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Writing Biomedical Research Papers

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Title: Writing Biomedical Research Papers


1
Writing Biomedical Research Papers
  • Ding-I Yang
  • Institute of Brain Science
  • National Yang-Ming University

2
  • Essentials of Writing Biomedical Research Papers.
    Second Edition. By Mimi Zeiger the McGraw-Hill
    Companies, Inc.

3
  • Title
  • Abstract
  • Introduction
  • Materials and Methods

4
The Title
5
Function of Title
  • To identify the main topic or the message of the
    paper
  • To attract readers

6
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.

7
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).

8
  • 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.

9
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.

10
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.

11
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.

12
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.

13
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.

14
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)

15
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

16
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.

17
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.

18
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.

19
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.

20
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???

21
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, bloodvs.
    extra-pulmonary) adjectives to express a message
    (reduced vs. reduction in), and noun clusters
    (NGF protection vs. protection by NGF).

22
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?).

23
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 ().

24
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.

25
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.

26
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?).

27
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

28
The Abstract
29
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.

30
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.

31
Organization of the Abstracts for
Hypothesis-Testing Papers
  • Overall organization
  • Organization of results

32
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.

33
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).

34
Writing of the Abstracts for Hypothesis-Testing
Papers
  • Continuity
  • Signaling Topics
  • Verb Tense
  • Sentence Structure
  • Word Choice
  • Abbreviations

35
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).

36
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.

37
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.

38
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.

39
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.

40
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.

41
Abstracts of Descriptive Papers
  • Contents and Organization
  • Writing including signaling topics, verb tense,
    sentence structure, word choice, and
    abbreviations.

42
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.

43
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.

44
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).

45
  • 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.

46
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.

47
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.

48
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.

49
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.

50
To ensure that your abstract provides a clear
overview, you must
  1. State the question you asked
  2. 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 clearly
  4. Write a hypothesis-testing abstract, not a
    descriptive abstract, when you are testing a
    hypothesis.

51
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.

52
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)

53
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54
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.

55
  • 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.

56
  • 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.

57
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.

58
Verb Tense
  • In the sentence that names the method, the verb
    is 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.

59
Indexing Terms
  • Some journals ask authors to supply a list of
    indexing terms, or key words, to guide indexers
    in selecting terms for the journals index.
    Indexing terms are sometimes printed after the
    abstract or after the title in the journals
    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.

60
  • 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.

61
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.

62
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.

63
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.

64
Introduction
65
Function
  • To awaken the readers 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.

66
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

67
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.

68
  • 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.

69
  • 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.

70
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.

71
  • 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).

72
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).

73
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.

74
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.

75
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.

76
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).

77
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.

78
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.

79
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.

80
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)

81
  • 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.

82
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.

83
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).

84
Answer to the question and length
  • The answer to the question should not be included
    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.

85
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.

86
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.

87
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.

88
Materials and Methods
89
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.

90
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).

91
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.

92
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.

93
Materials
  • Chemicals (drugs, culture media, buffers, gases)
  • What was examined (experimental materials,
    experimental animals, or human subjects)

94
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.

95
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.

96
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, Hams F-12 medium)
    without stating detailed components.

97
Materials gases
  • For gases, state the components and their
    concentrations (for example, 1 oxygen). Also
    state the flow rat if appropriate.

98
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.

99
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.

100
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 peoples 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.

101
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).

102
  • 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).

103
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.

104
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.

105
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.

106
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.

107
  • 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.

108
  • 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 Students 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.

109
  • 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.

110
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.

111
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).

112
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).

113
For animal studies
  • Materials
  • Animals
  • Preparation
  • Study Design
  • Interventions
  • Methods of Measurement
  • Calculations
  • Analysis of Data (or Statistical Analysis).

114
For Clinical Studies
  • Study subjects
  • Inclusion Criteria
  • Exclusion Criteria
  • Study Design
  • Interventions
  • Methods of Measurement
  • Calculations
  • Analysis of Data

115
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.

116
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.

117
  • Media and growth conditions
  • Plasmid constructions
  • Yeast strains
  • Plasmid rescue and DNA sequence analysis
  • Frame-shift rate determination

118
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.

119
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

120
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 5.11
  • The 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..

121
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.

122
  • 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.

123
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.).

124
  • 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

125
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.

126
Details animals, verb tense, and sample size
  • Use the animals 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.

127
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)

128
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.

129
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

130
  • 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-mm-diameter microspheres from the
    lungs in the second series, we measured the loss
    of 9-mm-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
    7525 mixture of nitrous oxide and oxygen and the
    other group anesthetized with halothane.

131
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.

132
  • 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.

133
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.

134
  • 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.

135
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.

136
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 stor
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