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  1. 1. How to write a manuscript Get your paper accepted Fukuoka University Warren Raye, PhD Senior Life Sciences Editor Edanz Group Japan November 24, 2010
  2. 2. Presentation Introduction Section One: Before you start writing Section Two: Manuscript structure Section Three: Tips for getting accepted Edanz Group Japan | 2
  3. 3. “… the preparation of a scientific paper has lessto do with literary skill than with organization. Ascientific paper is not literature.”How to Write and Publish a Scientific Paper - Robert Day Edanz Group Japan | 3
  4. 4. Why publish (in English)? English is the international language of science Increase the global knowledge base To share your research findings and opinions with the international research community More publications = funding success = career advancement It is your obligation/duty as a scientist! Edanz Group Japan | 4
  5. 5. Publish or perish Funding Bodies Grant Scientists / Writing Clinicians Journal Publication Edanz Group Japan | 5
  6. 6. Increased competition 1400 1200 1000 800 Journal numbers% Journal submissions 600 400 200 0 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 YearRelative growth from 100% baseline in 1990 Edanz Group Japan | 6
  7. 7. Publication procedureSubmit manuscriptEditor is assigned to manuscriptEditor assigns reviewers (associate editors) to inspectReviewers inspect and comment Accept, Reject, ReviseIf accepted subject to revision, manuscript is sent back toauthor for further developmentPossible second review processPublication! Edanz Group Japan | 7
  8. 8. Section One Before you start writing Hot topics Study design What do journal editors want? Choosing an appropriate journal Ethical issues Edanz Group Japan | 8
  9. 9. How to identify hot topicsLook for clues— Read the literature, Attendunexplained findings, including related internationalcontroversies fields meetings Greater interest = Greater competition Identify your advantages and use them Edanz Group Japan | 9
  10. 10. Study design Get it right first time Do you have a hypothesis or research question? Identify the appropriate methods and controls Are your sample sizes (n) large enough? Talk to a Which statistical tests? statistician Does your study comply with ALL ethics requirements Edanz Group Japan | 10
  11. 11. What do journal editors want?Good quality science! Will stand up to peer review Original research (advances a field of research) Interesting to the journal’s readership Active research area (many citations) Clear, concise writing Edanz Group Japan | 11
  12. 12. What do journal editors want?• [Among journal editors], there was a consensus that presentation could indeed make a difference in whether a paper is published or rejected.• A well-planned and executed project will address most manuscript pitfalls. However, the preparation of the manuscript DOES matter, and it can make the difference between acceptance or rejection. Professor Anthony N. DeMaria, MD, MACC Editor-in-Chief, JACC Edanz Group Japan | 12
  13. 13. Journal Selection Appropriate for your message What is the main focus of your research? Who will be interested in your work? How significant are your results? Does your work appeal to researchers in the same field or the broader scientific community? Journal circulation Edanz Group Japan | 13
  14. 14. Journal SelectionFactors to consider? Publishing frequency Access (open or subscriber) Impact factor Prior publications Target audience Publication fees Aims and scope Publication types Rejection rate Lead times Edanz Group Japan | 14
  15. 15. Journal Selection What are the differences? Nature Group Journal 12/year Special Issue: Childhood Obesity studies include ones that primarily influence family Elsevier interactions, food store 6/year policies, and television habits covers normal and 3.366 disordered eating and drinking, dietary attitudes and Elsevier 2.966 practices 12/year experimental nutrition research as it relates to: biochemistry, neurochemistry, molecular biology, toxicology, physiology4.288 and pharmacology Edanz Group Japan | 15
  16. 16. Publication ethicsUnethical behavior could lead to rejection and a possibleban from a target journal. Multiple submissions Redundant publications Plagiarism Data fabrication and falsification Improper use of human subjects and animals in research Improper author contribution Edanz Group Japan | 16
  17. 17. Section Two Manuscript structure Expanded IMRaD model Title Abstract Key words Introduction Methods Results Discussion References Acknowledgments Edanz Group Japan | 17
  18. 18. The ‘write’ orderFor maximum clarity and consistency, write yourmanuscript in this order: Methods Write during the research Results Introduction Discussion Write after selecting your Title target journal Abstract Edanz Group Japan | 18
  19. 19. The importance of your titleHook to catch Sells your Relevant readersreaders manuscript increase citations to the editor Edanz Group Japan | 19
  20. 20. A good title should … Accurately describe your work Be clear Be a suitable label for indexing Be concise (100 characters) Include species, if not human Avoid jargon, abbreviations and acronyms Edanz Group Japan | 20
  21. 21. Examples of titlesPoor Degeneration of neurons in the CA3 and DG following OA administration: involvement of a MAPK-dependent pathway in regional-specific neuronal degenerationBetter Region-specific neuronal degeneration after okadaic acid administration MAP kinase-dependent neuronal degeneration after okadaic acid administration Edanz Group Japan | 21
  22. 22. Good titles“Tumor–host cell interactions in the bone diseaseof myeloma”“Development of pharmacotherapies for drugaddiction: a Rosetta Stone approach”“Reprogramming bacteria to seek and destroy anherbicide”“Stress, memory and amygdala” Edanz Group Japan | 22
  23. 23. Abstract Many researchers will only read the abstract so it must be able to ‘stand alone’ It should give an accurate summary of your research within the specified word limit Structured or unstructured?Always consult your target journal’s Guide for Authorsfor specific requirements Edanz Group Japan | 23
  24. 24. A good Abstract should … State the objectives and scope of the study/investigation Describe the methods employed Summarize the results State the principal conclusions Avoid abbreviations unless necessary Avoid references Edanz Group Japan | 24
  25. 25. Structured AbstractsWhy? Easy for authors to write Easy for readers to understand Good for computerized indexingFollow the IMRaD format:INTRODUCTION, METHODS, RESULTS and DISCUSSIONCONSORT (Consolidated Standards of Reporting Trials)recommends Structured Abstract for RCT papers(randomized controlled trials). Edanz Group Japan | 25
  26. 26. Structured AbstractsMany clinical and medical journals have structuredabstracts: 250 words 300 words 150-250 words 250 words Edanz Group Japan | 26
  27. 27. Structured Abstracts Example 1 Edanz Group Japan | 27
  28. 28. Key wordsAbstracts are usually followed by key words: Choosing appropriate key words is important for indexing purposes → citations Use terms from the Medical Subject Headings (MeSH) list of Index Medicus Avoid general terms Some journals do not allow key words in the title Edanz Group Japan | 28
  29. 29. Key wordsManuscript title:Region-specific neuronal degeneration after okadaic acidadministrationPoor key words:neuron, brain, OA (as an abbreviation), regional-specificneuronal degeneration, signalingBetter key words:neurodegenerative diseases; CA1 region; hippocampal;okadaic acid; neurotoxins; MAP kinase signaling system;cell death Edanz Group Japan | 29
  30. 30. Introduction What question (problem) was studied? The answer to this question is contained within your Introduction Edanz Group Japan | 30
  31. 31. Introduction Provide background information to put your work into context What is the rationale/reason for your study? DO NOT write a comprehensive literature review of the field DO cite reviews that readers can refer to if they want more information Edanz Group Japan | 31
  32. 32. Introduction DO NOT state results from your study Briefly explain how you addressed the problem (1–2 sentences) Clearly state the aims of your study Citations must be balanced, current and relevant Edanz Group Japan | 32
  33. 33. Introduction Helpful phrases To determine whether … The purpose of this study was … 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 | 33
  34. 34. Materials and methods What you did Clear subheadings Describe methods in the past tense New methods must be described in sufficient detail for a capable researcher to reproduce the experiment Established methods can be referenced Give manufacturers/suppliers and their locations (city, state, country) Describe statistical tests used Edanz Group Japan | 34
  35. 35. The proteoglycan biglycan regulates expression of the B cell chemoattractant CXCL13 and aggravates murine lupus nephritis Kristin Moreth, Rebekka Brodbeck, Andrea Babelova et al.Clearsubheadings Established methods New methods The Journal of Clinical Investigation (doi:10.1172/JCI42213) Edanz Group Japan | 35
  36. 36. Results What did you find? Assemble your findings in a logical order to ‘make a story’ Use subheadings (similar to the methods section) Describe results in the past tense Refer to figures and tables in the present tense Simply present the facts, DO NOT discuss your results DO NOT duplicate data among figures, tables and text Include the results of statistical analyses, (e.g. P-values) in the text Edanz Group Japan | 36
  37. 37. The proteoglycan biglycan regulates expression of the B cell chemoattractant CXCL13 and aggravates murine lupus nephritis Kristin Moreth, Rebekka Brodbeck, Andrea Babelova et al. Subheading Refer to display itemsStatistics (Tables & Figures) The Journal of Clinical Investigation (doi:10.1172/JCI42213) Edanz Group Japan | 37
  38. 38. Display items Tables and figures Some readers will only look at your figures and their legends Figures and tables are VERY EFFECTIVE Data in figures and tables must be easy to understand — use separate panels if necessary Avoid duplication Clearly label all parts of your figure or table Include trendlines, scale bars and statistical significance Legends must be able to ‘stand alone’: write them in the present tense (except when describing methods) Must comply with journal guidelines Edanz Group Japan | 38
  39. 39. Display items Tables Tables are a great way to present large amounts of necessary data with minimal description requiredThe Journal of Clinical Investigation (doi:10.1172/JCI42213) Edanz Group Japan | 39
  40. 40. Display items FiguresFigure 1Overexpression of biglycan in the plasma and kidneys of patients suffering from LN.(A) Immunoblots for biglycan protein core after semipurification of 0.2 ml plasma from healthy controls (Cont) and patients with class IV LN followed by chondroitinase ABC digestion. Tostandardize the assay, 0.3 µg of intact biglycan (containing protein core and glycosaminoglycan chains) was added to plasma samples from a healthy control (Cont. 0.3) and a LN patient (LN0.3) prior to semipurification. All samples were purified simultaneously and under the same conditions. Standard (St) contained 0.3 µg of biglycan that was digested with chondroitinase ABConly. (B) Semiquantification of plasma biglycan calculated with consideration of assay recovery. The net biglycan gain was calculated by subtracting the control’s band intensity from that ofCont 0.3, or LN from LN 0.3, and expressed as a percentage of optical density as denominated by standard. Data are given as mean ± SD. *P < 0.05. (C and D) Correlations between levelsof plasma biglycan and albuminuria (C) or plasma CXCL13 (D) in individuals with LN versus healthy controls. (E–J) Immunostaining for biglycan (APAAP, red color) in renal sections from LNpatients (E–G) and healthy controls (H and I). Insert (G) shows a magnified view of an area with infiltrating mononuclear cells positive for biglycan. Counterstaining was done with Meyer’shematoxylin. The negative control (J) was performed in renal sections from LN patients by using an antigen-preadsorbed (human biglycan) antiserum. Scale bars indicate the respectivemagnifications. The Journal of Clinical Investigation (doi:10.1172/JCI42213) Edanz Group Japan | 40
  41. 41. StatisticsStatistical analysis is at the heart of scientific inquiryConsider statistical analysis when you design yourstudy. Before you start your research. Data Data Interpretation collection analysis Edanz Group Japan | 41
  42. 42. Statistics Poor statistics Poor statistics Poor study Poor analysis Poor interpretation design Data are valid e.g., sample size is too small Re-analysis or re-interpretation Difficult to recover… Revise manuscript Edanz Group Japan | 42
  43. 43. Statistics Basics Consult an expert about which test to use! Clearly describe the statistical tests used to analyze data Give the software, version number and maker of the statistical package that was used E.g. SPSS 11.0; SPSS Inc., Chicago, IL, USA Only use the word “significant” when describing statistically significant differences Alternatives: notable, substantial, marked Edanz Group Japan | 43
  44. 44. Statistics A few rulesUse appropriate amount of precision:Life expectancy of 22.085 years → 22 yearsAlways give numerator and denominator. E.g., 25% (650/2958)Avoid using percentages to summarize small samplesBe very clear with percentages within subgroups:“Of the 1000 patients, 800 (80%) were women; (31%) had a BMIof…” “Of the 1000 patients, 800 (80%) were women; of these, 250 (31%) had a BMI of…”Book As a full guide see the excellent book: How to report statistics in medicine by Thomas A. Lang and Michelle Secic (ACP Press, Second Edition) Edanz Group Japan | 44
  45. 45. Discussion What do these findings mean? The answer to this question is in the Discussion. Edanz Group Japan | 45
  46. 46. Discussion What does it all mean?The most difficult section for most authors to write.Present the principles, relationships and generalizationsshown by the results.Summarize and discuss your results – DO NOT justrepeat themInclude a beginning, middle, and end.Past tense to describe results (current and published)Present tense to describe their implicationsDiscuss other studies but only in the context of yourresults Edanz Group Japan | 46
  47. 47. Discussion Be humble Don’t overstate the importance of your results Our findings prove that… Our findings show that… Our findings suggest that… Edanz Group Japan | 47
  48. 48. Discussion BeginningAnswer the research questionBegin with a signal We found that … Blood pressure increased in patients who …Give your conclusions, based on your resultsGive your main result first Edanz Group Japan | 48
  49. 49. Discussion MiddleInterpret your resultsDiscuss key studies relevant to your workCompare your work with others’ workPresent ambiguous results and discrepancies with otherstudies objectivelyExplain unexpected findings to the best of your abilityDescribe limitations briefly Edanz Group Japan | 49
  50. 50. Discussion EndWrite a strong conclusionBegin with a signal In summary … In conclusion …Mention possible applications, implications andspeculation, if appropriateSuggest future work, if necessaryUse present tense except when making comparison toprevious studies or results Edanz Group Japan | 50
  51. 51. AcknowledgmentsThank people who helped with the research BUT who donot qualify for authorshipGive information on Grants and Funding including universityGive Grant numbersWrite funding organization names in fullIdentify who received funding for whatInclude those that provided intellectual assistance, technicalhelp (including writing and data analyses), specialequipment or materials. Edanz Group Japan | 51
  52. 52. References Always format your references: check your target journal’s Guide for Authors for the appropriate format Formatting is required both in text for citations and in the references section Use reference management software whenever possible (RefWorks, Mendeley, EndNote, Zotero, Papers) I highly recommend EndNote Edanz Group Japan | 52
  53. 53. Section Three Tips for getting acceptedCover letterRecommending reviewersLanguageWhat do reviewers look for?SubmissionFinal checksChecklist Edanz Group Japan | 53
  54. 54. Section Three General TipsOutlineConsult a statisticianGet IRB approvalSpell checkConsult grammar and writing websitesBuy the AMA Manual of StyleUse an editor Edanz Group Japan | 54Remember the question
  55. 55. Section Three General TipsInclude one thought per sentence, one idea perparagraph.Keep words simple. Be concise.Avoid adjectives and too much description. Keep yoursentences short (about 22 words).Use transitions and key wordsUse subject-verb-object construction and the active voicewhenever possible Edanz Group Japan | 55
  56. 56. Your cover letterGeneral rules for cover letters: Address to the editor personally Begin by giving your manuscript title and publication type Give a brief background, rationale and description of results Explain why your findings are important and why they would be of interest to the journal’s target audience Consult the journal’s Guide for Authors for cover letter requirements (e.g., disclosures, statements, potential reviewers) Give corresponding author details Edanz Group Japan | 56
  57. 57. Reviewers Recommendations and exclusionsRecommend Your work supports their hypotheses and ideas International collaborators in the same fieldExclude Competitors: researchers working on the same research question The findings in your manuscript are opposite to their findings or ideas Edanz Group Japan | 57
  58. 58. Reviewers What do they look for?Is the manuscript sufficiently novel?Is the manuscript of broad enough interest? Aims and Scope Impact Factor Novelty Significance Edanz Group Japan | 58
  59. 59. Reviewers About the researchThe research question is not interestingAre the methods used appropriate?Are any additional experiments/analyses necessary?Are the statistical tests used appropriate?Are all possible interpretations of the data considered?The data does not support the conclusion Edanz Group Japan | 59
  60. 60. Reviewers About the manuscriptAre the rationale and objectives defined? Is enough background given to understand the rationale?Could a capable researcher reproduce the experiments?Are the results clearly explained and in the best format?Are the findings described in context?Are the limitations discussed?Are the conclusions supported?Is the literature cited appropriate?Are there contradictions within the manuscript? Edanz Group Japan | 60
  61. 61. Revisions Rapid rejection Failure to state a hypothesis Not answering the hypothesis Contradictions within the manuscript Superficial or rambling discussion Inconsistent use of terms Conclusion that is not supported by the data 61
  62. 62. Revisions Post-referee revisionsOnly 1.5% of papers are immediately accepted withoutneed for any revisions Complete rejectionJournal editor Rejection with major revisions decision Rejection with minor revisions Acceptance Edanz Group Japan | 62
  63. 63. Summary Checklist for acceptance Appropriate study design Compliance with ethics guidelines Appropriate statistical tests Novel and interesting results Clear, concise, accurate writing Compliance with the Guide for Authors Significance of findings explained Appropriate choice of journal Edanz Group Japan | 63
  64. 64. Thank youGood luck!
  65. 65. Appendix: useful set phrases AbstractHere, we present…Here, we show…Here, we report…In this work we introduce… Edanz Group Japan | 65
  66. 66. Appendix: useful set phrases AbstractThese 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, weidentified ZZ Edanz Group Japan | 66
  67. 67. Appendix: useful set phrases Introduction We demonstrated previously… Previous studies have shown that… We have previously shown that… The topic of XX has recently been reviewed1. (insert reference) There are several challenges to the study of XX: first… second… Edanz Group Japan | 67
  68. 68. Appendix: useful set phrases Methods To test whether XX (past tense), we performed.... To examine if XX (paste tense) we performed… Edanz Group Japan | 68
  69. 69. Appendix: useful set phrases Results 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 | 69
  70. 70. Appendix: useful set phrases DiscussionIn the current study, we have shown…In summary…To conclude…In conclusion…In demonstrating XX, our findings showthat/illustrate that…Taken together these results suggest… Edanz Group Japan | 70
  71. 71. Appendix: useful set phrases Discussion 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 | 71
  72. 72. Appendix: useful set phrases Acknowledgments The authors wish to thank NAME for WHAT. This work was supported by funds from… We acknowledge the contribution of NAME for WHAT… Edanz Group Japan | 72