The Structure of Scientific Papers:

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-centered.

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.

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.

• 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.

The introduction

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.

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.
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).

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.

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 . . .

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.

For the task,

• use whoever did the work (normally, you and your colleagues) as the subject

of the sentence: we or perhaps the authors;

• use a verb expressing a research action: measured, calculated, etc.;

• set that verb in the past tense.

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.

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 . . .
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.
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.

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 . . .
The body
Even the most logical structure is of little use if readers do not see and understand it
as they progress through a paper. Thus, as you organize the body of your paper into
sections and perhaps subsections, remember to prepare your readers for the structure
ahead at all levels. You already do so for the overall structure of the body (the
sections) in the object of the document at the end of the Introduction. You can
similarly prepare your readers for an upcoming division into subsections by
introducing a global paragraph between the heading of a section and the heading of its
first subsection. This paragraph can contain any information relating to the section as
a whole rather than particular subsections, but it should at least announce the
subsections, whether explicitly or implicitly. An explicit preview would be phrased
much like the object of the document: "This section first . . . , then . . . , and finally . . .
"

Although papers can be organized into sections in many ways, those reporting
experimental work typically include Materials and Methods, Results,
and Discussion in their body. In any case, the paragraphs in these sections should
begin with a topic sentence to prepare readers for their contents, allow selective
reading, and — ideally — get a message across.

Materials and methods

Most Materials and Methods sections are boring to read, yet they need not be. To

make this section interesting, explain the choices you made in your experimental

procedure: What justifies using a given compound, concentration, or dimension?

What is special, unexpected, or different in your approach? Mention these things early

in your paragraph, ideally in the first sentence. If you use a standard or usual

procedure, mention that upfront, too. Do not make readers guess: Make sure the

paragraph's first sentence gives them a clear idea of what the entire paragraph is about.

If you feel you cannot or need not do more than list items, consider using a table or

perhaps a schematic diagram rather than a paragraph of text.

Results and discussion

The traditional Results and Discussion sections are best combined because results

make little sense to most readers without interpretation.

When reporting and discussing your results, do not force your readers to go through

everything you went through in chronological order. Instead, state the message of

each paragraph upfront: Convey in the first sentence what you want readers to

remember from the paragraph as a whole. Focus on what happened, not on the fact

that you observed it. Then develop your message in the remainder of the paragraph,

including only that information you think you need to convince your audience.

The conclusion

In the Conclusion section, state the most important outcome of your work. Do not

simply summarize the points already made in the body — instead, interpret your

findings at a higher level of abstraction. Show whether, or to what extent, you have

succeeded in addressing the need stated in the Introduction. At the same time, do not

focus on yourself (for example, by restating everything you did). Rather, show what

your findings mean to readers. Make the Conclusion interesting and memorable for

them.

At the end of your Conclusion, consider including perspectives — that is, an idea of

what could or should still be done in relation to the issue addressed in the paper. If

you include perspectives, clarify whether you are referring to firm plans for yourself

and your colleagues ("In the coming months, we will . . . ") or to an invitation to

readers ("One remaining question is . . . ").

If your paper includes a well-structured Introduction and an effective abstract, you

need not repeat any of the Introduction in the Conclusion. In particular, do not restate

what you have done or what the paper does. Instead, focus on what you have found
and, especially, on what your findings mean. Do not be afraid to write a

short Conclusion section: If you can conclude in just a few sentences given the rich

discussion in the body of the paper, then do so. (In other words, resist the temptation

to repeat material from the Introduction just to make the Conclusion longer under the

false belief that a longer Conclusion will seem more impressive.)

The abstract

The readers of a scientific paper read the abstract for two purposes: to decide whether

they want to (acquire and) read the full paper, and to prepare themselves for the

details presented in that paper. An effective abstract helps readers achieve these two

purposes. In particular, because it is typically read before the full paper, the abstract

should present what the readers are primarily interested in; that is, what they want to

know first of all and most of all.

Typically, readers are primarily interested in the information presented in a

paper's Introduction and Conclusion sections. Primarily, they want to know the

motivation for the work presented and the outcome of this work. Then (and only then)

the most specialized among them might want to know the details of the work. Thus,

an effective abstract focuses on motivation and outcome; in doing so, it parallels the

paper's Introduction and Conclusion.

Accordingly, you can think of an abstract as having two distinct parts — motivation

and outcome — even if it is typeset as a single paragraph. For the first part, follow the

same structure as the Introduction section of the paper: State the context, the need, the

task, and the object of the document. For the second part, mention your findings
(the what) and, especially, your conclusion (the so what — that is, the interpretation

of your findings); if appropriate, end with perspectives, as in the Conclusion section

of your paper.

Although the structure of the abstract parallels

the Introduction and Conclusion sections, it differs from these sections in the

audience it addresses. The abstract is read by many different readers, from the most

specialized to the least specialized among the target audience. In a sense, it should be

the least specialized part of the paper. Any scientist reading it should be able to

understand why the work was carried out and why it is important (context and need),

what the authors did (task) and what the paper reports about this work (object of the

document), what the authors found (findings), what these findings mean (the

conclusion), and possibly what the next steps are (perspectives). In contrast, the full

paper is typically read by specialists only; its Introduction and Conclusion are more

detailed (that is, longer and more specialized) than the abstract.

An effective abstract stands on its own — it can be understood fully even when made

available without the full paper. To this end, avoid referring to figures or the

bibliography in the abstract. Also, introduce any acronyms the first time you use them

in the abstract (if needed), and do so again in the full paper (see Mechanics: Using

abbreviations).