Transcript Diapositiva 1

Joint course with ERS “How to write an article”
Material and methods
Vito Brusasco
Department of Internal Medicine
Medical School
University of Genoa, Italy
Respiratory Pathophysiology Unit
San Martino University Hospital
Genoa, Italy
Material and methods
It is usually placed right after the Introduction
 Be concise but complete
 Organized as:
• Study subjects or animals
• Study design
• Procedures
• Analysis
Material and methods
General guidelines
Question to address
How to address them
How did you study the
problem?
Briefly explain the general type
of experimental procedure you
used.
What did you use? (Materials)
Describe what materials,
subjects, and equipment
(chemicals, experimental
animals, apparatus, etc.) you
used.
How did you proceed?
(Methods or Procedures)
Explain the steps you took in
your experiment.
Material and methods
Style
 Always use past tense
 Active or passive voice?
• Active: clearer and more direct, emphasizes the role
of the operator. “We chose method A instead of
method B because we found it more reproducible
(unpublished observations)”.
• Passive: it is often preferred (or mandatory) to
indicate objective procedures that can be replicated
by others. The individual doing the experiment is
therefore relatively unimportant. “Lung function was
measured by spirometry” is better than “We
measured lung function by spirometry”.
Material and methods
Style
 Active or passive voice?
• Active: Sometimes emphasizes the role of the subject
under study“To have lung volume measured, the
subject took a deep breath……..” .
• Passive: Sometimes emphasizes the role of the
operator “To have lung volume measured, subjects
were asked to take a deep breath……..”.
Either form is acceptable
Material and methods
Style
Avoid redundant wording such as
• a total of n subjects
• four different groups
• absolutely essential
• there were several subjects who completed…
•small in size
• period of time
• also included
• except for
• Use because instead of based on the fact that
• Use for or to instead of for the purpose of
• by means of
• during the course of
Material and methods
Style
Avoid ambiguity
Varying -- Distinguish from various or differing. Using
varying amounts means individually changing amounts
rather than a selection of various or different ones.
Apparent -- means obvious, clear, plainly evident, but also
means seemingly or ostensibly as well as observably. You
know the meaning that you intend, but readers may not.
Compare with, compare to -- Compare with means to
examine differences and similarities; compare to
means to represent as similar. “The music of Brahms
compares to that of Beethoven” but to say so, one must first
“compare the music of Brahms with that of Beethoven”.
Material and methods
Style
Avoid ambiguity
High(er), low(er) – Don’t use for other words such as
greater, lesser, larger, smaller, more, fewer. “Occurrences
of higher concentrations were lower at higher levels of
effluent outflow”. One interpretation is that greater
concentrations were less frequent as effluent volume
increased, but others also are possible.
Hyphening -- Often needed to clarify what is modifying
what. “a batch of 3 10-mL vials” is different from a “batch of
10 3-mL vials”, as “a man eating fish” is very different from
“a man-eating fish”!
Material and methods
Study subjects or animals
 Describe how they were identified
 State the inclusion criteria for case-controls or subjects
 Provide anthropometric characteristics of subjects in a
table, including physiological and clinical data that are not
variables of the study
 Provide details of animal species and/or strains
 Make statements on study approval from local Ethics
Committee (for all human studies) and regulatory
authority (for clinical trials) or compliance with the Helsinki
convention (for animal studies)
Material and methods
Study design
 Clearly state what are the main objective(s) of the study.
 Describe how the study was structured (e.g.,
randomization, blinding, parallel groups, cross-over)
 Describe the animals used in the study by giving:
• source (supplier or where and how they were
collected)
• typical size (weight, length)
• age (newborn, young, adults)
• how they were handled, fed, and housed before and
during the experiment(s)
Material and methods
Study design
 Always identify treatments by the variable or treatment
name, NOT by an ambiguous, generic name or number
“Bronchodilator group” and “Placebo group” instead of
“Group 1” and “Group 2”.
 When your paper includes more than one experiment,
use sub-headings to help organize your presentation by
experiment.
 State how the sample size was calculated in order to
have enough subjects (animals) to address the
question.
Material and methods
Study design
Give details on location and time of study only when
necessary.
• In field-based studies, usually authors describe the
study region in general terms in the Introduction and
then describe the study site and climate in detail in the
Materials and Methods section.
• For clinical trials, information on settings (hospital,
primary care) and location is essential to judge for
applicability and generalizability of results.
• For laboratory studies, usually unnecessary unless
you have performed experiments at a particular
location or lab because it is the only place to do it and
you want to give the opportunity to others to use it.
Material and methods
Procedures
 The usual order of presentation of methods is
chronological, but related methods may need to be
described together and strict chronological order cannot
always be followed.
 Describe the protocol for your study in sufficient detail
that other scientists could repeat your work to verify your
findings. Foremost in your description should be the
"quantitative" aspects (e.g., masses, amounts, volumes,
times, concentrations, temperature, dosage and route of
administration).
 Always use decimal metric system and degrees Celsius.
Material and methods
Procedures
 Equipment and materials available off the shelf should
be described exactly and sources of materials should be
given if there is variation in quality among supplies.
Modifications to equipment or equipment constructed
specifically for the study should be carefully described in
detail.
 Provide relevant citations for methods previously
published, but make sure to describe any modifications
you have made for the purpose of your study.
Material and methods
Procedures
Avoid wordy or overly details.
• “The petri dish was placed on the turntable. The lid was
then raised slightly. An inoculating loop was used to
transfer culture to the agar surface. The turntable was
rotated 90 degrees by hand. The loop was moved lightly
back and forth over the agar to spread the culture. The
bacteria were then incubated at 37 C for 24 h”. Bad
• “Each plate was placed on a turntable and streaked at
opposing angles with fresh overnight E. coli culture using
an inoculating loop. The bacteria were then incubated at
37 C for 24 h”. Better
• “Each plate was streaked with fresh overnight E. coli
culture and incubated at 37 C for 24 h”. Best
Material and methods
Procedures
Avoid using ambiguous terms.
• “A Spec 20 was used to measure A600 of Tubes 1,2, and
3 immediately after chloroplasts were added (Time 0) and
every 2 min. thereafter until the DCIP was completely
reduced. Tube 4's A600 was measured only at Time 0
and at the end of the experiment”.
• “A Spec 20 was used to measure A600 of the reaction
mixtures exposed to light intensities of 1500, 750, and
350 uE/m2/sec immediately after chloroplasts were
added (Time 0) and every 2 min. thereafter until the DCIP
was completely reduced. The A600 of the no-light control
was measured only at Time 0 and at the end of the
experiment”.
Material and methods
Analysis
 Clearly state and define the main outcome measure(s).
 Indicate what types of descriptive statistics were used
and which analyses (usually hypothesis tests) were
employed to answer each of the questions or
hypotheses tested and determine statistical significance.
 Briefly state the statistical methods you used if they are
standard. New methods should be described in detail
with justification.
Material and methods
Analysis
Be clear about what the outcome measure involves:
• Counting people, animals, or objects (categorical
data)
• Taking measurements on people, animals, or objects
(continuous data)
• Time-to event data (e.g., survival data)
Counting
people or
objects
•Relative risk
•Risk difference
Effect size
•Percentage
change in risk
Taking
Time-to-event
measurements on
data
people or objects
•Difference
•Hazard ratio
between 2 means •Risk difference
•Difference
at a specific time
between 2 medians point
Material and methods
Analysis
Use the appropriate test:
Counting people
or objects
Two separate Chi-square test
groups, 1
measurement
(unpaired data)
One group, 2 McNemar’s test
repeated
measurements
(paired data)
Taking measurements on
people or objects
Time-to-event
data
Unpaired t-test if the
difference between means is Log rank test
normally distributed
Mann-Whitney test if
difference distribution is
skewed
Paired t-test if difference is
Not applicable
normally distributed
Wilcoxon pairs test if
distribution of difference is
skewed
Allow for other Multivariate logistic
Multivariate linear regression Cox regression
factors
regression
Material and methods
Analysis
Use the appropriate test:
• Use ANOVA or Kruskall-Wallis test to compare
differences of the means for more than two groups.
• Use repeated-measure ANOVA or Friedman test to
compare paired data for more than two groups.
• Use mixed between-within groups ANOVA for repeated
measures in different groups.
• Use post-hoc tests for multiple comparisons when
ANOVA yields significant effects, or consider adjusting
p-values for multiple comparisons, or provide 99%
confidence intervals.
Material and methods
Analysis
Use the appropriate test:
• Be clear about repeated measures data. A study of 10
repeated measurements of a variable on 10 subjects is
not the same as 1 measurement on 100 subjects; there
are still only 10 subjects.
• Subgroup analyses tend not to produce reliable results if
there are (a) too few patients or (b) too few events.
Material and methods
Analysis
Use the appropriate test:
• For screening or diagnostic studies use "detection rate"
(sensitivity) and "false-positive rate" (1-specificity).
• Using specificity to compare two tests can mask an
important difference. For example, specificities of 96%
versus 98% both look high. However, the corresponding
false-positive rates are 4% versus 2% (one is twice as
large as the other).
Material and methods
Analysis
Use the appropriate test:
• For assessing agreement between methods do not use
correlation but Bland and Altman plot.
Good correlation r=0.94 (p<0.001)
Considerable lack of agreement (±80 L/min)
Material and methods
Analysis
Mean ± SD or Mean ± SEM?
SEM = SD / sqr(n)
 SD represents variation in the values of a variable, it
gives an idea of the variability of single observations.
 SEM represents the spread that the mean of a sample of
the values would have if you kept taking samples, it gives
an idea of the accuracy of the mean.
SEM does not convey
statistical significance!
Material and methods
Analysis
P<0.05, is there anything is special about it?
 An hangover from the days before computers, when it
was difficult to calculate exact p values for the value of a
test statistic.
 P<0.05 does not mean that there is a difference
 P>0.05 does not mean that there is no difference.
P values for these two
tests are p=0.051
and p=0.049, but nobody
can tell which is which.
Material and methods
Analysis
 P<0.05 is regarded as unlikely enough to reject the null
hypothesis. It allows to say “the effect is statistically
significant at the 5% level”. But some conclude “there is
a real effect”.
 P>0.05 means there is not enough evidence to reject the
null hypothesis. It allows to say “the effect is statistically
non-significant”. But some conclude “there is no effect”.
 For between-groups comparison, provide estimates of
effect sizes and the corresponding CI or p values.
 Report all main effect sizes whether statistically
significant or not.
Material and methods
Analysis
 State which is the probability level you accept as
significant.
 Calculate exact p values with 2 or 3 decimal digits
 There is no need to show the value of the test used (t, F,
chi-square, U).
 For regression and correlation calculate r2 to give an
estimate of the variance explained.
Material and methods
Analysis
 We can disprove things only in pure mathematics, not in
real life.
 Failure to reject the null hypothesis doesn't mean we
have to accept it.
 In any case, true effects are always "real”.
 The null hypothesis is always false!
 The P value is not a probability of anything in reality.
 Some useful effects aren't statistically significant.
 Some statistically significant effects aren't useful.
Non-significant is usually misinterpreted as unpublishable.
So good data don't get published.
Material and methods
Clinical trials
The International Committee of Medical Journals Editors
requires that clinical trials are registered before the
beginning of patient enrollment. For this purpose, a clinical
trial is defined as any research project that prospectively
assigns human subjects to intervention or comparison
groups to study the cause-and-effect relationship between a
medical intervention and a health outcome. Information on
the registry where the study was registered should be given.
Reporting of randomized controlled trials should conform to
the CONSORT statement, which provides a set of
recommendations comprising a list of items to report and a
patient flow diagram (www.consort-statement.org)
Joint course with ERS “How to write an article”
Discussion
Vito Brusasco
Department of Internal Medicine
Medical School
University of Genoa, Italy
Respiratory Pathophysiology Unit
San Martino University Hospital
Genoa, Italy
Discussion
Function
 To interpret your results in light of what was already
known about the subject of the investigation, and to
explain the new understanding of the problem in the light
of the results of the study.
 Connects to the Introduction by way of the question(s) or
hypotheses posed and the literature cited, but it does not
simply repeat or rearrange the Introduction.
 It tells how the study has moved us forward from the
place you left us at the end of the Introduction.
Discussion
General guidelines
Question to address
How to address them
What do your
observations mean?
Summarize the most important findings at the
beginning.
What conclusions can you
draw?
• Describe the patterns, principles, relationships
results show.
• Explain how results relate to expectations and to
literature cited in the Introduction.
• Explain plausibly any agreements, contradictions, or
exceptions.
• Describe what additional research might resolve
contradictions or explain exceptions
How do your results fit in a • Suggest their theoretical implications.
broader context?
• Suggest their practical applications
• Extend your findings to other situations or species.
• Give the big picture: do your findings help us
understand a broader topic?
Discussion
Style
 Past or present tense?
• Past tense, use it to summarize your findings or those
of previous studies
• Present tense, use it to make statements on the
interpretation of data and conclusions.
 Active or passive voice?
• Use the active voice whenever possible. Use of the first
person is okay, but too much use of the first person may
actually distract the reader from the main points.
Discussion
Content
 Comment on the methodological limitations of your
study. Some place this after the comments on results
but before is preferable.
 Address each of the experiments or studies for which
you presented results. Discuss each in the same
sequence as presented in the Results. The most
important findings should be presented first.
 Do not restate your results; if you need to remind the
reader of the result to be discussed, use "bridge
sentences" that relate the result to the interpretation.
"The greater response of the treated group relative to
controls suggests that...[interpretation]“.
Discussion
Content
 Comment on others’ studies that helps interpret your
own data, or reinterpret others' findings in light of yours.
 Consider how the results of other studies may be
combined with yours to derive a new or better
substantiated understanding of the problem.
 Don't ignore or bury the major issue. Did the study
achieve the goal presented in the Introduction?
 Don't overgeneralize.
 Avoid speculation that cannot be tested in the
foreseeable future.
Discussion
Content
 In general, new results should not be introduced in
the Discussion, but there are exceptions to this rule.
 You may include in this section tables and figures
which help explain something you are discussing.
 You may include flow diagrams, accumulation of data
from the literature, or something that shows how one
type of data leads to or correlates with another, etc.
 You may also include additional data that were not
part of the experimental design but may help explain
the results.
Discussion
Conclusions
The discussion should end up with one or more
conclusions.
Many times the authors are very cautious and this results
in ending of an manuscript with “Our findings suggest”, or
“Our preliminary results indicate”.
Many studies also end up with the recommendation that
more studies are needed, or higher number of subjects
should have been included.
These sentences weakens the message. Try to find a very
positive finding and state this clearly.