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Scientific paper outline example

Jun 17, 2018

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The Structure, Format, Content, and Style of a
Journal-Style Scientific Paper

Why 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 spacedfrom 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:

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 in 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:

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:

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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

1. Function: The function of the Introduction is to:

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 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(s) 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:

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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):

Organize your presentation so your reader will understand the logical flow of the experiment(s); subheadings work well for this purpose. Each experiment or procedure should be presented as a unit, even if it was broken up over time. The experimental design and procedure are sometimes most efficiently presented as an integrated unit, because otherwise it would be difficult to split them up. 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 work being reported is done, and was performed in the past, not the future. 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(s) used in the study. This includes giving the (1) source (supplier or where and how the orgranisms were collected), (2) typical size (weight, length, etc), (3) how they were handled, fed, and housed before the experiment, (4) how they were handled, fed, and housed during the experiment. In genetics studies include the strains or genetic stocks used. For some studies, age may be an important factor. For example, did you use mouse pups or adults? Seedlings or mature plants?

FOR FIELD STUDIES ONLY: 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(s) 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, ½ mi SW Grover, Maine" rather than "Grover Nature Preserve" or "Grover". When possible, give the actual latitude and longitude position of the site: these can be obtained using handheld GPS units, OR, from web resources such as Google Earth(TM) and MapQuest(TM). It is often a good idea to include a map (labeled as a Figure) showing the study location in relation to some larger more recognizable geographic area. Someone else should be able to go to the exact location of your study site if they want to repeat or check your work, or just visit your study area.

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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% NaCl" 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 worksheetis available to help plan your experiments in the core courses.

Describe the procedures for your study in sufficient detail that other scientists could repeat your work to verify your findings. Foremost in your description 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 vendor name and brand or category (e.g., ultracentrifuge vs. prep centrifuge), particularly if they are not commonly found in most labs. It is appropriate to report, parenthetically, the source (vendor) and catalog number for reagents used, e.g., "....poly-L-lysine (Sigma #1309)." When using a method described in another published source, you can save time and words by 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 descriptive statistics were used and which analyses (usually hypothesis tests) were employed to answer each of the questions or hypotheses tested and determine statistical siginifcance.

The information should include:

"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."

"Comparisons among the three pH treatment groups for each variable were done using one way ANOVA (with Tukey's post hoc test) or a Kruskal-Wallis Test (with Dunn's post hoc test)."

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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.

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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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."

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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 text and illustrative materials (Tables and Figures). The results section always begins with text, reporting the key results and referring to your figures and tables as you proceed. 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 Tables and/or Figures that should be sequenced to present your key findings in a logical order. The text of the Results section should be crafted to follow this sequence and highlight the evidence needed to answer the questions/hypotheses you investigated. Important negative results should be reported, too. Authors usually write the text of the results section based upon the 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:

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.

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 randomly selected 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.

Differences, directionality, and magnitude: Report your results so as to provide as much information as possible to the reader about the nature of differences or relationships. For eaxmple, if you testing for differences among groups, and you find a significant difference, it is not sufficient to simply report that "groups A and B were significantly different". How are they different? How much are they different? It is much more informative to say something like, "Group A individuals were 23% larger than those in Group B", or, "Group B pups gained weight at twice the rate of Group A pups." Report the direction of differences (greater, larger, smaller, etc) and the magnitude of differences (% difference, how many times, etc.) whenever possible. See also below about use of the word "significant."

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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:

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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(s) 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 problems to avoid:

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 that of female Biology majors, you might report this result (in blue) and your statistical conclusion (shown in red) as follows:

"Males (180.5 ± 5.1 cm; n=34) averaged 12.5 cm taller than females (168 ± 7.6 cm; n=34) in the AY 1995 pool of Biology majors (two-sample t-test, t = 5.78, 33 d.f., p < 0.001)."

If the summary statistics are shown in a figure, the sentence above need not report them specifically, but must include a reference to the figure where they may be seen:

"Males averaged 12.5 cm taller than females in the AY 1995 pool of Biology majors (two-sample t-test, t = 5.78, 33 d.f., p < 0.001; Fig. 1)."

Note that the report of the key result (shown in blue) would be identical in a paper written for a course in which statistical testing is not employed - the section shown in red would simply not appear except reference to the figure.

  • Avoid devoting whole sentences to report a statistical outcome alone.
  • Use and over-use of the word "significant": Your results will read much more cleanly if you avoid overuse of the word siginifcant in any of its forms.
    • In scientific studies, the use of this word implies that a statistical test was employed to make a decision about the data; in this case the test indicated a larger difference in mean heights than you would expect to get by chance alone. Limit the use of the word "significant" to this purpose only.
    • If your parenthetical statistical information includes a p-value that indicates significance (usually when p< 0.05), it is unncecssary (and redundant) to use the word "significant" in the body of the sentence (see example above) because we all interpret the p-value the same way.
    • Likewise, when you report that one group mean is somehow different from another (larger, smaller, increased, decreased, etc), it will be understood by your reader that you have tested this and found the difference to be statisticallysignificant, especially if you also report a p-value < 0.05.

Present the results of your experiment(s) in a sequence that will logically support (or provide evidence against) the hypothesis, or answer the question, stated in the Introduction. For example, in reporting a study of the effect of an experimental diet on the skeletal mass of the rat, consider first giving the data on skeletal mass for the rats fed the control diet and then give the data for the rats fed the experimental diet.

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Report negative results - they are important! If you did not get the anticipated results, it may mean your hypothesis was incorrect and needs to be reformulated, or perhaps you have stumbled onto something unexpected that warrants further study. Moreover, the absence of an effect may be very telling in many situations. In any case, your results may be of importance to others even though they did not support your hypothesis. Do not fall into the trap of thinking that results contrary to what you expected are necessarily "bad data". If you carried out the work well, they are simply your results and need interpretation. Many important discoveries can be traced to "bad data".

Always enter the appropriate units when reporting data or summary statistics.

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DISCUSSION

1. Function: The function of the Discussion is to interpret your results in light of what was already known about the subject of the investigation, and to explain our new understanding of the problem after taking your results into consideration. The Discussion will always connect to the Introduction by way of the question(s) or hypotheses you posed and the literature you cited, but it does not simply repeat or rearrange the Introduction. Instead, it tells how your study has moved us forward from the place you left us at the end of the Introduction.

Fundamental questions to answer here include:

2. Style: Use the active voice whenever possible in this section. Watch out for wordy phrases; be concise and make your points clearly. Use of the first person is okay, but too much use of the first person may actually distract the reader from the main points.

3. Approach: Organize the Discussion to address each of the experiments or studies for which you presented results; discuss each in the same sequence as presented in the Results, providing your interpretation of what they mean in the larger context of the problem. Do not waste entire sentences restating your results; if you need to remind the reader of the result to be discussed, use "bridge sentences" that relate the result to the interpretation:

"The slow response of the lead-exposed neurons relative to controls suggests that...[interpretation]".

You will necessarily make reference to the findings of others in order to support your interpretations.Use subheadings, if need be, to help organize your presentation. Be wary of mistaking the reiteration of a result for an interpretation, and make sure that no new results are presented here that rightly belong in the results.

You must relate your work to the findings of other studies - including previous studies you may have done and those of other investigators. As stated previously, you may find crucial information in someone else's study that helps you interpret your own data, or perhaps you will be able to reinterpret others' findings in light of yours. In either case you should discuss reasons for similarities and differences between yours and others' findings. Consider how the results of other studies may be combined with yours to derive a new or perhaps better substantiated understanding of the problem. Be sure to state the conclusions that can be drawn from your results in light of these considerations. You may also choose to briefly mention further studies you would do to clarify your working hypotheses. Make sure to reference any outside sources as shown in the Introduction section.

Do not introduce new results in the Discussion. Although you might occasionally include in this section tables and figures which help explain something you are discussing, they must not contain new data (from your study) that should have been presented earlier. They might be flow diagrams, accumulation of data from the literature, or something that shows how one type of data leads to or correlates with another, etc. For example, if you were studying a membrane-bound transport channel and you discovered a new bit of information about its mechanism, you might present a diagram showing how your findings helps to explain the channel's mechanism.

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ACKNOWLEDGMENTS (include as needed) | FAQs |

If, in your experiment, you received any significant help in thinking up, designing, or carrying out the work, or received materials from someone who did you a favor by supplying them, you must acknowledge their assistance and the service or material provided. Authors always acknowledge outside reviewers of their drafts (in PI courses, this would be done only if an instructor or other individual critiqued the draft prior to evaluation) and any sources of funding that supported the research. Although usual style requirements (e.g., 1st person, objectivity) are relaxed somewhat here, Acknowledgments are always brief and never flowery.

LITERATURE CITED

1. Function: The Literature Cited section gives an alphabetical listing (by first author's last name) of the references that you actually cited in the body of your paper. Instructions for writing full citations for various sources are given in on separate page. A complete format list for virtually all types of publication may be found in Huth and others(1994).

NOTE: Do not label this section "Bibliography". A bibliography contains references that you may have read but have not specifically cited in the text. Bibliography sections are found in books and other literary writing, but not scientific journal-style papers.

2. Format and Instructions for standard full citations of sources.

3. Literature Cited FAQs.

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APPENDICES


Function: An Appendix contains information that is non-essential to understanding of the paper, but may present information that further clarifies a point without burdening the body of the presentation. An appendix is an optional part of the paper, and is only rarely found in published papers.

Headings: Each Appendix should be identified by a Roman numeral in sequence, e.g., Appendix I, Appendix II, etc. Each appendix should contain different material.

Some examples of material that might be put in an appendix (not an exhaustive list):

Figures and Tables in Appendices

Figures and Tables are often found in an appendix. These should be formatted as discussed previously (see Tables and Figures), but are numbered in a separate sequence from those found in the body of the paper. So, the first Figure in the appendix would be Figure 1, the first Table would be Table 1, and so forth. In situations when multiple appendices are used, the Table and Figure numbering must indicate the appendix number as well (see Huth and others, 1994).

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