Making An English Biomedical Paper: Why, What, and How

1
Making An English Biomedical PaperWhy, What,
and How

• ??????????
• Ruiwen Zhang, MD, PhD, DABT ?????
• Professor, Pharmacology and Toxicology
• Director, Cancer Pharmacology LaboratorySr.
  Scientist, Comprehensive Cancer Center, Clinical
  Nutrition Research Center,
• Chemoprevention Center, Gene Therapy Center,
  Center for Aging,
• Center for AIDS Research University of Alabama
  School of Medicine
• Birmingham, AL 35294, USA
• ruiwen.zhang_at_ccc.uab.edu
• ????? (Editor-in-Chief)
• Jilin University, June 26, 2009
• This presentation does not necessarily represent
  the opinion or idea of UAB or ???.
• This presentation does not have any direct
  connection to UAB business.

2
Making An English Biomedical PaperWhy, What,
and How

• Outline
• Session 1A Why? General Instruction
• Session 1B What and How? Journal and Data
  selection
• Session 2 What and How? Specific Writing Tips
  for Major Sections
• Session 3 How? Communication with
  Editors/Reviewers

3
Making An English Biomedical PaperWhy, What,
and How

• ??????????Session 1A
• General Instruction

4
Q A Which of the following is Most Important
or Difficult to Perform?

• Select the data
• Select a target journal
• Write an English paper
• Prepare a cover letter
• Communicate with Editors

5
Writing and Speaking Well

• Learn to Write Well, or Not Write at All.
• John Dryden, Poet
• Avoiding Boring People.
• A book title from James Watson, Noble
  laureate
• Write or No Write, Speak or No Speak, Depending
  on Your Ability to Deliver.

My belief
Session 1
6
Obligations of a Scientist (Physician Scientist)

• Accomplish technically competent, thorough, and
  ethical research
• Employ objective scientific judgment and seek
  appropriate advice.
• Publish honest reports in a timely fashion.

Session 1
7
Types of Scientific Writing
Not public
Public
Peer-reviewed

• Grant Applications
• Fellowship proposals

• Original papers
• Reviews
• Meeting abstracts
• Conference reports

• Books, chapters
• Book reviews
• Teaching materials
• Theses/dissertations
• Editorial comments
• Letters to the editor
• Research reports (sometimes)
• Web pages

Not peer-reviewed

• Correspondence
• Confidential reports

Session 1
8
Overview The Research Process
Hypothesis
Session 1
9
Overview The Publication Process
Session 1
10
Major Techniques in Scientific Writing

• Definition
• Compare-contrast
• Enumeration/Illustration
• Cause-effect

Session 1
11
Characteristics of Scientific Writing (1)

• English the universal language of science
• - Eugene Garfield, 1987
• Reader-oriented ---- Sharing information
• Three Things to Avoid
• Laboratory jargon
• Invented words
• Non-standard abbreviations
• Purposeful ---- Convey information, ideas,
  concepts
• Precise ---- Choose words meant to be said
• Accurate ---- Conformity, actual (true) state

Session 1
12
Characteristics of Scientific Writing (2)

• Clear
• Reaches the audience with the same meaning it had
• Should NOT be interpreted in more than one way
  ---- Avoid
• When something is said for the first time,
  clarity is essential.
• Concise
• Expresses, covers much in few words
• The best English is that which gives the sense in
  the fewest short words. Instructions to
  Authors, Journal of Bacteriology.
• Simple ---- Easy to understand, not elaborate or
  artificial, not ornate, not complicated
• Illustrated ---- A picture is worth a thousand
  words. Make use of good figures and tables

Session 1
13
Sins of Language
excess
omission
Misunderstanding Misleading Harm
dishonesty
ignorance
malice
Session 1
14
Characteristics of a Valid Manuscript (1)

• First report of the data (original paper)
• Original research results (not me-too)
• Allow peers to repeat the reported experiments
  (not necessarily the results)
• Publish in a journal or other public source
  document
• Available to the scientific community
• Be received and understood

Session 1
15
Characteristics of a Valid Manuscript (2)

• Characteristic format ---- IMRAD
• (Introduction, Methods ( Materials), Results,
  and Discussion)
• Introduction What question was studied?
• Methods How was it studied?
• Results What were the findings?
• Discussion What do the findings mean?
• This logic helps the author organize and write
  the manuscript.
• Traditional format
• Cancer Research
• PNAS USA
• Alternative format Introduction, Results,
  Discussion, and Methods ( Materials)
• EMBO J
• Oncogene
• Letter format
• Nature
• Science

Session 1
16
Steps in Writing a Manuscript (1)
Reading
Thinking
Writing Revising
Q Professional Writing Service?
Session 1
17
Ten (10) Key Questions

• Is there a story to tell?
• What was the rationale for the project?
• Did I perform a thorough literature review?
• What is the historical context of the work?
• Did I have a clear hypothesis?
• Did the experiments test that hypothesis?
• Is the experimental design defendable?
• Can I justify what I did?
• Did I use appropriate controls?
• How do my findings relate to the existing
  knowledge?

Session 1
18
Steps in Writing a Manuscript (2)

• Search and Review the Literature
• Use MEDLINE other sources
• Search using all appropriate keywords
• Summarize relevant points of related articles
• Prepare an Outline
• Preparation forces you to think and organize.
• All points should be supported by appropriate
  data.
• Gives a logical, step-by-step order in which the
  manuscript will be presented.
• Gaps can be filled in, and extraneous material
  can be eliminated.
• Writing can be done with less interruption.

Session 1
19
Checklist for Preparing an Outline

• Ensure that you are up-to-date on the literature
  in the field
• Confirm that the results are real- i.e., they
  cannot be explained by experimental error and
  have been repeated
• Complete the initial statistical analyses
• Select a target journal
• Look over the Instructions for authors
• Decide on the authors, and decide who will be the
  corresponding author
• Verify the current institution and address for
  each of the authors
• Decide who will be responsible for the various
  parts of the manuscript Introduction____________
  _____Methods/Materials___________________
• Results____________________Discussion___________
  _______________
• Figures____________________Tables_______________
  ______________
• References_________________Overall
  formatting____________________
• Discuss who will be responsible for other parts
  of the submission process
• Cover letter_________________Online/mail
  submission________________
• Revisions___________________Letter for
  revision/rebuttal_____________
• Determine who should be included in the
  acknowledgements
• Select a targeted date for submission
• Select major references to be cited
• Make a list of the procedures and instruments
  used, along with the conditions for each
  experiment

Session 1
20
Steps in Writing a Manuscript (3)
Actual Writing (Turtle or Rabbit Writer?)

• General Approach to
• generating first draft
• Tables and Figures
• Results
• Methods
• Introduction
• Discussion
• Abstract
• Title
• References
• Other parts

• General Approach to
• Revising first draft
• Read the First Draft (From the beginning to the
  end
• Read it again
• Read literature again
• Revise
• Introduction, Results and Discussion
• Methods
• Abstract
• Title
• Abstract
• Title and other parts

Session 1
21
Steps in Writing a Manuscript (4)
Actual Writing (Turtle or Rabbit Writer?)

• General Approach to
• Revising 2nd and nth drafts
• 2nd Complete Draft
• Send to all authors
• Nth Draft
• Semi-final version
• Send to Outside reader/consultant/editing service
  
• Final version
• Send to all authors

• General Approach to
• preparing the final version
• Reading, reading, reading
• Checking, checking, checking
• Submission package
• Cover letter
• Suggested reviewers, if needed
• Submission
• Approve submission
• Waiting for the news

Session 1
22
Q A Do I Have to Work in a Lab to Write a SCI
Paper?

• The answer is NO.
• Your options (examples)
• Case Report
• Clinical Trials (including lab work)
• Retrospective Study
• Population Study
• Meta Analysis
• Review/Mini-review
• Theoretical Papers (Hypothesis)
• Letter to Editors
• Comments

23
Making An English Biomedical PaperWhy, What,
and How

• ??????????Session 1B
• Target Journals
• Data Preparation and Evaluation

24
Select an Appropriate Journal (1)
Target Journal

• Have a journal in mind as you design and perform
  your experiments.
• Basis for selection of a target journal
• Who is the target audience?
• General
• Multidisciplinary
• Specific
• How important is the contribution?
• If it is earth-shaking and of interest in
  several scientific fields or if it is a major
  advance in a particular discipline, submit the
  manuscript to Nature, Science, Cell, or PNAS.

Not Sure? Ask a trusted colleague!
Session 1
25
Select an Appropriate Journal (2)
SCI and Impact Factor

• What is the impact factor of the journal?
• Calculation for journal impact factor
• Example Nature 2007 Impact Factor
• Cites in 2007 to articles published in 2006
  25635  
•   2005 32644
• 
  Sum
  58279 
• Number of articles published in
  2006 962    
• 2005 1065    
• 
  Sum 2027 
• Calculation 58279 /202728.751      

Session 1
26
Select an Appropriate Journal (2)
2008 SCI Impact Factor

• Total Number of Journals in SCI? 6598
• IF distribution Number Cum
• gt50 2 0.03
• 30lt50 11 0.17
• 20lt30 20 0.30
• 15lt20 20 0.30 0.8
• 10lt15 63 0.95 1.75
• 5lt10 295 4.47 6.22
• 3lt5 736 11.15 17.37
• 1lt3 2948 44.68 62.05
• 0.5lt1 1410 21.37
• 0lt0.5 1047 15.87
• No IF 46 0.69

Session 1
27
Select an Appropriate Journal (2)
2008 SCI Impact Factor

• Top 10 Journals in SCI IF
• Journal 2008 IF 5-yr IF

Session 1
28
Select an Appropriate Journal (2)
2008 SCI Impact Factor

• Other interesting journals
• Journal 2008 IF 5-yr IF
• Lancet 28.409 28.965
• Science 28.103 30.268
• Nat Med 27.553 28.965

• Interesting Facts (2008 SCI IF)
• IF N Nature Family Cell Family Review
  Journals
• gt20 33 14
  2 17

Session 1
29
Select an Appropriate Journal (3)
SCI and Impact Factor

• Myths of Impact Factors (IFs)
• IFs do not reflect the quality of individual
  papers.
• Review journals generally have higher IFs.
• IFs are biased against some specialty or new
  fields of research.
• Not all journals are included in the index.
• IFs can be manipulated by editors/publishers.
• IFs fluctuate year to year for a given journal.
• Journals originated from Non-English country
  generally have lower IFs
• IFs cannot be used to compare publications in
  different fields (subject category)
• Simple math does not work here
• IF 10 IF1 X10?
• IF 5 IF5 IF10?
• IF 10X 6 IF60?
• IF 5.614 is better than IF 5.613?

Session 1
30
Select an Appropriate Journal (4)
Major Secondary Services

• Is it recognized by one or more of the major
  secondary services (Chemical Abstracts,
  Biological Abstracts, MEDLINE/PubMed)?
• MEDLINE (Medical Literature Analysis and
  Retrieval System Online) is an international
  literature database of life sciences and
  biomedical information. It covers the fields of
  medicine, nursing, pharmacy, dentistry,
  veterinary medicine, and health care and much of
  the literature in biology and biochemistry.
  (5000 serials)
• PubMed is a free search engine offering access
  to the MEDLINE database of citations and
  abstracts of biomedical research articles. It
  also provides access to many pre-1966
  publications.
• CA (Chemical Abstracts Service), a division of
  the American Chemical Society, produces Chemical
  Abstracts, an index of the scientific literature
  in chemistry and related fields. (9500 serials)
• Biological Abstracts directs users to
  information on life science topics, ranging from
  botany to microbiology to pharmacology. (gt3700
  serials)

Session 1
31
Select an Appropriate Journal (5)
More than IF

• What is the prestige of the journal?
• Is it a primary journal?
• Is it an open journal?
• What is the circulation of the journal?
• What is the review time for the journal?
• What is the publication time for the journal?

Most Journals publish the dates of submission,
review, and acceptance. You need to check the
publishing date Epub ahead of print In press
MS Open access online only PubMED submission
etc.
Session 1
32
Select an Appropriate Journal (6)
More than IF

• Who will be interested in reading the paper
  basic scientists, clinicians, or both?
• Whom do you want to read the paper members of
  the funding committee, the promotion committee,
  or the competitors?
• Is the paper within the Scope of the journal
  (in the Instructions for Authors ).
• Be familiar with the journal, especially papers
  published in the last 6-12 months

Still not sure Ask a trusted peer, and, if
possible, be acquainted with the editor.
Session 1
33
Select an Appropriate Journal (7)
Knew What You Wish For

• Check recent articles in various journals
  examine their format and content.
• Examine several articles in potential journals.
  How many figures and tables do they have?
• Read the Table of Contents of recent issues of
  potential journals.
• Consider Am I qualified to write an article for
  this journal?
• Consider Where were the papers you will cite as
  references published-were they published in a
  similar quality journal?
• Read the Instructions for Authors and examples
  of publications in these journals.

Keep in Mind Topic, Contents, Format, and Style.
Session 1
34
Select an Appropriate Journal (8)
Wrong Journal or Wrong Paper?

• If you submit to a wrong journal
• Your manuscript may be returned to you without
  review.
• It may be reviewed inadequately.
• Its publication may be unnecessarily delayed.
• Your work may remain unknown because it is not
  read after publication.

Still not sure Ask the Editor of the potential
journal. Do not overly depend on Professional
Editing Service
Session 1
35
Data Preparation and Evaluation (1)

• Checklist for finalizing data for a manuscript
• Make sure your results have been
  repeated/confirmed
• Select results that are representative of your
  repeats (for Western blots, photographs, spectra,
  etc) or prepare averages and standard deviations
  for your data (clinical parameters, animal
  studies, etc.)
• Ensure that your data are statistically
  significant, and that you indicate this in the
  text and figures.
• Prepare an appropriate number of figures and/or
  tables (many journals have a limit of 6 figures)
• Confirm that your figures and tables are
  supported by raw data
• Make sure that the raw data is retrievable (in
  laboratory records)
• Organize data by importance (key data,
  supporting evidence, and/or supplemental data)
• Determine they type of illustration that will
  best showcase the data (Figure? Table?
  Photograph?)
• Generate figures of sufficient quality for your
  selected journal (journals frequently require
  figure quality of 600 dpi)
• Format your illustrations according to the
  instructions for authors (font style and size)
  and, if possible, use a consistent size and style
  for each figure and table
• Avoid redundancy between tables, figures and the
  text
• The corresponding author needs to check the
  quality and accuracy of the data, and that the
  data is supported by raw data
• The figures and tables should indicate
  statistical significance (if applicable)
• Prepare supplemental illustrations (if applicable
  for your journal)
• Write figure and table legends (the legends
  should describe the figure and methods in
  sufficient detail so that the reader knows what
  the data indicate and how they were obtained)
• Check all the materials and methods and/or key
  references

Session 1
36
Data Preparation and Evaluation (2)

• Q Do I need All the data before beginning the
  writing
• No
• But You need
• All Key data
• Most supporting data
• Some supplemental data
• You need ALL the data before the completion of
  the first draft
• You still can add data before final submission

You should evaluate your data periodically and
prepare your outline and key data as soon as
possible.
Session 1
37
Data Preparation and Evaluation (3)

• Q Who should evaluate and check the data?
• All the authors
• Key persons
• Primary authors
• Corresponding author
• Technical staff
• Collaborators
• You may ask trusted colleagues to evaluate the
  data

Hot topic Can you trust the internet to send
your unpublished data?
Session 1
38
Data Preparation and Evaluation (4)

• Q Does the format of the data presentation
  matter?
• Yes
• You can present your data in various manners
• Table
• Simple
• Complex
• Number of the tables
• Figure
• Color?
• Number of the figures
• Number of panels in a figure
• Text
• The best way is to use all the above, but not
  redundant

Hot Topic The art of scientific data presentation
Session 1
39
Data Preparation and Evaluation (5)

• Q Why is statistical analysis so important?
• The following statements are frequently based on
  statistical analysis
• Significant
• Effective
• Correlation/relation
• Causal relation
• Safe
• Better or Worse
• Confirm or rule out a hypothesis
• Prediction/Extrapolation
• Other
• You Almost Always need help from a statistician,
  from planning to design to analysis to reporting
• It is almost too late if the reviewer/editor
  requests statistical analysis for your paper.

Hot topic You should know the difference between
statistical significance and biological
significance.
Session 1
40
Making An English Biomedical PaperWhy, What,
and How

• ??????????
• Session 2
• Writing Tips for Major Sections

41
Q AWhich Part (s) of A Paper is(are) Most
Important?Which Part (s) of is(are) Most
Difficult to Write?

• Title
• Abstract
• Introduction
• Materials and Methods
• Results (figures and tables)
• Discussion
• Acknowledgements
• References

42
General Order of Writing (1st Draft)

• Selecting and Finalizing Data
• Results
• Materials and Methods
• Introduction
• Discussion
• Title
• References
• Abstract
• Other sections

Session 2
43
Introduction/Background (1)

• Every Paper needs an Introduction section
• Original Article
• Review Article
• Case Report
• Technical/Method Report
• Letter
• Editorials
• Other
• This section is a critical showcase.
• May be written late in the process, e.g., after
  you complete Results and Methods section.

Session 2
44
Introduction/Background (2)

• The first sentence should stimulate the interest
  of the reader.
• Example 1
• Poor The purpose of this article is to show that
  case management can be a cost-effective approach
  in patient care. (unnecessary words)
• Improved Case management can be a cost-effective
  approach in patient care.

Session 2
45
Introduction/Background (3)

• The first sentence should stimulate the interest
  of the reader.
• Example 2
• Poor From the beginning of time, strokes have
  been a major health problem. (trite, negative)
• Improved Advanced treatments for stroke patients
  are giving them new hope.

Session 2
46
Introduction/Background (4)

• Three Important components in this section.
• The topic to be covered and why it is important
  (The rationale)
• The purpose of the studies.
• The hypothesis that led to the investigation.

Session 2
47
Introduction/Background (5)

• Try to state
• Whats new?
• Whats special?
• Whats significant?
• How to do it?
• Provide a brief review of the literature and cite
  findings that led to the present studies.
• Example
• Good In inner-city adolescents, the increased
  incidence of illnesses related to sexuality
  demonstrates a lack of understanding of these
  problems. Through counseling and referrals, nurse
  practitioners in our hospital developed a
  procedure to reach this population and reduce the
  occurrence of these diseases.

Session 2
48
Introduction/Background (6)

• This section should be short 500-1000 words.
• How to do it?
• Discuss any unknowns and controversies that exist
  , with respect to the rationale for the studies.
• The information should be fresh/novel,
  interesting, and specific.
• Much of the Introduction should be written in the
  present tense, when you mention the published
  data/hypothesis.
• This section is best written in the active voice.
  The active voice gives writing a sense of
  strength, energy, and direction. (It is also
  20-30 shorter than the passive voice.)

Session 2
49
Introduction/Background (7)

• You need a clearly stated HYPOTHESIS and
  Approaches.
• How to do it?
• State the hypothesis directly.
• Set up the problem and show how it was dealt
  with.
• It is acceptable to briefly state the conclusion.
• Use only the most important references. Do not
  refer to individual scientists unless it is
  necessary to contrast results from different
  laboratories. (This principle applies also to
  other sections of the manuscript.)
• Preliminary reports should be mentioned.
• If there are related publications that will be
  published soon, they should be mentioned. (But
  you need to check the journal format, with
  respect to unpublished data.)

Session 2
50
Introduction/Background Summary (1)

• Include in this section
• A brief review of the field (1 paragraph),
  including a description of areas in the specific
  field that are unclear or uncharacterized.
• An introduction to the present study (1
  paragraph), including hypothesis, major models
  and readouts, and key conclusions
• A brief comparison of the present study to the
  current knowledge, concluding with the
  significance and possible impact.
• A simple figure for testing system or agents that
  are new to the field, e.g., structure for a newly
  identified chemical that has been published.

Session 2
51
Introduction/Background Summary (2)

• DO NOT include in this section
• A lengthy review of the field or related fields
• Methods used for the paper
• For papers detailing the discovery or
  design of a new method, this may sometimes be
  mentioned.
• Results
• Discussion
• Unrelated materials
• Complex table or figures

Session 2
52
Introduction/Background Summary (3)

• Common problems
• Overly state the broad research area
• Inclusion of textbook information
• Lengthy citation of old research
• Descriptions of the results and methods from
  published studies or the present study
• Discussion of the results of the present study
• Inclusion of identical sentences from the
  Abstract or other sections, especially the
  discussion section.
• Inclusion of references that are not generally
  available, such as non-English publications
• Too short or too long
• Overly negative to studies of other groups
• Over-emphasize previous studies from the same
  group and or ignore studies from other groups
• Including complex table or figures

Session 2
53
Materials and Methods (1)

• General Suggestions
• For beginning authors, this section can be
  written first because it is easiest to write.
• The format is usually specific to the journal.
• Subheadings are characteristically used.
• Much of this section is written in the past
  tense, passive voice.
• Much of this section can be included in the
  supplementary data section
• This section can be placed after the Discussion
  section in many journals.

Session 2
54
Materials and Methods (2)

• This section should be specific, providing
  sufficient details that allow an experienced
  researcher in the related field to repeat the
  experiments in this study.
• How to do it?
• Provide sources of key materials and describe
  preparation of non-standard solutions.
• Experimental animals, plants, and microorganisms
  should be identified by genus, species, and
  strain, as well as age. Sources should be listed
  and special characteristics described.
• For human subjects, the criteria for selection
  should be described, and a statement relating to
  informed consent should be included.
• Provide sufficient details of the experiments.
  Descriptions of new methods should include all
  the needed details. If the methods have been
  published, references to the specific
  publications can be used. Do not describe
  previously published procedures in long detail,
  but do describe any modifications.
• Describe the study design and procedures for
  analysis of the data.
• Provide information on statistical analyses
  performed and state the number of observations in
  each group.

Session 2
55
Materials and Methods (3)

• Include in this section
• All the methods used to generate all of the data
  presented in the results section.
• Strains and ages of animals, doses used,
  treatment routes and durations, and other details
  that would allow the reader to repeat the
  experiments.
• Citations for protocols used previously.
• Detailed descriptions of new techniques/models or
  changes in standard techniques.
• Methods used to analyze data.
• A statement indicating that informed consent was
  obtained (if you are reporting a clinical study)
  or that your experiments were in compliance with
  your institutions animal regulations.
• Most used subheadings Chemicals and reagents
  Instruments Animals Subjects in vitro assays
  (specific) in vivo models and treatment
  Analytical methods Data and statistical analysis
  

Session 2
56
Materials and Methods (4)

• Do NOT Include in this section
• Standard instruments, common buffers, routine
  clinical chemistry
• Published synthetic pathway for test compounds
• Lengthy descriptions of commonly used procedures
  (Western blotting, RT-PCR)- a brief mention of
  the antibodies used and the primer sequences and
  PCR conditions is sufficient.
• Non-standard abbreviations for reagents or
  procedures.
• Results
• Discussion of the selection of the models and
  assays
• Acknowledgments

Session 2
57
Materials and Methods (5)

• Common Problems
• Overly detailed descriptions of common protocols.
• Too few details about new or difficult methods.
• Insufficient details about models (for example,
  no age or strain of animals is mentioned).
• Laboratory jargon and non-standard abbreviations.
• Too long or too Short.
• Methods section does not match the results
  section and/or the figure/table legends.
• No statistical analysis section.
• No mention on regulatory approval for animal use
  or human trials.
• Written as a laboratory protocol.
• No vendor information for specific
  agents/instruments (City, country)
• Redundancy and Inconsistency

Session 2
58
Results (1)

• General Guidelines
• Present results in a logical (not necessarily
  chronological) order.
• Give the big picture, especially for each set
  of experiments
• Present selected data.
• A fool collects facts the wise man selects
  them. John Wesley Powell.
• To maintain momentum, the evidence must tell a
  story and support the conclusion.
• Write in the past tense.
• Provide sufficient interpretation of data to lead
  the reader from one concept to the next but leave
  detailed analysis and comparison of findings for
  the Discussion section.
• Key previously published data can be referred but
  not the actual data
• Avoid duplication of information in the text and
  in tables and figure legends.

Session 2
59
Results (2)

• Include in this section
• The most interesting and clear data obtained from
  your studies.
• Illustrations of various types (for example
  figures, photographs, and tables).
• A clear and concise description of your studies
  and the data.
• Properly use subheadings to organize the data

Session 2
60
Results (3)

• Do Not Include in this section
• Discussion material. (The Results should not
  discuss the implications of the data.)
• Detailed methods and materials.
• Dont include titles on figures. This information
  should be in the figure legends.
• Too many figures and tables. (Well written
  manuscripts contain only a few important, clear
  figures). Include only enough to tell your
  story.
• Too many references. (A few may be cited if
  necessary, but these should be kept to a
  minimum.)

Session 2
61
Results (4)

• Common Problems
• Repetition of data in figures, tables and text.
• Inclusion of Discussion material. (For example,
  inclusion of what the results mean and how they
  are related to previous results.)
• Lack of sufficient details about the experiments.
  (Are the data representative of repeated
  experiments? Why were specific treatment
  durations or doses chosen?)
• Lack of statistical analysis and/or indication of
  significance in figures/tables.

Session 2
62
Results (5)

• Common Problems
• When the Methods section is placed after the
  Discussion section, the lack of experimental
  details in the Results section may result in
  difficulties in presenting and understanding the
  results.

Session 2
63
Illustrations (1)

• General Suggestions for Illustrations
• Check the journal to see how illustrations are
  presented.
• The text is easier to write after illustrations
  have been prepared.
• A goal is to simplify the message without
  falsifying the data.

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64
Illustrations (2)

• General Suggestions for Tables
• Tables present exact values and allow
  comparisons between data points.
• Tables should be understood without referring to
  the text.
• In general, use only one table per 1000 words of
  text.
• The text must refer to the table by number.
• Numbers should show no more decimal places that
  are essential for reasonable precision and
  accuracy.
• Captions should be concise, contain key words,
  and be parallel for all tables in the manuscript.
  Captions should not be sentences.
• Do not include columns containing only one
  repeated value.
• Tables should contain no vertical lines.
• Use straddle lines over all columns of items to
  which the heading refers.
• Comparisons between like elements are made down
  columns, not across rows.
• Align decimals in columns.

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65
Illustrations (3)

• General Suggestions for Graphs
• If you choose to use a graph, it should convey
  information better than a text or a table.
• Graphs should be understood without referring to
  the text.
• Graphs show trends, overall patterns, and
  interactions between variables.
• Graphs demonstrate change over time or
  concentration.
• Graphs do not emphasize individual values.
• Graphs should avoid wasted space.
• Place the independent variable on the x-axis and
  the dependent variable on the y-axis.
• On both axes, plot the length of intervals so
  that the curves are not excessively flat or
  steep.
• Captions should be concise, contain key words,
  and be parallel for all graphs in the manuscript.
  Captions should not be sentences.
• The number of curves on a graph should be limited
  to five.
• It is generally better to use symbols (?, , ?)
  than line patterns.
• The curves should be bold and easy to see the
  axes and tic marks can be smaller/less bold , but
  should still be easy to see.

Session 2
66
Sample Figures

• Fig. 6 Plasma concentrations of adaphostin
  following intravenous administration to each of
  two dogs at a dose of 7.5 mg/kg.

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67
Sample Figures

• General Suggestions for Other Illustrations
• Bar charts, which have only one measurable axis,
  dramatize differences, but they are not
  numerically specific.

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68
MDM2-p53 Interaction
Sample Figures

• General Suggestions for Other Illustrations
• Diagrams illustrate complex relationships,
  pathways, and interactions

Ub
Ub
Ub
Ub
Ub
Ub
Favors Nuclear Export
Ubiquitination
MDM2
p53
MDM2
p53
Inhibits Transactivation Activity
p53
p53 Target Genes
Tumor Suppressive Activity
Session 2
69
Sample Figures

• General Suggestions for Other Illustrations
• Flow charts show sequential processes and
  describe causation

Session 2
70
Sample Figures

• General Suggestions for Other Illustrations
• Pie charts show proportions, parts of a whole, or
  percentages.

MCF7 Cells
20(S)-PPD
20(S)-25-OCH3-PPD
MDA-MB-468 Cells
20(S)-PPD
20(S)-25-OCH3-PPD
71
Sample Figures

• General Suggestions for Other Illustrations
• Western blots and IHC data

72
Illustrations Summary (1)

• Include in this section
• Clear labels for all parts of the figure, table,
  or illustration.
• Consistent font styles and sizes (if possible)
  for each figure.
• Labels indicating statistical significance (where
  applicable).
• Legends describing the method used to obtain the
  data and what special symbols indicate.

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73
Illustrations Summary (2)

• Do Not Include in this section
• Too many parts per figure. (Four to six parts per
  figure is acceptable more than that leads to
  confusion.)
• Small fonts. (Ideally, the font should be at
  least 10 pt.)
• Large tables. (More than 5 columns or longer than
  2 type-written pages in length is too large.)
• Figures of poor quality. (Most journals now have
  minimum resolution requirements for photographs,
  figures and illustrations.)

Session 2
74
Illustrations Summary (3)

• Common Problems
• Unclear figures (low quality).
• Differences in font size and style between
  figures.
• Unclear figure labels.
• Misspelled labels.
• Missing units (hours? minutes? days?).
• Overly complex table or figures.
• Redundancy and inconsistency

Session 2
75
Discussion (1)

• General Suggestions
• The primary function is to relate the present
  work to previous reports and to point to future
  efforts.
• An introductory statement can describe again
  the purpose of the studies.
• If it is reasonable, the topics in the Discussion
  should be parallel to those in the Results.
• Main purpose is to present principles,
  relationships, and generalizations about the
  findings reported in the paper.
• The length of the Discussion is generally
  proportional to the amount of new information
  presented (1/4 text). It should contain about one
  word for every four words in other parts of the
  manuscript.

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76
Discussion (2)

• General Suggestions
• Use present and past tense, as appropriate.
• Present tense Other published work, including
  your own work.
• Past tense your present work
• Avoid re-stating the Background/Introduction
  information but prepare the Discussion in the
  context of the Background/Introduction.
• Avoid reiteration of Results, but discuss
  interpretations and conclusions based on the
  results.
• Show how your data agree with previous results
  point out exceptions.
• The conclusion should restate the thesis.

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77
Discussion (3)

• General Suggestions
• Do not recapitulate results. Discuss theoretical
  and practical applications.
• State the significance of the results and how the
  results advance knowledge.
• Limited speculation is acceptable.
• Identify future studies that are needed.
• Avoid undue claims of primacy (being first?).
• Present a strong ending.

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78
Discussion (4)

• General Suggestions
• Clearly and briefly state the conclusions and the
  significance.
• Conclusions should be logically derived from data
  presented.
• Compare how the conclusions agree or contrast
  with previously published work.
• Dont try to hide unclear thinking with excess
  words.
• Identify possible sources or error and
  inadequacies in the work.
• Present a strong ending.

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79
Discussion Summary (1)

• Include in this section
• Principles, relationships, and generalizations
  about the data.
• A description of how your data agree with
  previous results, and any exceptions.
• Conclusions logically derived from the data.
• A comparison of how the conclusions agree or
  contrast with previously published work.
• Most used structure (usually no subheading)
  purpose and significance of the study summary of
  key findings interpretation of the main results
  and comparison with previous works (do not have
  to be the same order as Results possible
  mechanisms limitation of the present study
  future studies summary or conclusions
  implication and translational potential.
• Additional illustrations can be used to
  facilitate discussion but not new data.

Session 2
80
Discussion Summary (2)

• Do Not Include in this section
• Textbook information
• Repetition of the Introduction, Methods/Materials
  or Results sections
• Extreme words, for example, extremely first
  very, super, and crucial
• Concepts that were not introduced earlier in the
  manuscript
• Similar discussion from similar published papers

Session 2
81
Discussion Summary (3)

• Common Problems
• Textbook information
• Repetition of the Introduction, Methods/Materials
  or Results sections
• Extreme words, for example, extremely first
  very, super, and crucial
• Concepts that were not introduced earlier in the
  manuscript
• Similar discussion from similar published papers
• Inconsistency with other sections
• Recite Illustrations
• Length too short or too long
• Overemphasis of the importance of the findings or
  previous work from your own group
• Too much speculation
• Misinterpret other published studies
• Overly use subheadings

Session 2
82
Abstract (1)

• General Suggestions
• It is a window that reveals the contents of the
  manuscript.
• Structured abstracts (more common nowadays),
• Background/objective
• Methods
• Results
• Conclusion
• It is usually a single paragraph.
• Limited length lt250 words for most journals
  (some lt100 lt350 words)
• It should summarize each of the main sections of
  the paper, including the following
• the background (1-3 sentences)
• the hypothesis (1 sentence)
• model systems used
• general methods
• a short description of the results
• a statement regarding the significance of the work

Session 2
83
Abstract (2)

• General Suggestions
• It should be complete and intelligible without
  reference to the text.
• Generally, it should be written in the past
  tense, especially methods and results .
• Within the space allowed, all key findings should
  be included.
• It should ordinarily be written after a
  semi-final draft of the manuscript has been
  prepared.
• In contrast to a meeting abstract, the abstract
  for a manuscript should ordinarily not include
  actual data values.

Session 2
84
Abstract (3)

• General Suggestions
• In general, citations should not be included.
• In general, abbreviations are not included,
  unless the same, long term is used repeatedly.
  (Abbreviate at the first use in the text)
• Terms included in the abstract will be included
  in various databases for literature searches.
• Importance of the Abstract Its contents can
  establish the interest of the editor and
  reviewers and will determine if the reader
  actually reads the manuscript. Editors will
  often use the abstract to determine whether the
  paper should be reviewed for their journal. After
  the paper is published, readers may read only the
  abstract.

Session 2
85
Abstract (4)

• Include in this section
• Background for the study
• The purpose of the study
• Sufficient details to allow the reader to
  understand what the manuscript is about and what
  the major points are
• (Experimental details would include, for
  example, the number of test subjects and
  controls, species of animals, drug dosages and
  routes of administration, and tumor yields.)
• Major findings (new and important)
• Principal conclusions
• Any items/sections required by the target journal

Session 2
86
Abstract (5)

• Do Not Include in this section
• Unnecessary abbreviations
• Detailed results (including numerical values for
  data)
• Statistical values (p-values) for the findings
• Overstatement of the significance
• Extreme words
• Vague statements, such as, The significance of
  the results is discussed or Future studies are
  needed.

Session 2
87
Abstract (6)

• Common Problems
• Not exciting
• Too long or too short
• Too much background information
• Not enough information about the results
• Unnecessary citations
• Excessive numerical data
• Inconsistency with other parts of the text
• Too much discussion or speculation

Session 2
88
Abstract (7)

• Example
• Down-regulation of p53 by MDM2-mediated
  proteasomal degradation makes cells resistant to
  apoptosis. The MDM2-p53 interaction is well
  characterized, but the mechanisms that regulate
  the interaction are not well understood. Here, we
  show that PA28?, a proteasome activator that
  inhibits apoptosis and promotes cell cycle
  progression through unknown mechanisms, exerts an
  effect as a cofactor in the MDM2-p53 interaction.
  The polymer form of PA28? interacts with both
  MDM2 and p53 proteins and facilitates their
  physical interaction. This promotes
  ubiquitination- and MDM2-dependent proteasomal
  degradation of p53, limiting its accumulation and
  resulting in inhibited apoptosis after DNA
  damage. Elimination of endogenous PA28? in human
  cancer cells abrogates MDM2-mediated p53
  degradation, increases the activity of p53, and
  enhances apoptosis. These findings reveal the
  mechanism by which PA28? affects apoptosis and
  proliferation. Manipulation of the level of
  PA28?, an approach that would regulate the
  cellular content of p53, may improve the efficacy
  of current cancer therapies.

Session 2
89
Title (1)

• General Suggestions
• Usually written in Title Case, with upper-case
  letters for nouns and other words of more than
  four letters.
• As far as possible, use specific terms, for the
  title is a key element of the manuscript.
• Key words should appear in the title.
• Use the fewest words possible to adequately
  describe the contents of the paper.

Session 2
90
Title (2)

• General Suggestions
• The first noun should be powerful.
• Sentence titles, which are now often used.
• Many people will read the title, including
  abstracting services.
• It is generally appropriate to choose the title
  when the manuscript is almost complete.
• Series titles and titles with colons (hanging
  titles) are generally not desirable.
• Titles should almost never contain abbreviations,
  chemical formulas, proprietary names, or jargon.

Session 2
91
Title (3)

• Comparisons
• Which of the following is preferable?
• Involvement of GREB1 (gene regulated by estrogen
  in breast cancer 1) in breast carcinogenesis
• Involvement of gene regulated by estrogen in
  breast cancer 1 (GREB1) in breast carcinogenesis
• Involvement of gene regulated by estrogen in
  breast cancer 1 in breast carcinogenesis
• Involvement of GREB1 in breast carcinogenesis

Session 2
92
Title (4)

• Comparisons
• Poor Action of Streptomycin on Mycobacterium
  tuberculosis
• Better Inhibition of Mycobacterium
  tuberculosis growth by Streptomycin
• Poor Mechanism of Suppression of
  Non-transmissible Pneumonia in Mice Induced by
  Newcastle Disease Virus
• Better Mechanism of Suppression of
  Non-transmissible Pneumonia Induced in Mice by
  Newcastle Disease Virus

Session 2
93
Title Summary (1)

• Include in the title
• A clear, specific, and concise statement
  reflecting the major findings reported in the
  manuscript.
• Key words that will attract the interest of the
  editor, the reviewer, and reader.

Session 2
94
Title Summary (2)

• Do Not Include in this section
• Roman or Arabic numerals showing that the paper
  is part of a series
• Jargon
• Abbreviations other than well-accepted standards
  such as, DNA, RNA, and RT-PCR
• Punctuation other than commas (and commas should
  be used sparingly)
• The words study, critical, very, or first
• Extensive prepositional phrases (ofinof)

Session 2
95
Title Summary (3)

• Common Problems
• Not exciting
• Too long or too short
• Not enough information about the finding
• Inconsistent with other parts of the text
• Extreme words
• Speculation

Session 2
96
Sample Titles (1)

• Example
• Poor The use of microbiological and enzymatic
  assays in studies on the disposition of
  2'-deoxycoformycin in the mouse.
• Better The disposition of 2-deoxycoformycin in
  mice as determined by microbiological and
  enzymatic assays.

Session 2
97
Sample Titles (2)

• Examples
• Controlling the Bollworm
• Investigations into the Effects of Several
  Selected Phenolic Acid Compounds on the Mortality
  Rate, Developmental Time, and Pupal Weight Gain
  of the Cotton (Gossipium hirsutum L.) Bollworm
  (Helicoverpa zea Boddie) in Studies Involving
  Larvae Fed a Synthetic Diet in the Laboratory
• The Effects of Selected Phenolic Compounds on the
  Mortality, Developmental Time, and Pupal Weight
  of Helicoverpa zea Boddie Synthetic Diet Studies
• Benzoic and Cinnamic Acids in Synthetic Diets
  Retard Development of Helicoverpa zea Larvae
• Influence of Benzoic and Cinnamic Acids on
  Mortality and Growth of Bollworm Larvae
• Toxicity of Benzoic and Cinnamic Acids to
  Helicoverpa zea Larvae

Session 2
98
Running Title

• A shortened, but descriptive version of the title
  (usually limited to about 60 characters and
  spaces)
• Placed on the title page
• Often appears on each page (or every other page)
  of the manuscript.

Session 2
99
Key words

• Most journals now ask for 3-6 key words to make
  it easier to link your article to search engines.
  
• These words should indicate the major focus of
  the manuscript (e.g., genistein, MDM2, and
  cancer).
• Suitable terms can be found in the Medical
  Subjects (MeSH) list of Index Medicus. See
  http//www.nlm.nih.gov/mesh/meshhome.html.

Session 2
100
List of Authors

• Example of authors
• Mao Li,1 Zhuo Zhang,1 Donald L. Hill,1,2 Xinbin
  Chen,2,3 Hui Wang,1,2 and Ruiwen Zhang1,2
• 1Department of Pharmacology and Toxicology,
  Division of Clinical Pharmacology 2Comprehensive
  Cancer Center, 3Department of Cell Biology,
  University of Alabama at Birmingham, Birmingham,
  AL
• Corresponding author. Department of
  Pharmacology and Toxicology, University of
  Alabama at Birmingham, 1670 University Blvd.,
  Volker Hall 113, Birmingham, AL 35294, USA. Tel.
  205 934 8558 Fax [phone] E-mail
  ruiwen.zhang_at_ccc.uab.edu

Session 2
101
References (1)

• General Suggestions Part A
• Limit the number of citations to a number
  consistent with articles published by the
  journal. For most publications (except reviews),
  fewer than 50 citations are adequate.
• For references, include primary sources if
  possible.
• Cite reviews rather than each article covered by
  the review. Instead of listing numerous
  references for a prior discov