
Edanz Group Japan | 14
Methods How did you carry out your work?
方法 - どのように研究を行ったか Subheadings
Easier to read
Past tense
New methods must be described in sufficient
detail that they can be reproduced
Established methods can be referenced
Save time and effort
Edanz Group Japan | 15
Methods Common headings & order
Materials/Reagents
Patients/Subjects
Animals
Study design
Ethics declarations
Clinical trial registration number
Treatments
Specific methodologies …
Statistics
Edanz Group Japan | 16
Materials and methods Example
Materials and methods
Materials. Culture media were obtained from Life Technologies
(Gaithersburg, MD). Okadaic acid was purchased from Alexis Company
(Läufelfingen, Switzerland). Antibodies to MEK1/2 and phosphorylated
MAPK were purchased from New England Biolabs (Beverley, MA).
Materials described first
Suppliers/locations given
Induction of cell death. Cell death was induced as described previously [15].
Briefly, cell death was induced by adding okadaic acid (0-300 nM, Alexis Co.)
after washing slice cultures in serum-free medium.
Clear subheadings
Refs used to save space
Light and electron microscopy. Cultures were fixed in 2.5% glutaraldehyde
and 1% formaldehyde, treated with 1% OsO4 in 0.1 M phosphate buffer, pH
7.4, dehydrated in a graded series of ethanol and propylene oxide, and flatembedded in an epoxy resin (Durcupan ACM, Fluka, Neu-Ulm, Germany).
Semithin sections were stained with toluidine blue, and ultrathin sections
were stained with 1% uranyl acetate for 20 min and 1% lead citrate for
2 min.
Enough information to
reproduce the experiment
Statistics. For statistical analysis, 2-tailed Student’s t test was used to assess
the significance of mean differences. Differences were considered significant
at a P value of 0.05 or less.
Statistical test parameters
provided
Edanz Group Japan | 17
Results What did you find?
結果 - 発見したもの Accurate, brief, clear
Use subheadings
Use past tense to describe your results
When referring to figures and tables, use present
tense
DO NOT explain your results
DO NOT duplicate data among figures, tables and
text
Edanz Group Japan | 18
Results Example
Results
Okadaic acid induces death of dentate gyrus neurons selectively.
Hippocampal slice cultures treated with OA (1–300 nM) showed selective
cell death of neurons in the dentate gyrus, but neurons in the CA1–3 regions
were largely unaffected. Cell death occurred in a time- and dose-dependent
manner. Propidium iodide staining of treated slides indicated….
Electron microscopy revealed a number of ultrastructural changes in
hippocampal pyramidal neurons, particularly those in the CA3 region, in
slices treated with 300 nM OA for 24 h (Fig 3). These changes included slight
nuclear aggregations (arrow in Fig 3A), accumulation of mitochondria
around nuclei (arrowheads in Fig 3B) and an increased amount of
endoplasmic reticulum (Fig 3C). As shown in Figure 4, the nuclei of
pyramidal neurons in the CA1 and CA3 regions…
Involvement of MAPK signaling in the effect of OA. Compared with slices
treated with medium only and treated slices at 0 h, slices treated with 300
nM OA showed increasing levels of phosphorylated MAPK at 4 h, 8 h, 16 h
and 24 h, with no corresponding change in the levels of total MAPK. This
increase was prevented in slices that were co-incubated with a protein
kinase inhibitor. In addition, the levels of phosphorylated Tau were higher in
OA-treated slices than in control slices…
Clear subheadings
Graphics used to save
space
Clear comparisons made
Edanz Group Japan | 19
Display items vs. text
Present a large amount of data quickly and
efficiently
Microarrays, flow cytometry, dose-response curves
Present most significant result as a figure or table
Simple descriptive statistics in text
Necessary?
Supplements text
Assists with communication
Edanz Group Japan | 20
Discussion So what?
発見内容が意味するもの
What do these findings
mean?
The answer to this question is in the
Discussion
Beginning → Middle → End
Edanz Group Japan | 21
Discussion Beginning
AVOID repeating the results section
Answer the research question(s) posed
Emphasize the major finding(s) first
What is your major conclusion, based on the
results you have presented?
Edanz Group Japan | 22
Discussion Middle
Interpret your results …
Compare with other studies
Same or different?
Possible reasons why?
Unexpected results
Briefly describe any limitations
Samples sizes
Complementary tests
How could experiments be improved?
Edanz Group Japan | 23
Discussion End
Restate major conclusion(s)
In summary … OR
In conclusion …
Possible real world applications and implications
Suggest future work
“Clinical and research priorities include furthering our understanding of the
pathogenesis of M. pneumoniae-associated CNS disease, development of
more reliable serologic assays, and defining the role of quantitative PCR in
distinguishing acute infection from asymptomatic carriage and prolonged
post-infection shedding”
– Bitun & Richardson Curr Infect Dis Rep 2010, 12:282-290
Pre-emptive defence
Edanz Group Japan | 24
Acknowledgments
You should acknowledge substantive contributions
from individuals and organizations
AVOID being casual, naming every member of your lab,
people unrelated to the work, ex-supervisors
Examples:
We thank Dr. Zhongshu Tang for the photoreceptor 661W cell
line and Dr. Maria M. Campos for technical support and
advice. (Wang et al. Journal of Neuroinflammation 2011,
8:173)
SEARCH is funded by programme grants from Cancer
Research UK (C490/A11019 and C490/A11024). (Ali et al.
Breast Cancer Research 2011, 13:R118)
Edanz Group Japan | 25
Acknowledgments Examples
We really appreciate the fantastic support provided by
all the members of the Maeda lab.
We thank Dr. Zhongshu Tang for the photoreceptor
661W cell line and Dr. Maria M. Campos for technical
support and advice.
Wang et al. Journal of Neuroinflammation 2011, 8:173
SEARCH is funded by programme grants from Cancer
Research UK (C490/A11019 and C490/A11024).
Ali et al. Breast Cancer Research 2011, 13:R118
Edanz Group Japan | 26
Conflicts of Interest
Actual OR perceived
“Authors MUST disclose interests that might APPEAR to affect
their ability to present or review data objectively”
Guidelines
Committee on Publication Ethics (COPE)
European Association of Science Editors (EASE)
Council of Science Editors (CSE)
International Committee of Medical Journal Editors (ICMJE)
Good publication practice for communicating company
sponsored medical research: the GPP2
Guidelines (BMJ 2009, 339:b4330)
Edanz Group Japan | 27
Conflicts of Interest
Acknowledge ALL financial support
Financial or personal connections to your work
Stocks, patents, consultancies, direct relationships
“Warren Raye is a member of a speakers’ bureau, has been a
consultant for, and has received research grants from WSR
Pharmaceuticals. Daniel McGowan is an employee of McG
Pharmaceuticals. Tom da Costa has stated that he has no conflicts of
interest.”
– adapted from Good publication practice for communicating
company sponsored medical research: the GPP2 Guidelines (BMJ 2009,
339:b4330)
Edanz Group Japan | 28
Conflicts of Interest Example
“The Clinical Trial Service Unit has a staff policy of not
accepting honoraria or other payments from the
pharmaceutical industry, except for the reimbursement of
costs to participate in scientific meetings. Coordinating centre
members of the writing committee (R Collins, J Armitage, S
Parish, R Peto) have, therefore, only had such costs
reimbursed. P Sleight has received honoraria and costs for
participating in meetings.”
– Heart Protection Study Collaborative Group The Lancet 2002,
360:7
Edanz Group Japan | 29
Resources and links
参考資料
http://edanzediting.co.jp/kyushu201201
This presentation
Templates
Guidelines
Edanz Group Japan | 30
Any questions?
Edanz Group Japan | 31
Appendix: useful set phrases Abstract
アブストラクトに役立つ表現
Here, we present…
Here, we show…
Here, we report…
In this work we introduce…
Edanz Group Japan | 32
Appendix: useful set phrases Abstract
アブストラクトに役立つ表現
These results show…
To test whether (past tense), we performed....
To examine if (past tense) we (past tense)
We used XX to YY. Using this approach, we
identified ZZ
Edanz Group Japan | 33
Appendix: useful set phrases Introduction
緒言に役立つ表現
We demonstrated previously…
Previous studies have shown that…
We have previously shown that…
The topic of XX has recently been reviewed1.
(insert reference)
To determine whether …
The purpose of this study was …
Edanz Group Japan | 34
Appendix: useful set phrases Introduction
緒言に役立つ表現
Therefore, we tested the hypothesis …
This report describes experiments designed to
determine whether …
Therefore, our first objective in these studies was
to determine whether …
In this study, we sought to extend our
observations and specifically test …
Edanz Group Japan | 35
Appendix: useful set phrases Methods
方法に役立つ表現
To test whether XX (past tense), we
performed....
To examine if XX (paste tense) we performed…
Edanz Group Japan | 36
Appendix: useful set phrases Results
結果に役立つ表現
Among the cases we analyzed…
XX was/were observed….
The results are summarized in Table 1.
Figure 2a shows the effect of X on Y.
Group X showed higher/lower levels of Y than
the control group.
Edanz Group Japan | 37
Appendix: useful set phrases Discussion
考察に役立つ表現
In the current study, we have shown…
In summary…
To conclude…
In conclusion…
In demonstrating XX, our findings show
that/illustrate that…
Taken together these results suggest…
Edanz Group Japan | 38
Appendix: useful set phrases Discussion
考察に役立つ表現
The above data collectively show…
Our data supports the idea that XX
Our study supports the hypothesis that ZZ
Our study is limited by…
There were some limitations to the current
study.
Edanz Group Japan | 39
Appendix: references
文献一覧
Pay attention to the referencing style in text:
Insect hunting is an ideal way to study predatory behavior (Suzuki et al., 2005).
Insect hunting is an ideal way to study predatory behavior (Tanaka and Honda).
Insect hunting is an ideal way to study predatory behavior [1].
Insect hunting is an ideal way to study predatory behavior (1).
Insect hunting is an ideal way to study predatory behavior. [1,2]
Insect hunting is an ideal way to study predatory behavior [1–3].
Insect hunting is an ideal way to study predatory behavior.¹
Tanaka reported that insect hunting was an ideal way to study predatory
behavior (2005).
Edanz Group Japan | 40
Appendix: references
文献一覧
If you need to abbreviate, use the following resources:
BIOSIS (BIOSIS Serial Sources)
CASSI (Chemical Abstracts Service Source Index)
Index Medicus
Title: Advances in drug research
Title: Medicine and science in sports
Abbreviation: Adv. Drug Res.
Abbreviation: Med. Sci. Sports
Some journals limit the number of references: check the Guide
for Authors
Check a sample paper if you are not sure of the style
Referencing styles: APA, Chicago, MLA, ACS, IEEE, Vancouver
Use reference managers such as EndNote or Mendeley
Edanz Group Japan | 41