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The Research Paper: Writing a Manuscript and Getting it Published Kathryn Stockbauer, Ph.D. Manager, Office of Academic Development Department of Pathology.

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Presentation on theme: "The Research Paper: Writing a Manuscript and Getting it Published Kathryn Stockbauer, Ph.D. Manager, Office of Academic Development Department of Pathology."— Presentation transcript:

1 The Research Paper: Writing a Manuscript and Getting it Published Kathryn Stockbauer, Ph.D. Manager, Office of Academic Development Department of Pathology and Genomic Medicine

2 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

3 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

4 GETTING STARTED Choosing a Journal Target audience, readership (translational, clinicians, basic science, cancer?) Likelihood of publication Impact Factor

5 Instructions to Authors GETTING STARTED Found on the home page of each journal Will tell you how to format the manuscript: Length, section titles and order Format figures, tables, and references Figure resolution and layout Nomenclature, abbreviations Not suggestions or guidelines, but instructions.

6 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

7 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

8 THE MANUSCRIPT “Science is a story. Tell it.” Wells, J Cell Biol., 165:757

9 THE MANUSCRIPT Discussion Introduction Materials and Methods Results Like any good narrative, your manuscript will answer: 1. Why? 2. How? 3. What happened? 4. What does it mean?

10 INTRODUCTION The “why” of the paper. What is known in the field (background) What gap does your study fill (hypothesis) End by stating what you will show (overview of results) Three main components:

11 The “how” of the paper. MATERIALS AND METHODS Provide enough detail so that someone can replicate your results Concentrations, incubation times, primer sequences, where your kits were purchased, etc. If it is a common procedure that has been done many times, put “as described in reference X” and reference it

12 DISCUSSION The “what does it mean?” Not a rehashing of the results Puts your findings in the context of the field What did you contribute? First paragraph: State what you have shown directly, declaratively, succinctly (Typically the most difficult section to write)

13 DISCUSSION Discussion We sought to determine whether the vascular pathology is linked to emphysema development and identified iNOS as a key molecular player in the underlying processes. Our data showed that alterations in lung vascular structure and function induced by tobacco smoke preceded emphysema in mice and were independent of hypoxia. We also showed that emphysema and PH occurred independently and are essentially associated with iNOS in different cell types. Finally, our data indicate that targeting iNOS by pharmacological inhibition can improve the functional and structural destruction caused by tobacco smoke. Inducible NOS Inhibition Reverses Tobacco-Smoke-Induced Emphysema and Pulmonary Hypertension in Mice, Seimetz et al Cell 147:

14 DISCUSSION Include: The major findings Their meaning and importance Relate the findings to the field Consider alternative explanations Acknowledge the study’s limitations Clinical importance/relevance Hess, Resp Care, 49:1238

15 DISCUSSION Avoid: Overinterpretation of the results Unwarranted speculation Inflating the importance of your findings Criticizing other studies Overly broad interpretation – stick to your hypothesis Hess, Resp Care, 49:1238 Remember two things: What scientific contribution have you made? Why is it relevant?

16 ABSTRACT If your abstract is not interesting or useful- They will not read the rest of your paper Four components to an abstract: 1.Clearly stated hypothesis 2.Methods used to test hypothesis 3.Summary of what you found 4.Conclusions, and how the study contributes to the unknown (mechanism/pathology of disease)

17 ABSTRACT PIK3R1 (p85a) Is Somatically Mutated at High Frequency in Primary Endometrial Cancer 1.Clearly stated hypothesis 2.Methods used to test hypothesis 3.Summary of findings 4.Conclusions, and how study contributes to the field

18 ABSTRACT Also: Limited to no abbreviations No references Usually words, depending on journal/article type Use present tense to tell what is known in the field and past tense to describe what you show

19 GETTING STARTED 1. Start with an outline of your figures Figure 1: Gene schematic Main Points: 1) Show gene order/arrangement 2) Show transcription start sights Figure 2: Western Blot, WT verses KO Main Points: 1) Gene expressed in WT 2) Gene not expressed in KO

20 GETTING STARTED 2. Write Results first You know what you did – often the easiest to write and good for getting words on paper What you show in Results will determine what you put in M&M, and what you have to Introduce and Discuss 3. After results I go to M&M, then Introduction, Discussion, and Abstract

21 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

22 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

23 SUBMITTING You are ready to submit The Manuscript: 1.Has been read and signed off on by all co-authors 2.Has been proofed for GSP and syntax 3.References reviewed for accuracy 4.Instructions to Authors have been followed

24 SUBMITTING The Cover Letter The cover letter is the first thing the editor will read, after the title, before the abstract U. Neill, JCI 117:3599 It is your first chance to present your work, its implications and how it fits in to the field Do NOT discount the importance of a good cover letter

25 SUBMITTING The cover letter should: U. Neill, JCI 117:3599 Be 3-4 paragraphs in length Introduce the study Briefly explain the premise, why it is important, and what your findings contribute Suggest referees and any exclusions (and why, e.g. direct competitor, known bias, etc.)

26 REVIEW Top Reasons an Article is Rejected: Adapted from G. Bordage, Acad Med, 76:889 1.Inappropriate or incomplete statistics 2.Overinterpretation of results 3.Sample size is too small 4.Incomplete or outdated literature review 5.Sloppy writing, or “poor” manuscripts

27 REVIEW Accepted manuscripts had the following in common: Adapted from G. Bordage, Acad Med, 76:889 1.The relevance and importance of the subject 2.Excellence in writing and data presentation 3.Quality of the study design

28 REVIEW Your paper is sent to 2-3 peers for review Turn around time is typically 1-2 months What types of reviews are you likely to see? Accepted with minor revisions Usually involves clarification to the text Option to resubmit with major revisions Could involve additional experiments Outright rejection Not appropriate for the readership, fatal flaws in design/findings/statistics, etc. Process

29 RESPONSE Important: Use the editor’s and reviewers’ responses to improve your manuscript Address all editor/review comments with: New experimental data Revised text Convincing, POLITE rebuttal as to why the reviewer/editor is not entirely correct

30 RESPONSE Response to Reviewers There is a correct way to present a point-by-point response: Reviewer 1 Comment 1: Materials and Methods section: The authors say that Hardy-Weinberg tests were performed, but no results are shown. It would be useful to have an individual list of polymorphisms not in HWE in each ethnic group, or an indication in the tables, or the proportion markers out of HWE overall should be shown. Response: A supplemental table with each SNP and the corresponding Fisher exact test P- values for each ethnic group has been added. Comment 2: Results section: It is not clear how and why a cut-off of <3% was used to define “rare” NSPs. This needs to be explained. Response: The cut-off lines for rare and common are usually 1% to 5%. In this study, we used 3% as cut-off line because the sample sizes in our adult case control study ranged from 110 to 375 in different ethnic groups of cases and controls. If an SNP had an allele frequency of 3% in one ethnic group, it will be have at least 6.6 alleles in the smallest group of having 110 individuals (e.g. Caucasian controls). It is statistically feasible for 2X2 Chi square test.

31 RESPONSE Response to Reviewers The point-by-point response is included in the cover letter of the resubmission Always be polite and professional in your response, even if you disagree! U. Neill, JCI 117:3599 Thank the editor/reviewers for their helpful suggestions

32 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

33 OVERVIEW 1.Getting Started 2.What goes where (Introduction, Methods, Results, and Discussion) 3.Submitting and Responding to Reviews 4.Writing Tips and Resources Presentation Outline:

34 WRITING WRITING TIPS Think back to freshman composition… Use short, declarative sentences Say what you need to say as simply as possible Be exact and concise Each paragraph has a topic sentence Each paragraph conveys one thought/theme

35 WRITING Genetic basis of virulence Pathogenesis and gene expression SNPs and RopB

36 GETTING STARTED Overcoming Writer’s Block Reasons for Writer’s Block: Too busy, low on the priority list Overwhelmed, don’t know where to start Harsh internal critic, aiming for perfection Wrong environment (distractions, other responsibilities)

37 “There is no such thing as writer’s block for writers whose standards are low enough.” GETTING STARTED Poet William Stafford

38 TIPS: Sit your butt in the chair and write Set aside a certain time every day, every week The first draft is just that – a first draft You will (and should) go through multiple iterations GETTING STARTED

39 RESOURCES There are 10s of 1000s of articles in PubMed and/or journal homepages Find ones you thought were well written, the data was well presented, and emulate them. Even though you’ve may not have written a manuscript before… you’ve read lots of them.

40 RESOURCES Links to articles used to create this presentation Office of Academic Development Website

41 Thank you! Questions?


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