How to write a manuscript

Transcription

1 How to write a manuscript Get your paper accepted Society for Neuroscience San Diego, CA, USA November 14, 2010 Daniel McGowan, PhD Science Director EdanzGroup Ltd / LiwenBianji

2 Presentation Introduction Section One: Preparations before writing Section Two: Manuscript structure Section Three: Tips for getting accepted Edanz Group Japan 2

3 Why publish? To share your research findings and opinions with the international research community Publication success is linked to funding success and career advancement Many PhD programs require candidates to achieve a set number of peer-reviewed publications Edanz Group Japan 3

4 Publish or perish Funding Bodies Grant Writing Scientists / Clinicians Journal Publication Regularly publishing research findings ensures ongoing grant support for new research Edanz Group Japan 4

5 Increased competition % Journal numbers Journal submissions Year Relative growth from 100% baseline in 1990 Edanz Group Japan 5

6 Section One Preparations before writing How to identify hot topics Study design What do journal editors want? Choosing an appropriate journal Ethical issues Edanz Group Japan 6

7 How to identify hot topics Look for clues unexplained findings, controversies Read the literature, including related fields Attend international meetings Greater interest = Greater competition Identify your advantages and use them Edanz Group Japan 7

8 Study design Get it right first time Have a hypothesis or research question Use appropriate methods and controls Ensure sample sizes are large enough Use appropriate statistical tests Remove investigator/researcher/patient bias Comply with ethical requirements Edanz Group Japan 8

9 Journal Selection Can be the difference between success and rejection What is the main focus of your research and who will be interested in it? (aims and scope, target audience) What are its strengths and weaknesses? (impact factor) How significant are your findings? (impact factor) Are your findings preliminary or are they sufficient to make a story? (publication type) How widely will your research appeal? To researchers in the same field or to the broader scientific community? (target audience) Edanz Group Japan 9

10 Journal Selection Open Access There are a growing number of open access journals and journals offering an open access option Author pays a publication feeto make the article freely available on the journal s website (rather than subscriber pays ) OA articles twice as likelyto be cited as non-os articles in the same journal in the period 4 10 mo after publication OA articles almost three times as likelyto be cited in the period mo after publication (Eysenbach, 2006, PLoS Biology 4(5):e157) Worth considering OA if seeking to reach a wide audience Edanz Group Japan 10

11 Journal Selection High publication frequency Online publication within 10 days of acceptance Impact factor Aims and Scope Brain Research publishes papers reporting interdisciplinary investigations of nervous system structure, function and chemistry at all levels of resolution, from molecular to behavioral and social that are of general interest to the broad community of neuroscientists. Your research: Your priorities Next step: Your research is preliminary but well enough developed to warrant publication You have interesting and novel findings from well controlled experiments Rapid publication Impact factor aim: Low to moderate but a good journal Check for relevant prior publications Make sure you mention future research plans to expand on your current results Edanz Group Japan 11

12 Journal Selection Focus on neurology and neurological science Dedicated to rapid publication Impact factor 9.49 Aims and Scope Brain gives preference to definitive papers on neurology and related clinical disciplines. Brain publishes animal studies but requires that they demonstrate a novel approach, elucidate mechanisms underlying the observations made, and have substantial clinical relevance. Your research: Your research has a clinical focus or translational aspect Your target audience is neurologists You have interesting and novel findings from well controlled experiments Your priorities Rapid publication Impact factor aim: High Next step: Clearly describe the clinical impact or translational potential of your findings Do you have mechanistic data to support any clinical data? Edanz Group Japan 12

13 Publication ethics Unethical behaviorcould lead to rejection and a possible ban 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 13

14 Section Two Manuscript structure The write order Title Abstract Keywords Introduction Materials and Methods Results Display items Statistics Discussion and Conclusions Acknowledgments Abbreviations References Examples Edanz Group Japan 14

15 The write order IMRaDmanuscripts: for maximum clarity and consistency, write in this order: Methods Results Introduction Discussion Title Abstract Write during the research Write afterselecting your target journal Edanz Group Japan 15

16 The importance of your title Hook to catch readers Sells your manuscript to the editor Relevant readers increase citations Edanz Group Japan 16

17 A good title should Convey the main findings of the research Be specific and concise without focusing on only one part of the content Avoidjargon, non-standard abbreviations and unnecessary detail Comply with character limits Some journals also require a short running title Edanz Group Japan 17

18 A good title Poor Degeneration of neurons in the CA3 and DG following OA administration: involvement of a MAPK-dependent pathway in regional-specific neuronal degeneration Better Region-specific neuronal degeneration after okadaic acid administration MAP kinase-dependent neuronal degeneration after okadaic acid administration Edanz Group Japan 18

19 Abstract Many researchers will only read the abstract so must be able to stand alone Must give an accurate summary of your research, and enough information so that readers can understand: What you did Why you did it What your findings are Why your findings are useful and important Edanz Group Japan 19

20 Abstract General rules for abstracts: Within the word limit Avoid technical jargon Avoid abbreviations unless necessary Avoidreferences Structured or unstructured? Always consult the target journal s Guide for Authors to determine allowable length, style and abbreviations Edanz Group Japan 20

21 Keywords Abstracts are usually followed by keywords: Choosing appropriate keywords is important for indexing purposes citations Be specific to your manuscript Avoid general terms Many medical journal require MeSH(Medical Subject Headings) terms Some journals do not allow keywordsin the title Edanz Group Japan 21

22 Keywords Manuscript title: Region-specific neuronal degeneration after okadaicacid administration Poor keywords: neuron, brain, OA (as an abbreviation), regional-specific neuronal degeneration, signaling Better keywords: neurodegenerative diseases; CA1 region, hippocampal; okadaicacid; neurotoxins; MAP kinasesignalingsystem; cell death Edanz Group Japan 22

23 Introduction Must give the reader enough background information to put your work into context Enough information to understand the rationalefor your study is all that is required Do not write a comprehensive literature review of the field Docite reviews that readers can refer to if they want more information Edanz Group Japan 23

24 Introduction Define technical and non-familiar terms Present the problem, research question and/or hypotheses to explain the rationale for the study Briefly explain how you addressed this problem and what was achieved (1 2 sentences for each) Citations must be balanced, current and relevant Edanz Group Japan 24

25 Region-specific neuronal degeneration after okadaic acid administration Daniel P McGowan, Thomas da Costa, Richard Parris, Benjamin Shaw and Kerry A Greer Introduction A number of neurodegenerative diseases are associated with excitotoxic neuronal death [1]. However, the causes of nerve cell damage in these diseases have been hotly contested. The balance between kinaseand phosphatase activity has been implicated in the pathogenesis of these diseases. Statement of the problem The algal toxin okadaicacid (OA), an inhibitor ofprotein phosphatases1and 2A, has been shown tocause hyperphosphorylationof tau, modification of synapse structure, destruction of stablemicrotubules, and apoptosis in neurons [2]. It alsokills a variety of cell types in culture, with disruption of the cell cytoskeleton [3]. Because OA induces neurodegenerative diseaselike phenotypes in animals, it is often used to model these disorders [4] However, although components of the MAP kinasesignalingpathway have been implicated, the mechanism of this action of OA in neurons has remained unknown. Background Rationale In the current study, we investigatedthe signalingpathways affected by OA treatment in vitro, and the areas of the brains of male Wistarrats that were preferentially damaged by OA treatment, using hippocampalslice culture. We found thathippocampalcells, in particular, underwent non-apoptotic cell death via a MAP kinase-dependent mechanism. What was done and found Edanz Group Japan 25

26 Materials and methods What you did Clear subheadings for methods/materials Describe methods in the past tense Novel methods must be described in sufficient detail for a capable researcher to reproduce the experiment Give manufacturers/suppliers and their locations Describe any statistical tests used Established methods can be referenced Edanz Group Japan 26

27 Region-specific neuronal degeneration after okadaic acid administration Daniel P McGowan, Thomas da Costa, Richard Parris, Benjamin Shaw and Kerry A Greer Methods and Materials Materials.Culture media were obtained from Life Technologies (Gaithersburg, MD). Okadaicacid 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 okadaicacid (0-300 nm, Alexis Co.) after washing slice cultures in serum-free medium. Light and electron microscopy. Cultures were fixed in 2.5% glutaraldehyde and 1% formaldehyde, treated with 1% OsO 4 in 0.1M phosphate buffer, ph 7.4, dehydrated in a graded series of ethanol and propylene oxide, and flatembedded in an epoxy resin (DurcupanACM, Fluka, Neu-Ulm, Germany). Semithinsectionswere stainedwithtoluidineblue, and ultrathin sections were stained with1% uranylacetate for 20min and 1% lead citrate for 2min. Statistics.For statistical analysis, 2-tailed Student s ttestwas used to assess the significance of mean differences. Differences were considered significant at a Pvalue of 0.05or less. Clear subheadings Refs used to save space Enough information to reproduce the experiment Statistical test parameters provided Edanz Group Japan 27

28 Results What did you find? Assemble your findings in a logical order to make a story Present your findings in subsections (the same as those in your methods section) Present complementary evidence when possible Describe results in the past tense Refer to figures and tables in the present tense Do not discuss implications do that in the discussion section Do not duplicate data among figures, tables and text Show the results of statistical analyses, (e.g., p values) Edanz Group Japan 28

29 Region-specific neuronal degeneration after okadaic acid administration Daniel P McGowan, Thomas da Costa, Richard Parris, Benjamin Shaw and Kerry A Greer Results Okadaic 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. Clear subheadings Electron microscopy revealed a number of ultrastructuralchanges in hippocampalpyramidal neurons, particularly those in the CA3 region, in slices treated with 300 nmoa 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 infigure 4, the nuclei of pyramidal neurons in the CA1 and CA3 regions Graphics used to save space Involvement of MAPK signalingin the effect of OA. Compared withslices treated with medium only and treated slices at 0 h, slices treated with 300 nmoa showed increasing levelsof phosphorylatedmapk 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 kinaseinhibitor. In addition, the levels ofphosphorylatedtau were higher in OA-treated slices than in control slices Clear comparisons made Edanz Group Japan 29

30 Display items Tables and figures Some readers will only look at the figures and their legends so they must stand alone Figures and tables are the best way to present your results concisely Data shown in figures and tables must be easy to interpret use separate panels if necessary Clearly label all components Show trendlines, scale bars and statistical significance Legends must be able to stand alone Comply with journal guidelines on display items Edanz Group Japan 30

31 Display items Tables and figures Tables are a great way to present large amounts of necessary data with minimal description required Clear concise heading Data divided into categories for clarity Abbreviations defined Edanz Group Japan 31

32 Display items Tables and figures Clear labels Significance indicated Arrows Clear, stand alone legend Scale bars Edanz Group Japan 32

33 Display items Tables and figures Illustrations are a great way to convey anatomy or a proposed model Edanz Group Japan 33

34 Statistics A man has one hand in boiling water The other hand in freezing water He is comfortable on average Edanz Group Japan 34

35 Statistics Statistical analysis is at the heart of scientific inquiry Consider statistical analysis when you design your study. Before you start your research. Data collection Data analysis Interpretation Edanz Group Japan 35

36 Statistics Poor statistics Poor statistics Poor study design e.g., sample size is too small Poor analysis Poor interpretation Data are valid Re-analysis or re-interpretation Difficult to recover Revise manuscript Edanz Group Japan 36

37 Statistics Questions Ask yourself these questions during study design: What are the independent and dependent variables? What is the scale of measurement of the study variables? Consider sample number for power analysis i.e., how many samples will you need? Have I met the assumptionsof the statistical test selected? Edanz Group Japan 37

38 Statistics Basics Reporting statistics in your manuscript: Consult a statistical expert about which test to use! Clearly describe the statistical tests used to analyze data Give the software, version number and maker Indicate the parameters described, e.g., means±s.d Only use the word significant when describing statistically significant differences Report p values, e.g., use p= rather than p<0.05 Edanz Group Japan 38

39 Discussion What does it all mean? Restate your research question and/or any hypotheses presented in the introduction Summarize your main findings make it clear how your study has advanced the field Begin with your most important finding Past tense to describe results (current and published) Present tense to describe their implications Minimize repetition with other sections Describe inconsistencies with other papers Describe the limitations of your study Edanz Group Japan 39

40 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 40

41 Conclusions Restate key findings and their significance Propose future studies that might follow on from your current study Give the reader a take-home message we can now conduct quantitative and functional genetic studies in natural populations (Science) Further, the structures reported here highlight the complex network of proteinprotein and protein-dna interaction (Nature) Edanz Group Japan 41

42 Region-specific neuronal degeneration after okadaic acid administration Daniel P McGowan, Thomas da Costa, Richard Parris, Benjamin Shaw and Kerry A Greer Discussion The mechanisms underlying the excitotoxicneuronal cell death observed in a variety of neurodegenerative diseases have remained unclear, despite a large number of hypotheses being put forward. The neurotoxin OA induces neurodegenerative disease-like phenotypes and non-apoptotic cell death in animals. We investigatedthe signalingpathways involved in induction of this form of cell death in hippocampal slice cultures obtained from. We observed selective neuronal cell death of dentate gyrusneurons in hippocampal slice cultures treated with OA (1 300 nm), occurring in a timeand dose-dependent manner. Neurons in the CA1 3 regions were relatively spared. However, electron microscopy revealed ultrastructuralchanges in pyramidal neurons in the CA3 region These findings suggestthat DG neurons in the hippocampus are particularly sensitive to OA, supporting the results of Wysonget al. [11] who described cell loss in the DG region of mice treated with OA. In contrast to the findings of Yimet al., who studied cultured Neuro2A cells, we observed a significant increase in the levels of phosphorylatedmapk in slices treated with OA. This difference could be due to the fact that. In conclusion, by treating hippocampalslice cultures with OA and a variety of kinaseand phosphataseinhibitors, we show that the excitotoxiccell death induced by this neurotoxin depends on MAPK activation and subsequent signaling. Future work shouldinvestigate the effects of protein kinaseinhibitors on preservation of learning and memory functions in animals treated with OA. Briefly restate the question or problem Restate main findings Put in context of previous work Concluding paragraph with future directions Edanz Group Japan 42

43 References Always format your references: check your target journal s Guide for Authors for the appropriate format Harvard style or Vancouver style or APA Formatting is required both in textand in the references section Use a reference manager like Endnote. Makes it easy to edit, reformat, add or remove references Some journal limit the number of references: check your target journal s Guide for Authors Edanz Group Japan 43

44 References Pay attention to reference 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 44

45 Section Three Tips for getting accepted Your cover letter Recommending reviewers Language Good writing Common language problems What do reviewers look for? Submission Final checks Post-referee revisions Checklist Edanz Group Japan 45

46 Cover letters Journal Editors receive hundreds of manuscripts each month They don t have time to read each manuscript Society journal editors are especially busy as they are usually practicing researchers too Your cover Letter is an opportunity to get the journal editor s attention Edanz Group Japan 46

47 Cover letters Competition for publication space and for editors attention is very high It is not enough to send a manuscript to a journal editor like this: Dear Editor-in-Chief, I am sending you our manuscript entitled Large Scale Analysis of Cell Cycle Regulators in bladder cancer by A. Honda, K. Tanaka, J. Suzuki, and myself. We would like to have the manuscript considered for publication in Pathobiology. Please let me know of your decision at your earliest convenience. With my best regards, Sincerely yours, Shinsuke Izumi, PhD Edanz Group Japan 47

48 Your cover letter General 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 the 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 48

49 Your cover letter Dear Dr Lisberger, Please find enclosed our manuscript entitled Amyloid-like inclusions in the brains of Huntington s disease patients, by McGowan et al., which we would like to submit for publication as a Research Paper in Neuroscience. Recent immunohistochemicalstudies have revealed the presence of neuronal inclusions containing an N-terminal portion of the mutant huntingtinprotein and ubiquitinin the brain tissues of Huntington s disease (HD) patients; however, the role of these inclusions in the disease process has remained unclear. One suspected disease-causing mechanism in Huntington s disease and other polyglutaminedisorders is the potential for the mutant protein to undergo a conformational change to a more stable anti-parallel β-sheet structure To confirm if the immunohistochemically observed huntingtin- and ubiquitin-containing inclusions display amyloid features, we performed Congo red staining and both polarizing and confocalmicroscopy on post-mortem human brain tissues obtained from five HD patients, two AD patients, and two normal controls. Congo red staining revealed a small number of amyloid-like inclusions showing green birefringence by polarized microscopy, in a variety of cortical regions....detected inclusions observed in parallel sections, suggesting that only a relatively small proportion of inclusions in HD adopt an amyloid-like structure. We believe our findings would appeal to a broad audience, such as the readership of Neuroscience. As a wide-reaching journal publishing original research on all aspects of neuroscience We confirm that this manuscript has not been published elsewhere and is not under consideration by another journal. All authors have approved the manuscript and agree with submission to Neuroscience. Wehave read and have abided by the statement of ethical standards for manuscripts submitted to Neuroscience. The authors have no conflicts of interest to declare. Please address all correspondence to. Addressed to editor Title and publication type provided Background What was done and what was found Why this is interesting to the journal s readership Conforms to the journal s requirements Correspondence information Edanz Group Japan 49

50 Language Journal editors are overloaded with quality manuscripts. They may make decisions on manuscripts based on formal criteria, like grammar or spelling. Don't get rejected for avoidable mistakes: make sure your manuscript looks perfect A senior executive at a large international publishing house Spelling errors are a sign of sloppiness, and a sloppy manuscript implies sloppy research A journal s instructions for authors Edanz Group Japan 50

51 Language screening Introduction of language screening protocols to check submissions Editors don t want to send poorly written manuscripts for peer review Editors receive enough well written submissions to reject poorly written manuscripts Edanz Group Japan 51

52 Scientific writing Good scientific writing possesses the following three C s: Clarity Conciseness Correctness (accuracy) Key points: Be as brief as possible without omitting essential details Be as specific as possible Edanz Group Japan 52

53 Scientific writing Common problems Avoid: Spelling and grammatical errors Insufficient detail/vagueness Repetition Redundancy Ambiguity Inconsistency They annoy editors, peer reviewers and readers Edanz Group Japan 53

54 Language Common English problems Tense Articles Plural or singular Proper nouns Hyphen or dash That/which Making comparisons Respectively Between or among Nomenclature Such as/namely Etc. Asian fonts UK or US spelling Presenting numbers Edanz Group Japan 54

55 Simple is best Use simple language: it is often clearer, more precise and more concise than using more complex language Say what you mean in as few words as possible Delete unnecessary words Avoid circular sentences, redundancies and repetition One sentence: one idea Edanz Group Japan 55

56 Reviewers What do they look for? Is the manuscript sufficiently novel? Is the manuscript of broad enough interest? Novelty Significance Aims and Scope Impact Factor Edanz Group Japan 56

57 Reviewers About the research The research question is not interesting Are 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 57

58 Reviewers About the manuscript Are 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 58

59 Submission Final checks Critically self-evaluate could anything be done better? Double check the Guide for Authors Are all files in the correct file format and of the appropriate resolution or size? Is your spelling/grammar correct? Do you have contact information for all authors and have they all approved the manuscript and target journal? Have you written a persuasive cover letter? Edanz Group Japan 59

60 Revisions Post-referee revisions Rejection from journals is an important part of the publication process It is not a negative experience It exists to ensure that your paper is as scientifically robust and complete as possible before joining the collective knowledge as part of the literature Edanz Group Japan 60

61 Revisions Post-referee revisions Only 1.5% of papers are immediately accepted without need for any revisions Complete rejection Journal editor decision Rejection with major revisions Rejection with minor revisions Acceptance Edanz Group Japan 61

62 Response Letter Say thank you to each reviewer Be polite Perform the requested additional experiments/analyses if possible: they will make your paper stronger If you disagree with a reviewer, say why Provide scientifically valid reasons in your rebuttal Respond to every comment Return within the stated deadline or it will be considered a new submission Edanz Group Japan 62

63 Response Letter Common phrases Explain any big structural changes: E.g., We removed table 1 and replaced Figure 3 Clearly indicate, which reviewer and which point you are responding to: E.g., Reviewer 1, comment 3: example example Response: example example Add page and line numbers to make it easy to locate changes: E.g., Please see page 4, line Clearly differentiate between Comments and Responses: Reviewer comment Response Response Deletions in strike through font Additions in font highlighted Reviewer comment Edanz Group Japan 63

64 Summary Checklist for acceptance Work in an area of interest Appropriate study design Compliance with ethical guidelines Appropriate statistical tests Novel and interesting results Appropriate choice of journal Clear, concise, accurate writing Compliance with the Guide for Authors Significance of findings clearly explained Edanz Group Japan 64