How to Write a Paper with Examples

1. How to Write a Paperwith Examples Dr. Steve Wallace

2. The IMRaD Format • Introduction • Methods • Results • And • Discussion • The IMRAD format was developed by Louis Pasteur to disprove the idea of spontaneous generation • IMRAD format lets people reproduce experiments

3. The IMRaD format ICMJE, “Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Writing and Editing for Biomedical Publication”, section IV.A.1.a: “The text of observational and experimental articles is usually (but not necessarily) divided into the following sections: Introduction, Methods, Results, and Discussion. This so-called “IMRAD” structure is not an arbitrary publication format but rather a direct reflection of the process of scientific discovery. Long articles may need subheadings within some sections (especially Results and Discussion) to clarify their content.” http://www.icmje.org

4. When Do We Write Each Section? IMRaD manuscripts should be written in the following order to achieve clarity and consistency: Write during the research Methods Results Write after selecting the target journal Introduction Discussion Abstract Title

5. Introduction The introduction contains the minimal amount of background to understand the reason for your study DO NOT write a comprehensive literature review of the field Cite reviews that readers can read for more information

6. Introduction Technical terms should be defined Present the problem, research question or hypotheses to explain the reason for the study Briefly explain how you answered this problem and what happened (1–2 sentences for each)

7. Knowledge Gap Motivation Literature Review Research Question Chemosphere (doi:10.1016/j.chemosphere.2009.06.045;)

8. Citing the Literature

9. Introduction Citations: Must be balanced, current, and relevant Avoid citing papers that do not directly relate to your research Cite all related papers, not only your own or those that support your hypothesis, but also papers that contradict your findings or propose alternative ideas Cite only the most recent papers showing a particular finding, unless referring to an older paper to explain the change of thought in the field or the development of a particular method

10. Common Mistakes in Citing Literature Don’t cite one source too much Don’t cite irrelevant literature Don’t over-cite definitions Don’t misattribute Don’t cite the citation Don’t cite implications as facts Don’t quote too much

11. Examples of Paraphrasing The Craft of Research (Booth, Colomb, and Williams 1995,169) Original Sentence: It is trickier to define plagiarism when you summarize and paraphrase. They are not the same, but they blend so seamlessly that you may not even be aware when you are drifting from summary into paraphrase, then across the line into plagiarism. No matter your intention, close paraphrase may count as plagiarism, even when you cite the source.

12. Plagiarized Version: It is harder to describe plagiarism when summary and paraphrase are involved, because they differ, their boundaries blur, and a writer may not know that she has crossed the boundary from summary to paraphrase and from paraphrase to plagiarism. Regardless of intention, a close paraphrase is plagiarism, even when the source is cited. This paragraph, for instance, would count as plagiarism of that one (Booth, Colomb, and Williams,169).

13. Borderline Plagiarized Version: Because it is difficult to distinguish the border between summary and paraphrase, a writer can drift dangerously close to plagiarism without knowing it, even when the writer cites a source and never meant to plagiarize. Many might consider this paragraph a paraphrase that crosses the line (Booth, Colomb, and Williams,169).

14. Correctly Summarized Version: According to Booth, Colomb, and Williams, writers sometimes plagiarize unconsciously because they think they are summarizing, when in fact they are closely paraphrasing (which counts as plagiarism), even when done unintentionally and sources are cited (169).

15. Identifying Plagiarism • Below are two versions of the same information, adapted from the Introduction in McNeill et al. (1997). In Version 2, identify where the writer has plagiarized by writing ideas in his or her own voice that originated in another document (as demonstrated in Version 1). • Version 1: Russel and Fillery (1996), using a stem-feeding technique, showed that in situ 15N-labelling of lupin plants growing in soil cores enabled total below-ground N to be estimated under relatively undisturbed conditions; but they indicted that the technique was not adaptable to all plants, particularly pasture species. • Version 2: Russel and Fillery (1996), using a stem-feeding technique, showed that in situ 15N-labelling of lupin plants growing in soil cores enabled total below-ground N to be estimated under relatively undisturbed conditions. However, this technique is not adaptable to all plants, particularly pasture species.

16. Verbs in the Literature Review Modifying strength of claims with verbs:

17. Materials and Methods • Subheadings for methods and materials • Describe methods in the past tense • Novel methods must be described so a capable researcher can reproduce the experiment • Established methods can be referenced

18. Materials and Methods • Suppliers and manufacturers must be provided, including locations if requested • Statistical methods should be described

19. The Journal of Clinical Investigation (doi:10.1172/JCI37155;)

20. Materials described first Past tense All required information provided Clear subheadings Reference to previous study and supplementary materials to save space Suppliers and locations Chemosphere (doi:10.1016/j.chemosphere.2009.06.045;)

21. Results Describe results in the past tense, but use the present tense to refer to figures and tables. Save discussion of implications for the discussion section. If the journal accepts a combined results/discussion, present results first within a subsection. Use figures and tables to summarize data except where data can be more easily summarized in the text. Do not repeat data among figures, tables, and text.

22. The Journal of Clinical Investigation (doi:10.1172/JCI37155;)

23. Combined results/discussion Clear subheadings, in a logical order to make a story Results presented first within a subsection, with graphics summarizing data Present tense to refer to table Past tense for describing results Chemosphere (doi:10.1016/j.chemosphere.2009.06.045;)

24. Figures and Tables Some readers will read the paper by looking at the figures and reading the legends. Comply with journal restrictions on the number of display items. Put less important findings in an appendix.

25. Figures and Tables Avoid repeating display information in text Label graph axes, table columns, and rows and components of diagrams Show trendlines, scale bars, and statistical significance Legends should stand alone and be in the present tense (except when describing methods)

26. Tables are a great way to present large amounts of necessary data with minimal description required Truncation of a table in a paper published in The Journal of Clinical Investigation (doi:10.1172/JCI37622;)

27. Tables present large amounts of necessary data with minimal description needed Clear, concise heading Data divided into categories for clarity Standard deviations presented Marine Chemistry (doi:10.1016/j.marchem.2009.04.004;)

28. Error bars Data unclear: needs to be separated into panels Clearly labeled axes Clear legends that can stand alone Marine Chemistry (doi:10.1016/j.marchem.2009.04.004;)

29. The Journal of Clinical Investigation (doi:10.1172/JCI37622;)

30. When to Use Tables, Graphs, and Figures… • When to use… Tables: when there isa large amount of repetitive data that makes a critical point. To compress and illustrate lots of data Graphs: when data show pronounced trends that are easy to see in graphical form Figures: when photographs are primary data, such as photographs of cell structures or electron micrographs of a silicon substrate. Or when illustrations point out a critical piece of evidence

31. When Not to Use Tables, Graphs, and Figures… Tables: when data can be summarized in one or two sentences. When there is a small amount of data or when data is repetitive Graphs: when data matches expectations. When compared data is similar. When you are trying to make boring data look better Figures: when the figure can be described in a few short sentences. When the photo is unclear or the drawing unnecessary

32. How to Make Good Tables • Clear brief labels, such as the title, column headings, and table entries • Put labels to the top and left and data below and to the right • Size should be large enough to make the point, and no more • Eliminate unnecessary data points that detract from the main point of the table

33. How to Present Tables Bad Table 1. This table is bad because it could be easily summarized with the sentence “Growth was only observed between 30-50 °C.”

34. How to Present Tables Bad Table 2. This table is bad because it makes data more complicated rather than less complicated. The organisms are simply divided into two categories. It would be easier to simply write a sentence dividing them into two categories.

35. How to Present Tables Bad Table 3. This table is bad because the arrangement of the labels makes the data difficult to read. The labels across the top should be switched with the labels along the left side.

36. How to Present Tables Good Table 1. Flipping around the labels of Bad Table 3 makes the data much easier to read. Good arrangement of table data is essential.

37. How to Present Tables Data are means and (standard deviations) * P < 0.05 vs. normoxic control, † P < 0.05 vs. hypoxic control Good Table 2. The data in this table is complex but arranged for scanning from left to right. The standard deviations are in parentheses so are easy to ignore.

38. How to Present Tables Data are means and (standard deviations) * P < 0.05 vs. normoxic control, † P < 0.05 vs. hypoxic control Good Table 3. Rearrangement of data in Good Table 2. Notice that the change in standard deviation numbers makes it easier to scan down columns, but harder to scan across each row. Also, the standard deviations are more difficult to ignore.

39. How to Make Good Graphs: • Choose the appropriate type of graph to display the data • Eliminate any unnecessary lines, and make sure everything is large enough to read

40. How to Present Tables, Graphs, and Figures Bad Graph 1. This graph doesn’t make sense, because I just entered in random values. If your graph doesn’t look better than this, don’t use it.

41. How to Present Tables, Graphs, and Figures Bad Graph 2. This graph is bad because the underlying data for each of the three dogs is so similar. Each of the three lines follows the same general pattern. This table is useless and would be better as a single sentence.

42. How to Present Tables, Graphs, and Figures Bad Graph 3. This graph is bad because the format of the graph is not suitable for the data. This data is numbers by date, but the radar chart turns it into a confusing mess. It would be much better as a line graph.

43. How to Present Tables, Graphs, and Figures Good Graph 1. The data looks much better as a line graph. It is very easy to see that something big happened to Staphylococcus on the 10th of January.

44. How to Present Tables, Graphs, and Figures Good Graph 2. Radar graphs can be useful for comparing the numerical measurements of a large number of factors between a few different subjects.

45. How to Present Tables, Graphs, and Figures Good Graph 3. The saturation density for FBS stands out strongly in this graph at 250%, much higher than the others. Despite not knowing any details of the study or the substances graphed, the point is clear.

46. How to Make Good Figures: • Figures can be drawings, photographs, or diagrams • Drawings are better than photographs for animals and equipment • For primary evidence such as radiographs, micrographs, gel electrophoretograms, and polygraph recordings, photographs are best • Crop and enlarge photos to show what you want to show

47. How to Present Figures Bad Figure 1. This figure is bad because it is a 3D representation of a box full of floating balls. Reading the caption only makes it more confusing. This is from a paper on glass transitions in polymer thin films.

48. How to Present Figures Bad Figure 2. This figure is bad because it is a literal drawing of a metaphor. It does not add anything to the paper at all. This is from a paper on technomimetic molecules.

49. How to Present Figures Bad Figure 3. This figure is bad because it does not add anything to the paper, except to help people remember the subject of a quantum-chain process that is made possible by ultra-fast energy transfer.

50. How to Present Figures Good Figure 1. Good figures are basically works of art. This is an electron microscopy image of human red blood cells.