One of the reasons readers find a research paper difficult to follow is that the hypotheses, observations of experimental results, and interpretations of the results are not clearly distinguished from each other, or they are in the wrong place, leaving the readers wondering why the study was carried out, what was actually done and observed by the authors, and whether the conclusions are reasonable.
The logical way, and the way expected by the reader, is to present your hypotheses first (Introduction), and then describe your observations (Results), followed by your interpretations (Discussion). If you have a combined Results and Discussion section, this order still should be followed; that is, in each subsection, state the observations first, followed by the interpretations. If results are given before descriptions of the hypotheses, the experiments will appear to have no purpose. If conclusions are presented before observations, the conclusions will appear to be not supported by any data and therefore not convincing at all.
Certain words and phrases can serve as clues to let the readers know which of these three categories a statement belongs to. In a journal article, we typically don’t say “Our hypotheses are…”; instead, hypotheses are phrased as objectives (“The aims of this study were….”; “In the current study, we sought to determine…..”; etc.). At the end of Introduction, you can give the overall hypotheses/objectives of the entire study, and at the beginning of each subsection in Results, the objective of experiments to be described in that subsection can be stated (e.g., “To determine if compound A inhibits tumor growth in vivo, we injected XYZ cells into nude mice and monitored tumor growth.”). In the Results section, if a statement is followed by a citation of the figure or table showing the data, then this is usually clear that you are describing your observations. However, in the Discussion section, citation of figures and tables is discouraged as it is not necessary, then it is essential to tell the reader whether your statement is about an observation (“In the current study, we found….”; “In our experiments, tumor growth was slow in mice administered compound A”; etc.) or an interpretation (e.g., “Our findings suggest that…”; “Thus, compound A has the potential to become a useful anti-tumor agent).
When you write a statement in your manuscript, think whether it is a hypothesis, observation, or interpretation. This will help you decide where in the paper to place that statement. Also, use the words and phrases given above or something similar to inform the readers. This way, your study will be presented in a logical way and will be easy for a reader to follow.