Structuring Your Scientific Paper

notes from https://www.nature.com/scitable/ebooks/english-communication-for-scientists-14053993/118519636/

1. Scientific papers are for sharing your own original research work with other scientists or for reviewing the research conducted by others. As such, they are critical to the evolution of modern science, in which the work of one scientist builds upon that of others. To reach their goal, papers must aim to inform, not impress. They must be highly readable — that is, clear, accurate, and concise. They are more likely to be cited by other scientists if they are helpful rather than cryptic or self-centred.
2. Scientific papers typically have two audiences: first, the referees, who help the journal editor decide whether a paper is suitable for publication; and second, the journal readers themselves, who may be more or less knowledgeable about the topic addressed in the paper. To be accepted by referees and cited by readers, papers must do more than simply present a chronological account of the research work. Rather, they must convince their audience that the research presented is important, valid, and relevant to other scientists in the same field. To this end, they must emphasize both the motivation for the work and the outcome of it, and they must include just enough evidence to establish the validity of this outcome.
3. Papers that report experimental work are often structured chronologically in five sections: first, Introduction; then Materials and Methods, Results, and Discussion (together, these three sections make up the paper’s body); and finally, Conclusion.

1. • The Introduction section clarifies the motivation for the work presented and prepares readers for the structure of the paper.
   • The Materials and Methods section provides sufficient detail for other scientists to reproduce the experiments presented in the paper. In some journals, this information is placed in an appendix, because it is not what most readers want to know first.
   • The Results and Discussion sections present and discuss the research results, respectively. They are often usefully combined into one section, however, because readers can seldom make sense of results alone without accompanying interpretation — they need to be told what the results mean.
   • The Conclusion section presents the outcome of the work by interpreting the findings at a higher level of abstraction than the Discussion and by relating these findings to the motivation stated in the Introduction.
     (Papers reporting something other than experiments, such as a new method or technology, typically have different sections in their body, but they include the same Introduction and Conclusion sections as described above.

4. Although the above structure reflects the progression of most research projects, effective papers typically break the chronology in at least three ways to present their content in the order in which the audience will most likely want to read it.

1. • First and foremost, they summarize the motivation for, and the outcome of, the work in an abstract, located before the Introduction. In a sense, they reveal the beginning and end of the story — briefly — before providing the full story.
   • Second, they move the more detailed, less important parts of the body to the end of the paper in one or more appendices so that these parts do not stand in the readers’ way.
   • Finally, they structure the content in the body in theorem-proof fashion, stating first what readers must remember (for example, as the first sentence of a paragraph) and then presenting evidence to support this statement.

5. The introduction reproduced here exhibits the four components that readers find useful as they begin to read a paper. In the Introduction section, state the motivation for the work presented in your paper and prepare readers for the structure of the paper. Write four components, probably (but not necessarily) in four paragraphs: context, need, task, and object of the document.
   • First, provide some context to orient those readers who are less familiar with your topic and to establish the importance of your work.
   • Second, state the need for your work, as an opposition between what the scientific community currently has and what it wants.
   • Third, indicate what you have done in an effort to address the need (this is the task).
   • Finally, preview the remainder of the paper to mentally prepare readers for its structure, in the object of the document.
6. Context and need. At the beginning of the Introduction section, the context and need work together as a funnel: They start broad and progressively narrow down to the issue addressed in the paper. To spark interest among your audience — referees and journal readers alike — provide a compelling motivation for the work presented in your paper: The fact that a phenomenon has never been studied before is not, in and of itself, a reason to study that phenomenon.
7. Write the context in a way that appeals to a broad range of readers and leads into the need. Do not include context for the sake of including context: Rather, provide only what will help readers better understand the need and, especially, its importance. Consider anchoring the context in time, using phrases such as recently, in the past 10 years, or since the early 1990s. You may also want to anchor your context in space (either geographically or within a given research field).
8. Convey the need for the work as an opposition between actual and desired situations. Start by stating the actual situation (what we have) as a direct continuation of the context. If you feel you must explain recent achievements in much detail — say, in more than one or two paragraphs — consider moving the details to a section titled State of the art (or something similar) after the Introduction, but do provide a brief idea of the actual situation in the Introduction. Next, state the desired situation (what we want). Emphasize the contrast between the actual and desired situations with such words as but, however, or unfortunately.
9. One elegant way to express the desired part of the need is to combine it with the task in a single sentence. This sentence expresses first the objective, then the action undertaken to reach this objective, thus creating a strong and elegant connection between need and task. Here are three examples of such a combination:

• To confirm this assumption, we studied the effects of a range of inhibitors of connexin channels . . . on . . .
• To assess whether such multiple-coil sensors perform better than single-signal ones, we tested two of them — the DuoPXK and the GEMM3 — in a field where . . .
• To form a better view of the global distribution and infectiousness of this pathogen, we examined 1645 postmetamorphic and adult amphibians collected from 27 countries between 1984 and 2006 for the presence of . . .

10. Task and object-An Introduction is usually clearer and more logical when it separates what the authors have done (the task) from what the paper itself attempts or covers (the object of the document). In other words, the task clarifies your contribution as a scientist, whereas the object of the document prepares readers for the structure of the paper, thus allowing focused or selective reading.
11. For the task,
12. use whoever did the work (normally, you and your colleagues) as the subject of the sentence: we or perhaps the authors;
13. use a verb expressing a research action: measured, calculated, etc.;
14. set that verb in the past tense.
15. The three examples below are well-formed tasks.

• To confirm this assumption, we studied the effects of a range of inhibitors of connexin channels, such as the connexin mimetic peptides Gap26 and Gap27 and anti-peptide antibodies, on calcium signaling in cardiac cells and HeLa cells expressing connexins.
• During controlled experiments, we investigated the influence of the HMP boundary conditions on liver flows.
• To tackle this problem, we developed a new software verification technique called oblivious hashing, which calculates the hash values based on the actual execution of the program.

16. The list below provides examples of verbs that express research actions:
    • apply-We applied Laklöter’s principle to . . .
    • assess We assessed the effects of larger doses of . . .
    • calculate We calculated the photoluminescence spectrum of . . .
    • compare We compared the effects of . . . to those of . . .
    • compute We computed the velocity predicted by . . .
    • derive We derived a new set of rules for . . .
    • design We designed a series of experiments to . . .
    • determine We determined the complete nucleotide sequence of . . .
    • develop We developed a new algorithm to . . .
    • evaluate We evaluated the efficacy and biocompatibility of . . .
    • explore We explored the relationship between . . .
    • implement We implemented a genetic algorithm for . . .
    • investigate We investigated the behavior of . .
    • measure We measured the concentration of cadmium in . .
    • model We modeled the diffraction behavior of . . .
17. For the object of the document,-use the document itself as the subject of the sentence: this paper, this letter, etc.;use a verb expressing a communication action: presents, summarizes, etc.;set the verb in the present tense.
18. The three examples below are suitable objects of the document for the three tasks shown above, respectively.
    • This paper clarifies the role of CxHc on calcium oscillations in neonatal cardiac myocytes and calcium transients induced by ATP in HL-cells originated from cardiac atrium and in HeLa cells expressing connexin 43 or 26.
    • This paper presents the flow effects induced by increasing the hepatic-artery pressure and by obstructing the vena cava inferior.
    • This paper discusses the theory behind oblivious hashing and shows how this approach can be applied for local software tamper resistance and remote code authentication.
19. The list below provides examples of verbs that express communication actions:
    • clarify This paper clarifies the role of soils in . . .
    • describe This paper describes the mechanism by which . . .
    • detail This paper details the algorithm used for . . .
    • discuss This paper discusses the influence of acidity on . . .
    • explain This paper explains how the new encoding scheme . . .
    • offer This paper offers four recommendations for . . .
    • present This paper presents the results of . . .
    • proposes This paper proposes a set of guidelines for . . .
    • provide This paper provides the complete framework and . . .
    • report This paper reports on our progress so far . . .
    • summarize This paper summarizes our results for 27 patients with . . .