Writing Biomedical Research Papers

Ding-I Yang

Institute of Brain Science

National Yang-Ming University

• Essentials of Writing Biomedical Research Papers. Second Edition. By Mimi Zeiger the McGraw-Hill Companies, Inc.

• Title

• Abstract

• Introduction

• Materials and Methods

The Title

Function of Title

• To identify the main topic or the message of the paper

• To attract readers

Hypothesis-testing Papers

• Stating the topic in the title: effects of X on Y in Z, Y in Z, and other pieces of information.

• Stating the message in the title: either in a phrase or in a sentence.

Independent and dependent variables: Effect of X on Y in Z

• The standard title of a biomedical research paper is a phrase that identifies the topic of the paper. For a hypothesis-testing paper, the topic includes three pieces of information: the independent variables that you manipulated (X), the dependent variables you observed or measured (Y), and the animal or population and the materials on which you did the work (Z).

• Where necessary, two other pieces of information may also be included in the title: the condition of the animals or subjects during the study and the experimental approach.

• Always include the animals studied unless in humans. However, when a subpopulation of humans was studied, the subpopulation is always included in the title.

Papers with only dependent variables: Y in Z

• Y is the dependent variables that are observed or measured, and Z is the animal or population and the material on which the work was done.

Other information in the title

• The condition the subjects or the animals were in during the experiments or the experimental approach.

• However, include these pieces of information only if such details are important.

Stating the message in the title: phrase title

• If the paper has a strong, unambiguous message supported by strong, unequivocal evidence, the title of the paper can state the message (the answer to the question) in a phrase or in a sentence.

• In a phrase title, the message is expressed by either an adjective or a noun (depending on the verb used in the question and answer) placed before the dependent variable at the beginning of the title.

Stating the message in the title: sentence title

• Using a sentence to state a message is stronger than using a phrase is. This is because verbs convey action more powerfully than nouns or adjectives. Thus, the same title stated as a phrase and as a sentence will sound stronger as a sentence.

• However, you should use a sentence title only if you have a clear message backed up by solid evidence.

Descriptive Papers

• For describing a new structure, the title names the structure being described and states its key function.

• The structure comes first in the title followed by the function.

Methods Papers

• A method, an apparatus, or a material: use the name in the title if the method has a name. If the method does not have a name, use a category term such as “method” or “apparatus”.

• Its purpose: for doing…• Name the animal or specific population in humans

the method is used for.• Whether the method is new or improved (for….,

describe the most important advantage of this method, or just “improved” if it is difficult to name a specific important feature)

Hallmarks of a Good Title Is…..

• Accurately, completely, and specifically identifies the main topic or the message of the paper, either in a sentence or in a phrase

• Unambiguous

• Concise

• To begin with an important term

Accurate

• For hypothesis-testing paper, check that your title is accurate by comparing it with the question and answer.

• For a descriptive paper, the terms used for the structure and the function in the title should be the same as those in the message stated in the Introduction and the Discussion.

• For a method paper, the name of the method, its purpose, and the animal or population should be the same in the title as in the Introduction, Discussion, and Abstract.

Complete

• In a paper with two messages, select the most important one for the title if you cannot create a title that reflect both messages.

• With several independent/dependent variables without a category term available to include them all, select the most important independent and dependent variable for the title.

• Announcing the main variables of the paper is stronger then trying to fit all into the title.

Specific

• And: use it only for parallel terms, NOT for joining the independent and dependent variables in the “X and Y in Z” instead of “Effect of X on Y in Z”. “And” does not implicate any relationship between X and Y.

• With: change with to a more specific word.

Unambiguous

• Avoid noun cluster (noun + noun: Blood-Brain Barrier CSF pH Regulation)

• Do not use abbreviation. Even if an abbreviation is well known in one specialty, it could be confusing to readers from other specialties.

• However, when the abbreviations are better known than the words they stand for, such as DNA and RNA, use abbreviations. In addition, abbreviations for chemicals, such as NO (nitric oxide), can be used. Nevertheless, if you have space, spell it out if it is a short familiar word like “oxygen”.

Concise

• A concise title is a short title without sacrificing accuracy, completeness, specificity, or clarity.

• Keep your titles shorter than 100 characters and spaces (120 is the outer limit). But how???

To make titles concise…

• Omit unnecessary words such as “nature of”, “studies of”, “effects of”, omit “the” at the beginning of the title.

• Compact the necessary words as tightly as possible by category terms (liver, blood…vs. extra-pulmonary) adjectives to express a message (reduced vs. reduction in), and noun clusters (NGF protection vs. protection by NGF).

Important word first

• Either the dependent variable or the independent variable can be the most important word (considering the journal you are submitting your manuscript, who are the readers?).

Subtitles

• A technique for putting an important word first is to use a main title followed by a subtitle.

• The main title states the general topic and the subtitle states the specific topic.

• A subtitle is separated from the main title by a colon (:).

Relation of the subtitle to the main title

• Material: Variables Studied• Variable Studied: Experimental Approach• Variable: Function• You need to figure out the appropriate preposition

between the subtitle and the main title in order to reconstruct the full title.

• Whatever the relation, a crucial element in the use of subtitles is that the relation between the subtitle and the main title must be obvious.

• Subtitles for a series of papers: a risky idea….• Use subtitle only if it is the best way to put an important

word first.

Details

• Word choice: “increased” and “reduced” should be used to modify quantitative words; “improved” and “impaired” should be used for qualitative words.

• Determining the length of a title: count both characters (a category term for letters and punctuation marks) and spaces between words.

Running titles

• Also known as running heads. Short phrases that appear at the top or bottom of every page, or every other page, in a journal article. The purpose is to identify the article. Some journals use the authors’ names instead.

• The running title is shorter then the title (probably less specific?).

Running titles for three types of articles

• Hypothesis-testing papers: name the independent and dependent variables, but not the animal/population.

• Descriptive papers: name the structure and a brief version of the function.

• Method papers: name the method only or the population

The Abstract

Contents of the Abstracts for Hypothesis-Testing Papers

• Question: as a question or as a hypothesis

• Experiments: state the materials and experimental approach, including dependent and independent variables

• Results: give data, if at all, only in percent change

• Answer: state the answer to the question. Do not write vague statements.

Background and Implication

• At the beginning of the abstract, you can include one or two sentences for background introduction. This is for those readers who may wonder why you are asking your question. This sentence should be the same as that given at the beginning of the Introduction, only briefer.

• You can include a sentence stating the implication, speculation or recommendation, at the end of the abstract. However, DO NOT substitute implication for answer.

Organization of the Abstracts for Hypothesis-Testing Papers

• Overall organization

• Organization of results

Overall Organization

• Often the details of the experiments done (specific independent and dependent variables, doses, methods) are given in the sentences that state the results found. This organizational strategy avoids repetition.

• Although the overall organization of the abstract follows the organization of the paper, the abstract does not give equal weight to all sections of the paper. The abstract include much of the Introduction but only a few details from Methods, only key results/data from Results, and only the answer and maybe an implication from the Discussion.

Organization of Results

• If you include two or more results in the abstract, arrange them in a logical order, such as chronological order, most to least important or least to most important.

• When organizing from most to least important, describe control results last (if you include them at all).

Writing of the Abstracts for Hypothesis-Testing Papers

• Continuity

• Signaling Topics

• Verb Tense

• Sentence Structure

• Word Choice

• Abbreviations

Continuity

• Repeat key terms

• Use consistent order for details

• Keep the same point of view in the question and the answer

• Use either parallel form or consistent point of view for comparisons and other parallel ideas (Example 10.3: four different drugs).

Signaling Topics

• Abstracts are conventionally written as one single paragraph, albeit with exceptions. Therefore, it helps the readers if you signal the parts of an abstract both visually (by starting a new sentence) and verbally (by signaling the topic at the beginning of the sentence).

• Begin a new sentence for the question, the results found, and the answer. The question and the experiment done are often in the same sentence, so only the question needs to be signaled. However, if the sentence is too long, the question and experiment can be in separate sentences, each having its own signal.

Signaling Topics

• Be careful to distinguish the implication from the answer by using a cautious signal such as “These results suggest that …..”. The verb in the suggestion can also be cautious, “may inhibit”, “may play a role in,” etc.

• Always put answer and implication in separate sentences.

Verb Tense and Word Choice

• Verb tenses in the abstract should be the same as those in the paper: present tentse for the question and the answer; past tense for the experiments done and the results found.

• Use simple words. Avoid jargon.

Abbreviations

• Avoid abbreviations wherever possible. You can use widely accepted abbreviations such as DNA, but semi-standard and nonstandard abbreviations should be avoided.

• If you must use a nonstandard abbreviation that is not widely accepted, define it the first time you use it in the abstract. Try to have only one abbreviation in an abstract and certainly no more than three.

Length of the Abstracts for Hypothesis-Testing Papers

• Most journals limit the length of the abstract usually to 250 words or less. It is better to keep it within 150 words.

• If no limit is stated, make your abstract no longer than the abstracts in recent issues of the journal.

• If you can summarize your apper in fewer words than the maximum allowed, do so. Do not add more and more details. The overview is easiest to see in a short abstract.

• Do not write in the style of a telegram; that is, do not omit necessary “a”, “an” and “the”.

Abstracts of Descriptive Papers

• Contents and Organization

• Writing including signaling topics, verb tense, sentence structure, word choice, and abbreviations.

Contents of the Abstracts for Descriptive Papers

• The message of the paper

• The results that support the message

• The implication of the message

• If necessary, background information can be added at the beginning of the abstract.

Organization

• Since there is no hypothesis to be tested in descriptive papers, the message is stated at the beginning of the abstract.

• The results that support the message come immediately after the message, to convince the reader that the message is true.

• The implication is stated at the end. Methods, if any, are included in the sentences that state the results.

Writing of the Abstracts for Descriptive Papers

• Only the message and the implication are signaled in a descriptive abstract.

• Verb tenses are a little trickier in descriptive abstracts than in hypothesis-testing abstracts. If a statement is still true, use present tense; if the statement is about something done or found in the past, use past tense. Use present tense to describe a structure; use past tense to describe the result of an experiment.

• For implications, the verbs can be cautious or not (use the present tense).

• As usual, sentences should be short, words should be simple, and abbreviations should be avoided.

• Keep the abstract as short as possible, never more than 250 words.

Common Problems in Abstracts of Hypothesis-Testing Papers

• Deviations from the standard for, including omitting the question, stating the question only vaguely, stating an implication instead of an answer, and substituting a descriptive abstract for a hypothesis-testing abstract.

Question omitted or stated vaguely

• Without the question, the readers read the abstract blindly. They understand the abstract only at the end and then have to reread it to fit the details into the picture.

• In a question stated vaguely, only the dependent variable is named, like “Y was studied”. You should use a verb to join the independent and dependent variables. For questions that have only a dependent variable, the specific aspect of the dependent variable studied must be named.

Answer Not Stated• The function of the abstract is to provide an

overview of the story and the answer is the culmination of the story, not stating the answer undermines the abstract.

• Further, most of the readers do not realize that the answer is missing, so they could be confused without knowing it.

• Therefore, for a clear abstract that has an unmistakable message, the answer must be stated and clearly signaled.

• The answer should use the same key terms, the same point of view, and the same verb as in the question, so it is easy to see that the answer answers the question asked.

Substitution of a Descriptive Abstract for a Hypothesis-Testing Abstract

• A descriptive abstract implies that you had no hypothesis, but rather made a discovery. This implication is misleading and makes the story of the science unclear.

• If your study tested a hypothesis or asked a question, you should include the hypothesis in the abstract and write a hypothesis-testing abstract, not a descriptive abstract.

To ensure that your abstract provides a clear overview, you must

1. State the question you asked2. Make the statement of the question specific

rather than vague or general (by naming both the independent and the dependent variables, using the same key terms and the same point of view as in the answer, using the same verb as in the answer)

3. State the answer clearly4. Write a hypothesis-testing abstract, not a

descriptive abstract, when you are testing a hypothesis.

Excessive Length

• Retain the essential information and omits less important details, such as definition, experimental preparation, details of methods, confirmatory results, and comparisons with previous results.

• Omit exact data; instead percent change is given.

• Note that the solution to condensing an excessively long abstract is not to use abbreviations.

Variations

• Follow the form requested by the journal.

• Clinical journals (Stroke, Annals of Internal medicine) may request a specific form, known as structured abstracts.

• Rather than having a single paragraph, these abstracts contain a sequence of short paragraphs, each preceded by a subheading.

• British Journal of Pharmacology (next slide)

Abstracts of Methods Papers

• The abstract of a method paper should include the following information: the name; the purpose; the animal or population; the key features of the apparatus or material or how the method or apparatus works, or both; the advantages; how the method, apparatus, or material was tested; and how well it works.

• Name: use the name or a category term or if possible, add an adjective that states a key feature of the method before the category term. You can add “improved’ if this is an improved version of an existing method. It is not usually necessary to indicate that a method is new, but it is OK to do so.

• Purpose: “for doing X” or “to do X”.• Animal or population: unless the population

studied was all humans.• Key features and how the method works, or

both: this is to give the reader an idea of what the method, apparatus, or material is.

• Advantages: to convince the reader that a new method is a good one or that an improved method is better than existing methods. The advantages of an improved method should solve the problems of the existing methods. Stating the advantages is important so that the reader knows why the method is needed.

• How it was tested and how well it works: this is included to convince the reader that the method is reliable, accurate, etc.

Organization

• The abstract should always begin with the name of the method followed by its purpose and the animal or population and then by its key features or how it works. Either the advantages or how the method was tested and how well it works can come at the end.

• More than one kind of information can be included in one sentence. Specifically, the name of the method, its purpose, and the animal or population are virtually always in one sentence, and how the method was tested and how well it works are often in one sentence.

Verb Tense• In the sentence that names the method, the verb i

s in past tense (or present perfect tense) or present tense, depending on the verb used. For example, “an improved method has been developed” or “an improved method is described”.

• Verbs in sentences that describe the method and its advantages are in present tense. For example, “the system includes…”; “the method simplifies the conventional procedure..”.

• Verbs in sentences that describe how the method was tested and how well it worked are in past tense. For example, “the flowmeter accurately measured a wide range of tidal volumes.”

Indexing Terms

• Some journals ask authors to supply a list of indexing terms, or key words, to guide indexers in selecting terms for the journal’s index. Indexing terms are sometimes printed after the abstract or after the title in the journal’s table of contents.

• Indexing terms should name important topics in your paper. Select terms that you would look up if you were trying to find your own paper and that would attract the readers you hope to reach.

• When selecting indexing terms, use the most specific terms possible. For example, in a paper about erythromycin, “erythromycin” should be used instead of a more general term “antibiotics”. It is easy to extrapolate from the specific to the general terms if necessary, but it is not to do it in the opposite way.

• Indexing terms can be phrases as well as single words.

• Because it is easy to pick indexing terms out of the title of the paper, some journals ask authors to supply only indexing terms that are NOT in the title.

• Words used as indexing terms do not have to be in the paper.

Abstracts for Meetings

• Function: to show that you have a valuable contribution and to lure an audience to your talk/poster.

• Content: similar to the abstracts for papers except that abstracts for meetings are likely to include more details of methods and to display data in a table or a graph. The extra information helps the selection committee evaluate the validity of the work. In addition, the abstracts for meetings are more likely to include implications than are abstracts of papers, to indicate the importance of the work.

Amounts of Details and Use of Abbreviations

• Do not cram as many methods details, data, and statistical details as possible into an abstract for a meeting. It is better to give one good result than to give a lot of data.

• Do not use abbreviations.• Keep in mind that even a detailed abstract for a

meeting cannot replace the paper. Thus, judicious use of details and abbreviations, not the maximal use, shows that your contribution is valuable and lures an audience to your talk.

Presentation of Data and Results

• Data included in an abstract for a meeting, unlike data in an abstract of a journal article, are sometimes presented in a table or a graph, which should be designed clearly. The only differences are that in abstracts no title is given for tables and no legends are included for graphs.

• Do not omit the statement of the results that the data support. For greatest clarity, the table or graph should be placed after the sentence that states the results that the data support, not instead of the results sentence.

Introduction

Function

• To awaken the reader’s interest: direct to the point, as short as possible, and consistent with clarity and informativeness

• Be informative enough to prepare readers (whether or not they are the specialists in your fields) to understand the paper: written in a readable style.

Introduction: the first step of the story line

• Hypothesis-testing paper: question

• Descriptive paper: message-the key features of a new structure

• Method paper: new or improved method, material, or apparatus

Content of introduction for hypothesis-testing papers

• Known, unknown, question: what the question of the study and why the author is asking this question. The question is stated either as a hypothesis or as a question. The story of where the question came from is composed of what is known or believed about the topic and what is still unknown or problematic.

• Materials and animals or populations: name the materials (cell lines, organs, tissues, animal or human population). Where necessary, this statement can be expanded into experimental approach taken to answer the question.

• No answer, results, or implication: they belong to other sections of your manuscript. Introduction is to lead into the paper. Answers, results, and implications sound like the end of the abstract. They close off rather than leading in.

• Retrospective vs. prospective study design: if a question is asked after the data were gathered, the fact that the study was retrospective must be stated in the introduction. If the experiments were designed and the data were gathered to specifically answer this question, that fact does not need to be stated. If a study is partly retrospective and partly prospective, each part should be identified in the Introduction.

• References: the statement about what is known must include references, which should be chosen to reflect the key work that led to the question of your paper. The number of references should be kept minimum. If a lot of work has been done on the topic, select papers describing the first, the most important, the most elegant, and the most recent studies. You can also cite review articles (for a recent review, see Hsu et al., 2008).

• Newness (novelty) and importance: new, true, important, and comprehensible. The introduction is the place to make clear that this work is new by stating the “unknown”. The importance can be stated in Introduction, if it is not obvious, or in Discussion.

Organization for hypothesis-testing papers-funnel shape

• Known, unknown, question: the question is the focal point (p. 108).

• Known: the first step in the funnel, often includes many sentences that narrow by appropriate scientific logic to the unknown.

• Unknown: often just one sentence. It is important for two reasons. The unknown indicates that the work is new. The unknown links the known and the question, creating a story line. Unknown is virtually the same as the question. Thus, once unknown is stated, the question is determined.

• Question: specific topic of the paper and the end of the funnel. General topic of the paper is named in the first sentence of what is known.

• Experimental approach: if the experimental approach is included, the logical place for it its after the question. Putting the experimental approach before the question is like treating it as background, which does not work. The background (known, unknown) is what leads to the question. The experimental approach does not lead to the question, it follows from the question.

• Importance: there is no particular spot in the funnel to indicate the importance of the work (p. 109 and examples 4.1, 4.2).

Continuity• In longer Introduction, you tell the story in two levels.

One is the overall story with known, unknown, and question, which run throughout the Introduction. The second one is the “mini stories”, which run within paragraphs or parts of paragraphs.

• Overall story: see p. 111• The techniques of continuity: (1) start a new

paragraph. (2) transition phrase with repeated key terms after an intervening mini-story. (3) repeating earlier step as the subject of the sentence that states the next step is an effective way to use repeated key terms to create continuity, especially after a mini-story that interrupts the two steps (p.111).

Topic sentences

• Mini-story: see p.112.• Topic sentences help ensure that the story

line is clear in longer introductions. Longer introduction, unlike shorter one in which every sentence or part of a sentence is a step in the story, have separate sentences of supporting details. Therefore, the sentences in the overall story supported by the supporting sentences become topic sentences.

The question as a super-topic sentence

• The question is a topic sentence of the paper as a whole.

• Just as a topic sentence gives an overview of a paragraph, the question gives an overview of the paper. Just as every sentence in a paragraph relates to the topic sentence, so every sentence in the paper relates to the question. This is one reason why a precise statement of the question is so important.

Writing of a hypothesis-testing paper: the unknown

• State (clearest) or imply the unknown. One way to imply an unknown is to state a suggestion or a possibility. Thus, if you say something is possible, that implies that it is not yet known.

• See example 4.3.

Writing of a hypothesis-testing paper: the question

• Precision: the most scientific way of stating the question of hypothesis-testing research is as a hypothesis. The advantage is that the question is precise, the reader can easily anticipate the answer. The reader can also read the paper in a direct way rather than blindly.

• If a question is stated as a question, it should be equally precise. That is, the question should name the variables studied and use a precise verb in present tense (examples 4.1 and 4.3).

Writing of a hypothesis-testing paper: inevitability

• The question should follow inevitably from the previous statements of what is known or believed and what is still unknown or problematic.

• See example 4.1.

Question based on suggestive evidence

• Sometimes, the question is not stated immediately after the unknown or the problem. Instead, evidence suggesting a possible answer is stated. In this case, the question should follow inevitably both from the unknown and from the suggestive evidence.

• Example 4.4. In this example, the hypothesis is based on the earlier statements because key terms from the known, from the unknown, and from the suggestive evidence all appear in the hypothesis.

Two questions, linked questions, and questions stated in the Unknown

• In a paper with two questions, both questions must follow inevitably from the previous statements. If the background information leading to the second question is omitted, as frequently happens, the reader does not know where the second question comes from. See Example 4.5.

• If the second question depends on the answer to the first one, the questions can be linked by “if so” or a similar phrases. No background information needs to be added. See Example 4.6.

• If the question is presented in the statement of the unknown, then it is unnecessary to sate the question again. Instead, use “to answer this question” or “to test this hypothesis”. See Example 4.7.

Experimental approach

• Sometimes the Introduction can end after a statement of the question. However, it is helpful for the reader to know the experimental approach to answering the questions, especially if the approach is new, unusual or complicated, or if the study needs to be identified as having been done in vitro or retrospectively.

• In general, the experimental approach is short, usually in one sentence; at most two or three. Usually the experimental approach describes one of the variables (independent or dependent) in addition to naming the animal studied (Example 4.1)

• If your paper have no “Study Design” subsection in the Methods section, but instead run the story of the experiments done to answer the question through the Results section, then including a complete overview of the experiments at the end of the Introduction is crucial.

• In these papers, the experimental approach at the end of the Introduction is the only overview we get of the experiments done. In Results section, the story is fractionated, one or two sentences per paragraph. The overview of the experiments should be stated compactly in one spot – at the end of the Introduction.

Signals of the question and the experimental approach

• The signals vary depending on whether the question is stated as a hypothesis or as a question, and on whether the question and the experimental approach are in the same sentence or in separate sentences.

• See P. 118 for details.

Animal or human population and material

• The animal and the material studied must be stated in the Introduction. Where the animal is stated depends on the kind of question you are asking. If the question is about a particular animal, name the animal in the question, as in Example 4.8.

• If the question is not limited to the animal studied, usually because the animal is serving as a model of a human condition, name the animal in the experimental approach (examples 4.1, 4.2, and 4.5). If the model is a new one, also establish its validity.

• Humans are frequently not mentioned in the question (example 4.3). Specific human population is always stated in the question (example 4.9).

Answer to the question and length• The answer to the question should not be include

d in the Introduction. The reader knows the answer from having read the abstract.

• The Introduction section should be as short as possible consistent with clarity and informativeness. Generally, shorter is better. For a typical journal article, one double-spaced page (about 250-300 words) is often sufficient. When a longer Introduction is needed, try to keep it to two double-spaced pages (500-600 words).

• Do not review the topic; that is what review articles are for. The purpose of the Introduction is to awaken interest and to prepare the reader to understand the paper. Long introductions kill off interest and are often confusing and misleading.

Content and organization for Descriptive Papers

• Known – message.• Descriptive papers do not have questions

or hypotheses. Thus, the introductory funnel in a descriptive paper can have only two steps: known and message.

• The message is the discovery being reported in the paper. Its relation to the known is that it extends or contrasts with what is known. See Example 4.10.

Content and organization for Methods Papers

• The introduction of a method paper begins by stating that a method, an apparatus, or a material is needed and then goes on to give the reasons.

• The Introduction then states one or more problems or limitations of the existing method, apparatus, or material and ends by stating what the new method, apparatus, or material is and what its advantages are. The advantages should be the solution to the problem or limitation.

• See example 4.11.

Details: verb tense

• Verb tenses in the introduction, like verb tense everywhere in the paper, depend partly on the type of statement and partly on the meaning of the verb.

• Most importantly, the verb in the question must be in present tense, because the question asks if something is true in general and not just in your experiments. See p. 121 for details.

Materials and Methods

Function

• To tell the reader what experiments you did to answer the question posed in the Introduction in hypothesis-testing papers.

• To tell the reader what experiments you did to obtain the message stated in Introduction in descriptive papers.

• To describe the new method in complete details and to tell the readers what experiments you did to test the new method.

Story Line

• For hypothesis-testing papers and descriptive papers, the first step is respectively the question and the message (structure) being described.

• The second step i-n the story line is an overview of the experiments you did. This overview gives the strategy of the experiments, the plan that connects the methods to each other and to the question or the message (Page 127).

Story Line

• For a method paper, the first step in the story line is a statement that you are presenting a new or improved material, method, or apparatus.

• The second step has two parts: a complete description of new method (materials or apparatus), and a description of how this new method (materials or apparatus) was tested. Both are described in the Methods section.

Content

• Cookbook: the main content of the Materials and Methods section is a detailed description of the materials and methods you used.

• In addition, in hypothesis-testing papers in which all the experiments are designed in advance, the Materials and Methods should also include an overview of the experiments done to answer the question. This overview is known as “Study Design”.

Materials

• Chemicals (drugs, culture media, buffers, gases)

• What was examined (experimental materials, experimental animals, or human subjects)

Methods• Essential information include: what you did

(including Study Design), in what order, how you did it, and why you did it (especially if the reasons are not so obvious).

• Other information (as needed): preparation, assumptions, definitions of indicators.

• The Methods section also includes references.• The Methods section does NOT include results.

However, intermediate results (results used in calculations done to obtain results that answer the question) can be included in the Methods section. Putting intermediate results in Methods is a better choice than in Results because intermediate results are more relevant to methods that to results.

Materials: drugs

• For drugs, state the generic name, manufacturer (including city, state, and country), purity and concentration. If the drug is in solution, state the solvent, pH, temperature, total volume infused, and rate of infusion, if appropriate.

• State the amount of drug administered per kilogram of body weight and the duration of the injection. If the drug is placed in an organ bath or reservoir, calculate its concentration in fluid.

Materials: culture media, buffers

• For culture media and buffers, state the components and their concentrations. Also state the temperature, volume, and pH, if appropriate.

• However, for those commonly used buffers such as phosphate-buffered saline (PBS), sometimes you can omit the detailed components. Also for culture media, you can only name the commonly used media (for example, Ham’s F-12 medium) without stating detailed components.

Materials: gases

• For gases, state the components and their concentrations (for example, 1% oxygen). Also state the flow rat if appropriate.

Experimental Materials

• If you studied a molecule, cell line, tissue, etc., specify it.

• For cell line, specify the numbers of passages or the ranges of generations in which the cells were used for your experiments.

Animals• For animals, state the species and weight, and

also the strain, sex, and age, if they are important. • Give details of sedation and anesthesia agent

used, amount, route, administration (single, repeated, or continuous), depth of anesthesia and how it was assessed. If anesthetics were not used, state the reasons. State that the research was approved by the appropriate committee at your institution. If necessary, state that the numbers of animals sacrificed were kept minimal or all efforts were exerted to minimize the suffer of these animals.

Materials: human subjects• Give enough information about age, sex, race,

height, weight, state of health or disease, and specific medical and surgical management to be of use to researchers who want to compare your data with theirs or other people’s or to clinicians who want to see if your findings are applicable to their patients.

• Much of this information can be presented in tables. These tables should be cited in the Methods section, not in the Results section. Tell how the subjects were selected (inclusion and exclusion criteria). State that the research was approved by the appropriate committee at your institution.

Methods: what you did

• Study Design: for hypothesis-testing research in which all experiments are designed in advance, including physiology studies, clinical studies, and some biochemistry studies, the overview of the experiments should be given in a separate subsection of Methods, called “Study Design”.

• The Study Design should include the following information: Questions asked, Independent variables, dependent variables, and all the controls (baseline, sham, placebo etc).

In addition, the Study Design should make clear:

• What one experiment consisted of• Order of the interventions, of the

measurements, of the experiments• Duration of the interventions, of the

measurements, of the experiments• Sample sizes (n): unless indicated in a

different subsection of the Methods section such as Animals, Subjects, Data Analysis etc.

See Example 5.1 (p. 130-131).

Study Design versus Experimental Approach

• In papers that have a Study Design subsection in the Methods section and experimental approach at the end of the Introduction, some overlap exists. This overlap helps to keep the story line that runs from the Introduction to the Methods section clear.

• Often the experimental approach is brief. In other cases the experimental approach gives a more complete overview including both independent variables, dependent variables and controls. Despite the overlaps, however, the Study Design is always more extensive than even the most complete experimental approach. This is because Study Design includes specific details (timing and dosages) that are not included in experimental approach.

• In hypothesis-testing papers in which all experiments are designed in advance, Study Design is necessary for readers to know the strategy you used to answer your question.

Study Design as “Topic Sentence”

• Because the Study Design gives an overview of the experiments done to answer the question and is followed by cookbook details, it can be viewed as a sort of topic sentence for the methods subsections of the Materials and Methods section.

• Like all topic sentences, the Study Design should be as brief as possible, so that the overview is clear.

Cookbook: how you did the experiments

• Methods and apparatus: the amounts of details needed when describing a method or an apparatus depends on how well known the methods or apparatus is. A well known method or apparatus needs not be described. All that is needed is the reference.

• See Example 5.2-4 on p. 132 for well known method, less well known method, and modified method.

Analysis of data (Statistical Analysis)

• Provide the reader with information about both the magnitude of the data and the variability.

• If the data seem to have been drawn from a normal distribution, it is reasonable to use the mean and standard deviation (SD) to summarize the data. The mean provides the overall magnitude of the data. The SD provides a measure of the variability in the sample.

• Standard error of the mean (SEM) equals SD divided by the square root of the sample size. However, mean and SEM is generally not a good way to summarize data for two reasons.

• One reason is that the SEM does not indicate the variability in the sample as an estimate of the variability in the underlying population; rather, SEM quantifies the uncertainty in the estimate of the true mean (that is, the mean of the underlying population). Another reason is that many readers do not know the difference between SD and SEM. When these readers see a SEM, they misinterpret it as indicating the variability in the sample.

• When the data appear to come from a skewed distribution (that is, an inordinate number of high or low values, compared to the mean), the mean and SD do not provide an accurate summary of the data. In this case, you may report the median and the interquartile range (that is, the range between the 25th and the 75th percentiles).

• For statistical analysis, state the statistical tests that you used and, for tests that are not well known, give a reference to the report or book that describes the tests as you used them. Well known tests include Student’s test, chi square, standard forms of analysis of variance, linear regression, correlation.

• If you used a computer program to analyze your data, stat which program, including version or release number, and which non-default options you used.

• If the size of the sample analyzed for each comparison (n) is not obvious from the Study Design, state the sample size in the Analysis of Data subsection.

• State the P value at which you considered differences statistically significant. In addition, give specific P values in figure legends, footnotes to tables, or the Results section, where each P values can be linked with the relevant data.

• To determine whether to accept or reject a hypothesis, a P value is not always sufficient. A difference can be statistically significant but biologically or clinically unimportant. For example, a difference can be statistically significant because the sample size is larger rather than because a treatment has a large effect. Thus, it is often useful to assess the size of the difference in comparison with the variability in the data sample by calculating the 95% confidence interval.

Other information: preparation, assumptions, and indicators

• Preparation consists of procedures done before the experiments can be done. In physiology experiments, for example, preparation often includes anesthesia and insertion of catheters (see Example 5.16 on p. 141).

• If your experimental design is based on assumptions, state the assumptions and your reasons for believing that they are valid. If your reasons are lengthy, they can be presented in Discussion.

• If you assessed an indicator of a variable, make clear what variable it is an indicator of.

Why you did the experiments: purposes and reasons

• It is not always obvious to the reader why you did certain procedures, so state the purpose or reason for any procedure whose relation to the question is not obvious.

• Purposes are commonly signaled by an infinitive phrase (“to” plus the verb) or a prepositional phrase (“for” plus the noun made from a verb).

• See Examples 5.6-9 on p. 134-135).

Organization: overall organization

• The natural organization of the Materials and Methods section is chronological order.

• Materials and Methods is divided into subsections based on the type of information. Each subsection has its own subheading. For hypothesis testing papers that design all experiments in advance, these subheadings are generic (next slide).

For animal studies

• Materials• Animals• Preparation• Study Design• Interventions• Methods of Measurement• Calculations• Analysis of Data (or Statistical Analysis).

For Clinical Studies

• Study subjects• Inclusion Criteria• Exclusion Criteria• Study Design• Interventions• Methods of Measurement• Calculations• Analysis of Data

Omission of some subheadings• For examples, the Materials and the Animals subsections

are omitted if there are not enough details to warrant a separate subsections. Instead, the details are included in Methods of Measurement and Surgical Preparations, respectively.

• If no preparation (such as surgical placement of catheters) was done, the Preparation subsection its subheading are omitted.

• Similarly, interventions may not need to be described in more detail than given in the Study Design, so the interventions subsection can be omitted.

• Sometimes inclusion and exclusion criteria can be combined into a single subsection having a single subheading, or they can be brief enough to be included in the Study Subjects subsection.

Overall organizations

• For hypothesis-testing papers in which results of one experiment determine what the next experiment will be, the subheadings of the subsections are specific. The subheadings name the specific material or variable worked on or the specific procedure done.

• See next slide for example.

• Media and growth conditions

• Plasmid constructions

• Yeast strains

• Plasmid rescue and DNA sequence analysis

• Frame-shift rate determination

Overlap between Study Design and Methods of Measurement

• The dependent variables are always mentioned twice in the Methods section: once in the Study Design as part of the overview and once in the Methods of Measurement (cookbook).

• Although the dependent variables are mentioned twice, what is said about the variables is different: the Study Design tells that the dependent variables were measured; the Methods of Measurement tells how the dependent variables were measured.

• This overlap is similar to the repetition of key terms in the topic sentence and supporting sentences of a paragraph and is what keeps the story line going.

Signaling the Organization by Subheadings

• Subheadings signal topics of subsectins that can include one or more paragraphs.

• Example 5.10

Gel Filtration. After centrifugation at ……

Signaling the Organization by Topic Sentences

• Topic sentences can be used to signal the topic of a paragraph, especially when a subsection has more than one paragraph.

• Example 5.11The effects of intra-arterial pressure gradients on steady-state circumflex pressure-flow relations derived during long diastoles were examined in five dogs (as follows). To obtain each pressure-flow point, we first…..

Signaling the Organization by Transition Phrases or Clauses

• Transition phrases or clauses that state purposes can be used to signal the topic of a paragraph in the Materials and Methods section. The transition phrase or clause comes at the beginning of the first sentence of the paragraph, and the end of that sentence states the first step in the procedure. The remaining sentences in the paragraph state the subsequent steps.

• Next slide.

• To prepare the enzyme solution, the cells were first incubated in lipoprotein-deficient serum for 48 h. Then, after being washed….. The homogenate was centrifuged at 700 g for 10 min and the resultant supernatant was used as the enzyme solution.

Relationship of Parts

• Relate the Methods to the Results. For every result in the Results section there should be a method in the Methods section.

• Relate the Study Design to the Question it answers. To ensure that the Study Design relates clearly to the question it answers, restate the question before describing the study design. The question can be restated in a topic sentence (The effect of high-frequency ventilation of the … was ascertained as follows.) or in a transition phrase (To determine the effect of beta-adrenergic agonists on .., we instilled….).

• When there is more than one question, restate the appropriate question at the beginning of each study design, so that the reader knows which study design relates to which question.

• When restating the question, be sure to use the same key terms, the same verb, and the same point of view, as in the original question, so that the reader can easily recognize that this question is the same question asked in the Introduction.l

Length

• The Methods section should be as long as necessary to describe fully and accurately what was done and how it was done.

• However, Methods should be written in the fewest words possible and should not contain fussy detail. What constitutes fussy detail depends on what the readers of the journal to which you submit your paper can be expected to know.

Details: animals, verb tense, and sample size

• Use the animal’s name (mice, rats) rather than the general term “animal”.

• Methods are reported in past tense. However, to describe how data are presented in the paper, use present tense, because this information is still true.

• When you have several different sample sizes, be sure that the numbers add up correctly throughout the Methods section and the whole paper. For studies of human subjects, make clear how the numbers of subjects relate to each other. See p.139 for details.

Details: information in parentheses

• In the Methods section, details are often placed in parentheses so that the flow of ideas in the sentence will not be interrupted. Some details that are commonly placed in parentheses are weights of animals or human subjects, concentrations, doses, manufacturers’ names, and model numbers.

• Horse red blood cells (Colorado Serum Company, Boulder) were washed…

• 10 mg nitroglycerin versus nitroglycerin (10 mg)

Details: precise word choice

• Use the verb that indicates precisely what you did: measured, calculated, estimated….

• For example, “We measured heart rate and ventricular pressure and calculated maximal positive dP/dt.”

• If you want to discuss measurements and calculations together, using one term that includes both, use “determined”. For the same example, “We determined heart rat, ventricular pressure, and maximal positive dP/dt.”

Avoid interchanging the following terms:

• Study: A sustained, systematic inquiry into, or examination of, a phenomenon, development, or question

• Experiment: A test done to examine the validity of a hypothesis (referred to as a “study” when the subjects are human)

• Series: A set of two more related experiments

• Group: A number of experimental animals or human subjects treated similarly or having similar characteristics

One paper is equivalent to one study, but it can report many experiments, series of experiments, and groups of animals or subjects. See example below.

In this study, the experiments were organized into two series. In the first series, we measured the loss of 9-m-diameter microspheres from the lungs; in the second series, we measured the loss of 9-m-diameter microspheres from the left ventricular myocardium. Each series of experiments was performed on two groups of dogs, one group anesthetized with Innovar-Vet and a 75:25 mixture of nitrous oxide and oxygen and the other group anesthetized with halothane.

Details: point of view

• Point of view of the experiment: Blood samples were drawn.

• Point of view of the experimenter: We drew blood samples.

• If you choose the point of view of the experimenter, many of your sentences will begin with “We”, which is obnoxious. There are several techniques to reduce the numbers of sentences beginning with “We”, as shown in next slide.

• Put all the steps of a single procedure in one sentence. We dehydrated the pellets, cleared them with propylene oxide, and embedded small pieces of each pellet in blocks of resin.

• Begin some sentences with a transition word or phrase indicating time sequence. After 30 s, we centrifuged the samples. Then we centrifuged the suspension as before.

• Begin some sentences with purposes. To prepare isolated surface layers for electron microscopy, we resuspended…

• Begin some sentences with reasons. Because these surface layers did not stick well to polylysine, we processed them as small pellets.

• Begin some sentences with phrase subordinating the first step of a procedure. After fixing the surface layers for 2 h, we rinsed them three times….

Handling Point of View in the Methods Section: simplest level

• At the simplest level of sophistication, you can choose to write entire Methods section from one point of view.

• The point of view of the experiments has the advantage of making the topic the subject of the sentence, thus emphasizing what is important (the method, the variable, etc.). The disadvantage is that most sentences will be in passive voice, which is dull. However, since people read Methods to get precise information, the disadvantage of dullness is generally outweighed by the advantage of making the topic the subject.

• Alternatively, the point of view of the experimenter, is undeniably more lively because it usually requires the use of active voice. However, it sacrificed having the topic as the subject of the sentence. Also, using “we” is inappropriate if someone other than the authors (such as technicians) actually did the work.

• Nevertheless, if “we” is well handled, choosing to write the Methods section from the point of view of the experimenter is also a defensible choice. So pick up the one you feel comfortable with.

Handling Point of View in the Methods Section: higher level

• At higher level of sophistication, you can write some subsections from one point of view and other subsections from another point of view.

• For example, you can use “we” in Study Design, but not in the Methods of Measurement. An advantage of this choice is that subsections that are difficult to write from one point of view can be written from the other.

Handling Point of View in the Methods Section: highest level

• At the highest level of sophistication, you can choose one point of view for a given subsection but write some sentences from another point of view when you have a specific and obvious reason.

• For example, you can use the point of view of the experimenter (“we”) for sentences that do not move the story forward, as shown in Example 5.16. the advantage is that the writing is smooth and clear. However, you want to avoid changing back and forth from one point of view to another several times within one paragraph for no apparent reason.

Units of Measurement

• The International System of Units (SI units) should be used.

• Young DS. Implementation of SI units for clinical laboratory data: style specifications and conversion tables. Ann Intern Med 1987;106;114-129.