Scientific Writing 101

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A general overview of composing a scientific article for publication in a peer reviewed journal

A general overview of composing a scientific article for publication in a peer reviewed journal

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  • 1. Scientific Writing 101 “ In science the credit goes to the man who convinces the world, not to the man to whom the idea first occurs.” -Sir Francis Darwin Parham Mirshahpanah 20 July, 2007
  • 2. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 3. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 4. Journal Selection Aims & Scope Reference Relevance Impact Factor Editorial Board Scientific class: i.e. biology, chemistry, etc… Clinical application: derm, oncology, cardiology, etc… Quality of data: novelty, value to scientific community Utilize familiar names: references & associations Correspondence type: letter, original article, review… Similar journal as the majority of your references
  • 5. Getting started: formatting Refer to journal home page for individual formatting styles; varies by journal Immunity
    • Title
    • Authors & Affiliations; corresponding author
    • Running Title (displayed in Journal TOC)
    • Abstract/ Summary
    • Introduction
    • Results
    • Discussion
    • Materials & Methods
    • References
    • Figure Legends
    • Tables & Figures
    • Total number of display items
    • High resolution images (300-500 dpi minimum)
    • color versus b/w
    • MS Word/ Excel/ PPT/ PDF
    • Display item configuration: heading, body, description
    • References: textual reference and bibliography formatting
    Additional factors to consider:
  • 6. Getting started: formatting JBC Contact Dermatitis Gene Therapy Different journals have varying aesthetic properties that are handled by publisher and not to be considered by author
  • 7. Getting started: formatting Submission Proof
  • 8. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 9. Getting started: data Choose the course of presentation based on the highest added value to the scientific community, which will also yield the optimal journal Develop an outline & order data to support story What information do you have and how can you best present it? Animal model Chemistry Molecular biology
  • 10. Figures: basics After your abstract, readers will look to figures to gain the most information with the least time investment; therefore your figures should accurately depict and explain your findings in the simplest possible form
    • Consider:
    • axes/ titles
      • labeling
      • values
    • breaks to amplify points of interest
    • balanced amount of information
    • consistency (c o l o r s and symbols)
    Mirshahpanah et al. Exp Dermatol 2007 light gray = MF dark gray = MPA
  • 11. Figures: breaks & dual axes Thickness Weight no info small window Dual axes allows incorporation of two relevant parameters into a single graph, which allows for better comparison break decreases the amount of space used for irrelevant info and allows for expansion of point of interest sparse graph
  • 12. Figures: tables Maintain consistency, simplicity, and completeness Mirshahpanah et al. Exp Dermatol 2007
    • Informative title
    • clear labeling across headings (along with measurement parameters)
    • consistent presentation of information: mean ± SD
    • Legend describes fundamental properties necessary to read table
  • 13. Figures: titles & legends
    • First sentence summarizes results of figure
    • Followed by a brief “materials and methods” explanation specific for this figure
    • Then describes actual results with values and significance where appropriate ( p- values)
    • Ends with statistical evaluation methods and representative value definition
    Zollner et al. JCI 2002
  • 14. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 15. Results: basics
    • Describes findings that are presented in figures, without duplicating the figures
      • DO provide guided description of findings, including trends or correlations
      • DO cite other papers that are directly relevant to your data; not in terms of implications but pure results
      • DO provide basic interpretation of results without alluding to larger implications
      • DO NOT simply restate that which is clearly presented in the figures
      • DO NOT discuss the role of results in the greater scheme of your paper – save this for the discussion
    Language : use past tense to describe events that have occurred in your experiment and present tense for conclusions you draw from the results
  • 16. Results: example Zollner et al. JCI 2002
    • Leading sentence summarizes results
    • Transitory sentence from previous section links different paragraphs and guides reader in the intended direction and flow of information (data presentation)
    • References used to support results
    • Minimal interpretational statements allow for unbiased presentation of data with subtle guidance from the author to address the issue: why do I care?
    • Only data points that are relevant to the point of the study are discussed, not every single point needs to be mentioned
    • Correlations may be drawn to support other data or to gain support from other results
  • 17. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 18. Materials & Methods: basics
    • Accurately and concisely summarizes materials and methods used to carry out experimental procedures
      • Animals and models employed along with appropriate authorization statement
      • Reagents used including company name and location (city, state/country)
      • Provides enough detail to reproduce results in another lab of similar capacity; write with a general scientific audience in mind:
        • not necessary to write:
          • We poured 50% sodium dodecyl sulfate (SDS) buffer into a graduated cylinder until the bottom of the meniscus was at the 20ml line. We then poured 80ml de-ionized water to make 10% SDS buffer and divided it into five equal tubes.
        • instead summarize:
          • We aliquoted 20ml of 10% SDS to 5 tubes.
      • You may cite other papers for detailed explanation of methods and briefly state the main points to align the reader
      • Order methods according to the logical flow of the experiment, often paralleling the order of results and figures
      • Include Statistics – these are methods used to evaluate data
    Language : past tense, passive voice (the reader is not interested in who did the experiment, but instead what was done) - i.e. avoid “we”
  • 19. Materials & Methods: example
    • Concise descriptions
    • Approval for animal model statement
    • Topic sentence summarizing subsequent method description
    • Referencing of detailed descriptions instead of re-writing it
    • Brief description summarizing main experimental procedure
    • Statistics used in various steps; often involves several procedures; again, referencing other sources saves space and allows reader to locate detailed description if necessary
    Mirshahpanah et al. Exp Dermatol 2007
  • 20. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 21. Introduction: format Basic background: what clinical implication does your study fit into? Introduce history Past studies and their results; what information is still unknown/ what questions arose? Description of specific parameters addressed in your study, align reader with language and readouts State your objective, process and allude to the significance your results aim to provide
  • 22. Introduction: basics
    • Guides reader into the specific material you are about to discuss
      • Where does the clinical implication of your study lay?
        • disease-specific?
        • Basic biological process?
        • Drug discovery?
      • Introduce basic background and concepts: history and references
        • characterize the background of the issues you will address in your study
        • outline the evolution of the topic of interest by discussing previous study’s results and conclusions; use primary references
        • i.e. drug/ therapy development, animal models, molecular biology, etc…
      • What studies already exist that are similar to your investigation
        • what were their conclusions?
        • what are they lacking; what still requires elucidation?
        • describe how your study fits into the larger picture of these previous findings
      • The final paragraph should briefly describe what you did, why you did it, and how you did it – all with relevance to the previous studies you have mentioned
        • allude to your broader implicated findings: what have you done that makes this an important study that adds value, what gap have you filled?
      • Intro should give reader a working knowledge of history, implications, some specifics, and providing the reason your study adds value
  • 23. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 24. Discussion: constituents results literature theory clinical applications Discussion contradictions patterns future studies
  • 25. Discussion: format Summarize your findings Discuss each major result in the context of previous studies, pointing out supportive and contradictory findings Suggest implications and practical applications of results; extend to other species if appropriate Provide “big picture” conclusion of results; integrating results, literature, theory and future direction for further studies
  • 26. Discussion: basics
    • Innovative facet of scientific article, allowing for guided interpretation of results
      • First paragraph summarizes findings in a clear manner
      • Draw conclusions from each major result
        • Briefly describe results without repeating previous sections
        • Cite literature that your results build upon or contradict
        • Explain possible reasons for your findings (appropriately supported by data or references); provide reasons for deviations
        • Provide evidence for conclusions combining previous work with current findings
        • Suggest future studies to further elucidate or verify your results
      • Be open about your results, describe deviations from hypothesis or expected results, what future experiments would clarify these issues?
      • Broader implications
        • Suggest theoretical implications of your results
        • Suggest practical application of your results
        • Discuss findings in a broader topic – extend to clinical situations if applicable
      • The final paragraph should state what your findings added to the scientific community (why is this study important?) and provide suggestions for future direction
  • 27. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 28. Abstract Most frequently read section of your paper; must be concise and complete
    • Brief introductory sentence to topic – i.e. clinical issue addressed
    • Background/ purpose of experiment
    • Methods – brief description of study design
    • Results – using actual values or stating major trends and findings from results
    • Conclusion – summary of discussion stating the major contribution of your study
    • Notes: Do not include brand names and try to avoid abbreviations
  • 29. Abstract: example
    • Introduction – topical glucocorticoids
    • Purpose – assessment of two leading compounds: function & side effects
    • Methods – in vitro and in vivo rodent models for compound atrophogenicity
    • Results – one compound superior to the other in both respects
    • Conclusions – better drug in this test system, must be tested in clinic to confirm
    Mirshahpanah et al. Exp Dermatol 2007
  • 30. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 31. Formatting & Submission
    • Order
    • Cover Page
    • Key Words
    • Abstract
    • Introduction
    • Materials & Methods
    • Results
    • Discussion
    • References
    • Figure Legends
    • Figures
    • Supplemental data
    • Submission
    • Cover letter to the editor
    • Online electronic submission & correspondences
  • 32. Formatting & Submission: cover letter
    • Properly address the editor
    • Introduce manuscript including title
    • Provide a brief paragraph about your study
      • relevance
      • scope
      • results
    • Conclude with reasoning for choosing this journal
      • Why is your study relevant and important for the readership of this particular journal?
      • What conclusions can you draw from your study?
  • 33. Process
    • Journal
    • Data & Figures
    • Results
    • Materials & Methods
    • Introduction
    • Discussion
    • Abstract
    • Formatting & Submission
    • Reviewer Response
  • 34. Reviewer Response
    • Thank each reviewer for his/her contributions, they volunteer their time to review papers and are ultimately responsible for accepting your manuscript
    • Provide complete point-by-point response to detail exactly how you have adapted your manuscript or fully refuted comments; if necessary, break up reviewer’s paragraph to respond to each query
    • Follow guidelines for review process in each journal; generally, track changes in MS Word and be prepared to provide original, changed, and revised versions
    • Resubmit as soon as possible to ensure timely publication
  • 35.  
  • 36. EndNote: reference manager
    • Create a new library for each publication; allows for simple reformatting when necessary
    • Many available journal styles, which may be further formatted for those missing from the database
    connect to PubMed to search and directly download into database format bibliography specifically for each journal
  • 37. EndNote: remote searches Multi-field searching capacity allows for specific location of topics by various search fields and associations
  • 38. EndNote: output styles Edit  Output Styles  Edit “current style” (use the style closest to your journal of interest)
  • 39. SigmaPlot: basics
    • Scaling
    • Axes
    • Breaks
    • Grouping
    • Error bars
  • 40. SigmaPlot: scaling resize scales to maximize data presentation
  • 41. insert break to enhance differences SigmaPlot: breaks
  • 42. SigmaPlot: enhancement Basic Plot (original) Aesthetically Enhanced Plot
  • 43. General Tips
    • Use consistent tenses – don’t switch between past, present and future
    • Simple is preferred over complex – words/ sentences/ structure
    • Use the active voice (except in methods)
      • We found correlations… (active voice)
      • Correlations were found… (passive voice)
    • Subject-verb agreement (The mice from each study were sacrificed.)
    • Use affirmative (+) rather than negative (-) constructions
    • Numbers beginning a sentence must be spelled (Twenty-five vs. 25)
    • Avoid phrases such as:
      • four different groups
      • absolute essential
      • in close proximity
      • very close to zero
      • much better
  • 44. General Writing: flow
    • Simple is better ; writing should be easy to read
    • Flow of paper should follow an hourglass shape
      • Introduction starts broadly (top), narrows to specific point(s) addressed (neck)
      • Materials, Results & Figures detail exactly what was observed (grains)
      • Discussion applies findings in a broader setting (base)
  • 45. General Writing: example A good paragraph generally possesses several key features that contribute to its clarity and effectiveness in presenting information. The first feature is a topic sentence that provides the reader with a general overview of the topic covered in the ensuing paragraph. The body of the paragraph should provide substantial information with references and evidence supporting the topic sentence. The final sentence serves to wrap up the ideas and prepare the reader for material to follow in the next paragraph, also known as a transition sentence. Upon reading the final sentence, the reader should be able to name the topic of the following paragraph. Topic Sentence Body: supporting evidence Concluding/ transition sentence