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
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