Scientific paper structureWhy a Scientific Format?
The scientific format may seem confusing for the beginning science writer due
to its rigid structure which is so different from writing in the humanities.
One reason for using this format is that it is a means of efficiently
communicating scientific findings to the broad community of scientists in a
uniform manner. Another reason, perhaps more important than the first, is
that this format allows the paper to be read at several different levels. For
example, many people skim Titles to find out what information is available on
a subject. Others may read only titles and Abstracts. Those wanting to go
deeper may look at the Tables and Figures in the Results, and so on. The take
home point here is that the scientific format helps to insure that at
whatever level a person reads your paper (beyond title skimming), they will
likely get the key results and conclusions.

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The Sections of the Paper
Most journal-style scientific papers are subdivided into the following
sections: Title, Authors and Affiliation, Abstract, Introduction, Methods,
Results, Discussion, Acknowledgments, and Literature Cited, which parallel
the experimental process. This is the system we will use. This website
describes the style, content, and format associated with each section.

The sections appear in a journal style paper in the following prescribed
order:

Experimental process
Section of Paper

What did I do in a nutshell?
Abstract

What is the problem?
Introduction

How did I solve the problem?
Materials and Methods

What did I find out?
Results

What does it mean?
Discussion

Who helped me out?
Acknowledgments (optional)

Whose work did I refer to?
Literature Cited

Extra Information
Appendices (optional)

Section Headings:
Main Section Headings: Each main section of the paper begins with a heading
which should be capitalized, centered at the beginning of the section, and
double spaced from the lines above and below. Do not underline the section
heading OR put a colon at the end.

Example of a main section heading:

INTRODUCTION

Subheadings: When your paper reports on more than one experiment, use
subheadings to help organize the presentation. Subheadings should be
capitalized (first letter in each word), left justified, and either bold
italics OR underlined.

Example of a subheading:

Effects of Light Intensity on the Rate of Electron Transport



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Title, Authors' Names, and Institutional Affiliations
1. Function: Your paper should begin with a Title that succinctly describes
the contents of the paper. Use descriptive words that you would associate
strongly with the content of your paper: the molecule studied, the organism
used or studied, the treatment, the location of a field site, the response
measured, etc. A majority of readers will find your paper via electronic
database searches and those search engines key on words found in the title.

2. Title FAQs

3. Format:

The title should be centered at the top of page 1 (DO NOT use a title page -
it is a waste of paper for our purposes); the title is NOT underlined or
italicized.
the authors' names (PI or primary author first) and institutional affiliation
are double-spaced from and centered below the title. When more then two
authors, the names are separated by commas except for the last which is
separated from the previous name by the word "and".
For example:



Ducks Over-Winter in Colorado Barley Fields in Response to
Increased Daily Mean Temperature



Ima Mallard, Ura Drake, and Woodruff Ducque
Department of Wildlife Biology, University of Colorado - Boulder

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The title is not a section, but it is necessary and important. The title
should be short and unambiguous, yet be an adequate description of the work.
A general rule-of-thumb is that the title should contain the key words
describing the work presented. Remember that the title becomes the basis for
most on-line computer searches - if your title is insufficient, few people
will find or read your paper. For example, in a paper reporting on an
experiment involving dosing mice with the sex hormone estrogen and watching
for a certain kind of courtship behavior, a poor title would be:

Mouse Behavior

Why? It is very general, and could be referring to any of a number of mouse
behaviors. A better title would be:

The Effects of Estrogen on the Nose-Twitch Courtship Behavior in Mice

Why? Because the key words identify a specific behavior, a modifying agent,
and the experimental organism. If possible, give the key result of the study

Scientific paper structurein the title, as seen in the first example. Similarly, the above title could
be restated as:

Estrogen Stimulates Intensity of Nose-Twitch Courtship Behavior in Mice

4. Strategy for Writing Title.

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ABSTRACT

1. Function: An abstract summarizes, in one paragraph (usually), the major
aspects of the entire paper in the following prescribed sequence:

the question  you investigated (or purpose), (from Introduction)
state the purpose very clearly in the first or second sentence.
the experimental design and methods used, (from Methods)
clearly express the basic design of the study.
Name or briefly describe the basic methodology used without going into
excessive detail-be sure to indicate the key techniques used.
the major findings including key quantitative results, or trends (from
Results)
report those results which answer the questions you were asking
identify trends, relative change or differences, etc.
a brief summary of your interpetations and conclusions. (from Discussion)
clearly state the implications of the answers your results gave you.
Whereas the Title can only make the simplest statement about the content of
your article, the Abstract allows you to elaborate more on each major aspect
of the paper. The length of your Abstract should be kept to about 200-300
words maximum (a typical standard length for journals.) Limit your statements
concerning each segment of the paper (i.e. purpose, methods, results, etc.)
to two or three sentences, if possible. The Abstract helps readers decide
whether they want to read the rest of the paper, or it may be the only part
they can obtain via electronic literature searches or in published abstracts.
Therefore, enough key information (e.g., summary results, observations,
trends, etc.) must be included to make the Abstract useful to someone who may
to reference your work.

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How do you know when you have enough information in your Abstract? A simple
rule-of-thumb is to imagine that you are another researcher doing an study
similar to the one you are reporting. If your Abstract was the only part of
the paper you could access, would you be happy with the information presented
there?

2. Style: The Abstract is ONLY text. Use the active voice when possible, but
much of it may require passive constructions. Write your Abstract using
concise, but complete, sentences, and get to the point quickly. Use past
tense. Maximum length should be 200-300 words, usually in a single paragraph.

The Abstract SHOULD NOT contain:

lengthy background information,
references to other literature,
elliptical (i.e., ending with ...) or incomplete sentences,
abbreviations or terms that may be confusing to readers,
any sort of illustration, figure, or table, or references to them.
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3. Strategy: Although it is the first section of your paper, the Abstract, by
definition, must be written last since it will summarize the paper. To begin
composing your Abstract, take whole sentences or key phrases from each
section and put them in a sequence which summarizes the paper. Then set about
revising or adding words to make it all cohesive and clear. As you become
more proficient you will most likely compose the Abstract from scratch.

4. Check your work: Once you have the completed abstract, check to make sure
that the information in the abstract completely agrees with what is written
in the paper. Confirm that all the information appearing the abstract
actually appears in the body of the paper.

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INTRODUCTION
[ strategy | FAQs | style | structure | relevant literature review |
statement of purpose | rationale ]
1. Function: The function of the Introduction is to:

Establish the context of the work being reported. This is accomplished by
discussing the relevant primary research literature (with citations) and
summarizing our current understanding of the problem you are investigating;
State the purpose of the work in the form of the hypothesis, question, or
problem you investigated; and,
Briefly explain your rationale and approach and, whenever possible, the
possible outcomes your study can reveal.
Quite literally, the Introduction must answer the questions, "What was I
studying? Why was it an important question? What did we know about it before
I did this study? How will this study advance our knowledge?"

2. Style: Use the active voice as much as possible. Some use of first person
is okay, but do not overdo it.

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3. Structure: The structure of the Introduction can be thought of as an
inverted triangle - the broadest part at the top representing the most
general information and focusing down to the

Scientific paper structure specific problem you studied.
Organize the information to present the more general aspects of the topic
early in the Introduction, then narrow toward the more specific topical
information that provides context, finally arriving at your statement of
purpose and rationale. A good way to get on track is to sketch out the
Introduction backwards; start with the specific purpose and then decide what
is the scientific context in which you are asking the question  your study
addresses. Once the scientific context is decided, then you'll have a good
sense of what level and type of general information with which the
Introduction should begin.

Here is the information should flow in your Introduction:

Begin your Introduction by clearly identifying the subject area of interest.
Do this by using key words from your Title in the first few sentences of the
Introduction to get it focused directly on topic at the appropriate level.
This insures that you get to the primary subject matter quickly without
losing focus, or discussing information that is too general. For example, in
the mouse behavior paper, the words hormones and behavior would likely appear
within the first one or two sentences of the Introduction.
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Establish the context by providing a brief and balanced review of the
pertinent published literature that is available on the subject. The key is
to summarize (for the reader) what we knew about the specific problem before
you did your experiments or studies. This is accomplished with a general
review of the primary research literature (with citations) but should not
include very specific, lengthy explanations that you will probably discuss in
greater detail later in the Discussion. The judgment of what is general or
specific is difficult at first, but with practice and reading of the
scientific literature you will develop e firmer sense of your audience. In
the mouse behavior paper, for example, you would begin the Introduction at
the level of mating behavior in general, then quickly focus to mouse mating
behaviors and then hormonal regulation of behavior. Lead the reader to your
statement of purpose/hypothesis by focusing your literature review from the
more general context (the big picture e.g., hormonal modulation of behaviors)
to the more specific topic of interest to you (e.g., role/effects of
reproductive hormones, especially estrogen, in modulating specific sexual
behaviors of mice.)
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What literature should you look for in your review of what we know about the
problem? Focus your efforts on the primary research journals - the journals
that publish original research articles. Although you may read some general
background references (encyclopedias, textbooks, lab manuals, style manuals,
etc.) to get yourself acquianted with the subject area, do not cite these,
becasue they contain information that is considered fundamental or "common"
knowledge wqithin the discipline. Cite, instead, articles that reported
specific results relevant to your study. Learn, as soon as possible, how to
find the primary literature (research journals) and review articles rather
than depending on reference books. The articles listed in the Literature
Cited of relevant papers you find are a good starting point to move backwards
in a line of inquiry. Most academic libraries support the Citation Index - an
index which is useful for tracking a line of inquiry forward in time. Some of
the newer search engines will actually send you alerts of new papers that
cite particular articles of interest to you. Review articles are particularly
useful because they summarize all the research done on a narrow subject area
over a brief period of time (a year to a few years in most cases).
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Be sure to clearly state the purpose and /or hypothesis that you
investigated. When you are first learning to write in this format it is okay,
and actually preferable, to use a pat statement like, "The purpose of this
study was to...." or "We investigated three possible mechanisms to explain
the ... (1) blah, blah..(2) etc. It is most usual to place the statement of
purpose near the end of the Introduction, often as the topic sentence of the
final paragraph. It is not necessary (or even desirable) to use the words
"hypothesis" or "null hypothesis", since these are usually implicit if you
clearly state your purpose and expectations.
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Provide a clear statement of the rationale for your approach to the problem
studied. For example: State briefly how you approached the problem (e.g., you
studied oxidative respiration pathways in isolated mitochondria of
cauliflower). This will usually follow your statement of purpose in the last
parag

Scientific paper structureraph of the Introduction. Why did you choose this kind of experiment or
experimental design? What are the scientific merits of this particular model
system? What advantages does it confer in answering the particular question 
you are posing? Do not discuss here the actual techniques or protocols used
in your study (this will be done in the Materials and Methods); your readers
will be quite familiar with the usual techniques and approaches used in your
field. If you are using a novel (new, revolutionary, never used before)
technique or methodology, the merits of the new technique/method versus the
previously used methods should be presented in the Introduction.

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MATERIALS AND METHODS
This section is variously called Methods or Methods and Materials.

1. Function: In this section you explain clearly how you carried out your
study in the following general structure and organization (details follow
below):

the subjects used (plant, animal, human, etc.) and their pre-experiment
handling and care, and when and where the study was carried out (if location
and time are important factors);
if a field study, a description of the study site, including the physical and
biological features, and precise location;
the experimental OR sampling design (i.e., how the experiment or study was
structured. For example, controls, treatments, the variable  measured, how
many samples were collected, replication, etc.);
the protocol for collecting data, i.e., how the experimental procedures were
carried out, and,
how the data were analyzed (statistical procedures used).
Organize your presentation so your reader will understand the logical flow of
the experiment ; subheadings work well for this purpose. Each experiment or
procedure should be presented as a unit, even if it was broken up over time.
In general, provide enough quantitative detail (how much, how long, when,
etc.) about your experimental protocol such that other scientists could
reproduce your experiments. You should also indicate the statistical
procedures used to analyze your results, including the probability level at
which you determined significance (usually at 0.05 probability).

2. Style: The style in this section should read as if you were verbally
describing the conduct of the experiment. You may use the active voice to a
certain extent, although this section requires more use of third person,
passive constructions than others. Avoid use of the first person in this
section. Remember to use the past tense throughout. The Methods section is
not a step-by-step, directive, protocol as you might see in your lab manual.

3. Strategy for writing the Methods section.

4. Methods FAQs.

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Describe the organism  used in the study. This includes giving the source
(supplier or where and how collected), size, how they were handled before the
experiment, what they were fed, etc. In genetics studies include the strains
or genetic stocks used.

Describe the site where your field study was conducted. The description must
include both physical and biological characteristics of the site pertinant to
the study aims. Include the date  of the study (e.g., 10-15 April 1994) and
the exact location of the study area. Location data must be as precise as
possible: "Grover Nature Preserve, ? mi SW Grover, Maine" rather than "Grover
Nature Preserve" or "Grover". When possible, give the actual latitude and
longitude position of the site (the WWW has sites which provide this
service). It is most often a good idea to include a map (labeled as a Figure)
showing the location in relation to some larger more recognizable geographic
area. Someone else should be able to go to the exact location of your study
if they want to repeat or check your work, or just visit your study area.

NOTE: For laboratory studies you should not report the date and location of
the study UNLESS it is relevant. Most often it is not.
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Describe your experimental design clearly. Be sure to include the hypotheses
you tested, controls, treatments, variables measured, how many replicates you
had, what you actually measured, what form the data take, etc. Always
identify treatments by the variable or treatment name, NOT by an ambiguous,
generic name or number (e.g., use "2.5% saline" rather than "test 1".) When
your paper includes more than one experiment, use subheadings to help
organize your presentation by experiment. A general experimental design
worksheet is available to help plan your experiments in the core courses.

Describe the protocol for your study in sufficient detail that other
scientists could repeat your work to verify your findings. Foremost in your
desc

Scientific paper structureription should be the "quantitative" aspects of your study - the masses,
volumes, incubation times, concentrations, etc., that another scientist needs
in order to duplicate your experiment. When using standard lab or field
methods and instrumentation, it is not always necessary to explain the
procedures (e.g., serial dilution) or equipment used (e.g., autopipetter)
since other scientists will likely be familiar with them already. You may
want to identify certain types of equipment by brand or category (e.g.,
ultracentrifuge vs. prep centrifuge). It is appropriate to give the source
for reagents used parenthetically, e.g., "....poly-l-Lysine (Sigma #1309)."
When using a method described in another published source, you can save time
and words by referring to it and providing the relevant citation to the
source. Always make sure to describe any modifications you have made of a
standard or published method.

Describe how the data were summarized and analyzed. Here you will indicate
what types of data summaries and analyses were employed to answer each of the
questions or hypotheses tested.

The information should include:

how the data were summarized (Means, percent, etc) and how you are reporting
measures of variability (SD,SEM, etc)
this lets you avoid having to repeatedly indicate you are using mean ± SD.
data transformation (e.g., to normalize or equalize variances)
statistical tests used with reference to the particular questions they
address, e.g.,
"A Paired t-test was used to compare mean flight duration before and after
applying stablizers to the glider's wings."

"One way ANOVA was used to compare mean weight gain in weight-matched calves
fed the three different rations."

any other numerical or graphical techniques used to analyze the data


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Here is some additional advice on particular problems common to new
scientific writers.

Problem: The Methods section is prone to being wordy or overly detailed.

Avoid repeatedly using a single sentence to relate a single action; this
results in very lengthy, wordy passages. A related sequence of actions can be
combined into one sentence to improve clarity and readability:
Problematic Example: This is a very long and wordy description of a common,
simple procedure. It is characterized by single actions per sentence and lots
of unnecessary details.

"The petri dish was placed on the turntable. The lid was then raised
slightly. An inoculating loop was used to transfer culture to the agar
surface. The turntable was rotated 90 degrees by hand. The loop was moved
lightly back and forth over the agar to spread the culture. The bacteria were
then incubated at 37 C for 24 hr."

Improved Example: Same actions, but all the important information is given in
a single, concise sentence. Note that superfluous detail and otherwise
obvious information has been deleted while important missing information was
added.

"Each plate was placed on a turntable and streaked at opposing angles with
fresh overnight E. coli culture using an inoculating loop. The bacteria were
then incubated at 37 C for 24 hr."

Best: Here the author assumes the reader has basic knowledge of
microbiological techniques and has deleted other superfluous information. The
two sentences have been combined because they are related actions.

"Each plate was streaked with fresh overnight E. coli culture and incubated
at 37 C for 24 hr."

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Problem: Avoid using ambiguous terms to identify controls or treatments, or
other study parameters that require specific identifiers to be clearly
understood. Designators such as Tube 1, Tube 2, or Site 1 and Site 2 are
completely meaningless out of context and difficult to follow in context.
Problematic example: In this example the reader will have no clue as to what
the various tubes represent without having to constantly refer back to some
previous point in the Methods.

"A Spec 20 was used to measure A600 of Tubes 1,2, and 3 immediately after
chloroplasts were added (Time 0) and every 2 min. thereafter until the DCIP
was completely reduced. Tube 4's A600 was measured only at Time 0 and at the
end of the experiment."

Improved example: Notice how the substitution (in red) of treatment and
control identifiers clarifies the passage both in the context of the paper,
and if taken out of context.

"A Spec 20 was used to measure A600 of the reaction mixtures exposed to light
intensities of 1500, 750, and 350 uE/m2/sec immediately after chloroplasts
were added (Time 0) and every 2 min. thereafter until the DCIP was completely
reduced. The A600 of the no light control was measured only at Time 0 and at
the end of the experiment.

Scientific paper structure"

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RESULTS

1. Function: The function of the Results section is to objectively present
your key results, without interpretation, in an orderly and logical sequence
using both illustrative materials (Tables and Figures) and text. Summaries of
the statistical analyses may appear either in the text (usually
parenthetically) or in the relevant Tables or Figures (in the legend or as
footnotes to the Table or Figure). The Results section should be organized
around a series of Tables and/or Figures sequenced to present your key
findings in a logical order. The text of the Results section follows this
sequence and highlights the answers to the questions/hypotheses you
investigated. Important negative results should be reported, too. Authors
usually write the text of the results section based upon this sequence of
Tables and Figures.

2. Style: Write the text of the Results section concisely and objectively.
The passive voice will likely dominate here, but use the active voice as much
as possible. Use the past tense. Avoid repetitive paragraph structures. Do
not interpret the data here. The transition into interpretive language can be
a slippery slope. Consider the following two examples:

This example highlights the trend/difference that the author wants the reader
to focus:
The duration of exposure to running water had a pronounced effect on
cumulative seed germination percentages (Fig. 2). Seeds exposed to the 2-day
treatment had the highest cumulative germination (84%), 1.25 times that of
the 12-h or 5-day groups and 4 times that of controls.

In contrast, this example strays subtly into interpretation by referring to
optimality (a conceptual model) and tieing the observed result to that idea:
The results of the germination experiment (Fig. 2) suggest that the optimal
time for running-water treatment is 2 days. This group showed the highest
cumulative germination (84%), with longer (5 d) or shorter (12 h) exposures
producing smaller gains in germination when compared to the control group.

3. Strategy for Writing the Results Section

4. Frequently asked questions (FAQs).



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Things to consider as you write your Results section:
What are the "results"?: When you pose a testable hypothesis that can be
answered experimentally, or ask a question that can be answered by collecting
samples, you accumulate observations about those organisms or phenomena.
Those observations are then analyzed to yield an answer to the question. In
general, the answer is the " key result".

The above statements apply regardless of the complexity of the analysis you
employ. So, in an introductory course your analysis may consist of visual
inspection of figures and simple calculations of means and standard
deviations; in a later course you may be expected to apply and interpret a
variety of statistical tests. You instructor will tell you the level of
analysis that is expected.

For example, suppose you asked the question, "Is the average height of male
students the same as female students in a pool of Biology majors?" You would
first collect height data from large random samples of male and female
students. You would then calculate the descriptive statistics for those
samples (mean, SD, n, range, etc) and plot these numbers. In a course where
statistical tests are not employed, you would visually inspect these plots.
Suppose you found that male Biology majors are, on average, 12.5 cm taller
than female majors; this is the answer to the question.

Notice that the outcome of a statistical analysis is not a key result, but
rather an analytical tool that helps us understand what is our key result.
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Organize the results section based on the sequence of Table and Figures
you'll include. Prepare the Tables and Figures as soon as all the data are
analyzed and arrange them in the sequence that best presents your findings in
a logical way. A good strategy is to note, on a draft of each Table or
Figure, the one or two key results you want to addess in the text portion of
the Results. Simple rules to follow related to Tables and Figures:

Tables and Figures are assigned numbers separately and in the sequence that
you will refer to them from the text.
The first Table you refer to is Table 1, the next Table 2 and so forth.
Similarly, the first Figure is Figure 1, the next Figure 2, etc.


Each Table or Figure must include a brief description of the results being
presented and other necessary information in a legend.
Table legends go above the Table; tables are read from top to bottom.
Figure legends go below the figure; figures are usually viewed from bottom to
top.


When referring to

Scientific paper structure a Figure from the text, "Figure" is abbreviated as
Fig.,e.g.,
Fig. 1. Table is never abbreviated, e.g., Table 1.
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The body of the Results section is a text-based presentation of the key
findings which includes references to each of the Tables and Figures. The
text should guide the reader through your results stressing the key results
which provide the answers to the question  investigated. A major function of
the text is to provide clarifying information. You must refer to each Table
and/or Figure individually and in sequence (see numbering sequence), and
clearly indicate for the reader the key results that each conveys. Key
results depend on your questions, they might include obvious trends,
important differences, similarities, correlations, maximums, minimums, etc.

Some things to avoid:

Do not reiterate each value from a Figure or Table - only the key result or
trends that each conveys.
Do not present the same data in both a Table and Figure - this is considered
redundant and a waste of space and energy. Decide which format best shows the
result and go with it.
Do not report raw data values when they can be summarized as means, percents,
etc.

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Statistical test summaries (test name, p-value) are usually reported
parenthetically in conjunction with the biological results they support.
Always report your results with parenthetical reference to the statistical
conclusion that supports your finding (if statistical tests are being used in
your course). This parenthetical reference should include the statistical
test used and the level of significance (test statistic and DF are optional).
For example, if you found that the mean height of male Biology majors was
significantly larger than 

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