Competências Básicas de Investigação
Científica e de Publicação
Lecture 3: Reading and writing skills
August 2014
The scientific research process
[Greatly simplified!]
Experiments
Problem definition
Grant proposal
More
experiments
Seminar
Conference proceedings
Writing-up
Publication
Key:
Experiments
Reading and writing
Verbal communication
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The importance of reading and writing
• Good science begins and ends in the literature
• Good experimental design requires an awareness of the latest
research trends and findings in your area together with a clear
definition of the problem you are trying to solve
• Acceptance of your work for publication requires clear logical
presentation of your results together with a clear explanation
of how they advance our understanding
• Analysis of the literature is a constant component of a good
researcher’s daily routine
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The importance of regular reading
A strategy for reading
• Search Scopus, WoS, PubMed, etc regularly for new
articles, or look at articles citing landmark papers
• The worst way is to read from title to references,
digesting every word along the way without any
reflection or criticism, so…
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–
–
–
Read often
Skim the articles and identify their structure.
Distinguish the main points, starting with the results.
Generate questions and be aware of where your
understanding begins and ends
– Draw inferences – where are the gaps?
– Take notes as you read.
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Finding a place to start
• Understanding the background
– Review journals
• Trends in…, Current Opinions in…, Annual Reviews in…, Nature
Reviews in…
– Use ‘cited by’ functionality in Scopus and WoS
– Use ‘related article’ functionality in PubMed
• Finding the frontier
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–
–
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Scientific weeklies, Nature, Science
Top international journals in your field
Conference reports
Talk to a leader in the field
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Nature News and Views format
Current Opinion review style
Systematic reviews
Search for reviews as a specific document type
Beware of choosing a topic because “little
is known about it”
• This means either the area is of little interest,
or you haven’t done your literature search
effectively
• Use a comparative or inductive approach and
look for examples in similar systems - this
technique is particularly useful in any field
with a molecular component
• But it also works for the caatinga!
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Styles of communication
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Conversation
Meeting minutes
Chemical patent
Legal document, e.g. a contract, a will
Car owner manual
Yellow pages
Computer software
Newspaper article
– Which styles are similar to those of a scientific journal
article ?
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Scientific writing is linear
• Scientific writing must be unambiguous and
logical
• Since logic tends to be linear, learn to express
yourself that way
Scientific writing has structure
Title
Document
Summary
Sections
Introduction
Paragraphs
Discussion
Sentences
Conclusions
Phrases
Phrases are the basic building blocks
• [Noun phrase][Verb phrase][Noun phrase]
• Breathing exercises improve functional exercise capacity in
people with COPD .
• There are no consistent effects on dyspnoea or healthrelated quality of life.
• Outcomes were similar across all the breathing exercises
examined.
• Treatment effects for patient-reported outcomes may have
been overestimated owing to lack of blinding.
• Breathing exercises may be useful to improve exercise
tolerance in selected individuals with COPD.
• However, these data do not suggest a widespread role for
breathing exercises in the comprehensive management of
people with COPD.
Phrase order and stress
Readers expect context first, with the take-home message
in the stress position at the end of the sentence.
For example:
• Treatment effects for un-blinded patient-reported
outcomes may have been overestimated
• Lack of blinding may have led to an overestimate in the
treatment outcomes reported by patients.
• Patients report better treatment outcomes due to lack
of blinding
Often writers will chain sentences using the item stressed
in the preceding sentence as the context for the next.
Example of chaining sentences
• Nociceptor sensory neurons are specialized to detect potentially
damaging stimuli
• These stimuli initiate the sensation of pain.
• However, bacterial infections produce pain by unknown molecular
mechanisms.
• These mechanisms are presumed to be secondary to immune
activation.
• Here we demonstrate that bacteria directly activate nociceptors.
• So the immune response mediated through TLR2, MyD88, T cells, B
cells., neutrophils and monocytes is not necessary for bacteriainduced pain in mice.
• Instead, mechanical and thermal hyperalgesia in mice is correlated
with live bacteria load rather than tissue swelling or immune
activation.
Structure tips – sentence order
• The smallest of the URF's* (URFA6L), a 207-nucleotide (nt) reading frame
overlapping out of phase the NH2-terminal portion of the
adenosinetriphosphatase (ATPase) subunit 6 gene has been identified as the
animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene.
• The functional significance of the other URF's has been, on the contrary,
elusive.
• Recently, however, immunoprecipitation experiments with antibodies to
purified, rotenone-sensitive NADH-ubiquinone oxido-reductase [hereafter
referred to as respiratory chain NADH dehydrogenase or complex I] from
bovine heart, as well as enzyme fractionation studies, have indicated that six
human URF's (that is, URF1, URF2, URF3, URF4, URF4L, and URF5, hereafter
referred to as ND1, ND2, ND3, ND4, ND4L, and ND5) encode subunits of
complex I.
• This is a large complex that also contains many subunits synthesized in the
cytoplasm.
* URF = uncharacterized open reading frame
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Structure tips – sentence order (edit)
• The smallest of the URF's, URFA6L, has been identified as the animal functional
equivalent of the recently discovered yeast H+-ATPase subunit 8 gene.
• However, the functional significance of other URF's has been more elusive.
• Recently, several human URF's have been shown to encode subunits of
rotenone-sensitive NADH-ubiquinone oxido-reductase.
• This is a large complex that also contains many subunits synthesized in the
cytoplasm - it will be referred to hereafter as respiratory chain NADH
dehydrogenase or Complex I.
• Six subunits of Complex I were shown by enzyme fractionation studies and
immunoprecipitation experiments to be encoded by six human URF's (URF1,
URF2, URF3, URF4, URF4L, and URF5)
• These URF's will be referred to subsequently as ND1, ND2, ND3, ND4, ND4L and
ND5.
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Structure - paragraphs
• Start with generalities and then move towards
more specific ideas.
• There should be an obvious logical connection
between paragraphs.
• There should be one main or theme point per
paragraph; if the paragraph contains too many
themes, create a new paragraph or
paragraphs.
• Now some examples…
REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Introduction: Chronic heart failure (CHF) is a complex syndrome caused by functional or structural cardiac abnormalities, leading to defects in
ventricular filling/ejection. As a result, the heart is unable to adequately supply the blood demand of tissues.1,2
The main symptoms of CHF are dyspnea and fatigue,3,4 caused by a physiopathological interaction beyond the hemodynamic disorder itself.3-6
Research shows that the lungs, with the exception of possible pulmonary function damage, are not responsible for reduced functional capacity in
patients with chronic heart failure (CHF).4 Since hemodynamic and pulmonary limitations do not sufficiently explain the appearance of fatigue and
dyspnea in CHF sufferers, several studies suggest that skeletal muscle abnormalities may contribute to these symptoms among subjects with CHF.6,7
Fatigue and dyspnea hamper performance in activities of daily living and exercise among patients with CHF.8 These symptoms are caused by skeletal
muscle atrophy, lower percentages of type I fibers in relation to type II, a decline in oxidative enzymes with rapid depletion of glycolytic mechanisms,
as well as a decrease in the size and number of mitochondria.9 In addition, respiratory muscle weakness may be involved in increased breathing
effort during hyperpnea required to perform activities with greater energy expenditure.10
Inspiratory muscle dysfunction is characterized by a reduction in their ability to generate pressure and force. This decreased strength is the result of
histological and biochemical changes. Based on diaphragm biopsies of individuals with CHF, histological studies recorded an increase in type I fibers,
suggesting a compensatory mechanism for the ventilation overload of these muscles. 11 Moreover, weakness in these muscles can also be explained
by the reduced diameter of muscular fibers, causing mechanical alterations.12 Clinically, this dysfunction may lead to limited exercise ability and
diminished quality of life, as well as a less favorable prognosis among individuals affected.10
In an attempt to reduce respiratory muscle dysfunction in CHF sufferers, several investigations have demonstrated the effects of Inspiratory Muscle
Training (IMT). 8,10,13 Inspiratory muscles, particularly the diaphragm, exhibit plasticity and are therefore susceptible to the principles of training.14 In
accordance with the specificity of training, IMT improves respiratory function in daily activities with regard to the type of muscle recruitment pattern
required during exercise or activities of daily living of patients. 15
A recent study by Chiappa et al 13, recorded a 72% increase in MIP among individuals who underwent IMT and suffered from CHF related to
inspiratory muscle weakness, compared to patients not submitted to training. Using ultrasound testing, the investigation also found that IMT
provoked notable diaphragmatic hypertrophy.
Another clinically significant aspect in CHF sufferers is the presence of cardiomegaly in some patients. In this condition expansion of the chest wall is
limited and extrapulmonary restriction, caused by competition between the lungs and heart for space inside the chest, may occur. As the disease
advances and worsens, in association with cardiomegaly, episodes of dyspnea become more frequent and severe with minimal effort and muscle
fatigue sets in progressively sooner.14-15
Thus, the present study aims to assess regional lung ventilation distribution in patients with CHF after completing an inspiratory muscle training
program
and correlate it with functional capacity and quality of life
amongAssociates
these individuals.
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REGIONAL LUNG VENTILATION DISTRIBUTION AMONG INDIVIDUALS WITH
CHRONIC HEART FAILURE AFTER AN INSPIRATORY MUSCLE TRAINING
PROGRAME: A RANDOMIZED CONTROLLED CLINICAL TRIAL
Introduction: Chronic heart failure (CHF) is a complex syndrome caused by functional or structural cardiac
abnormalities, leading to defects in ventricular filling/ejection.
The main symptoms of CHF are dyspnea and fatigue,3,4 caused by a physiopathological interaction beyond the
hemodynamic disorder itself.3-
Fatigue and dyspnea hamper performance in activities of daily living and exercise among patients with CHF.8
Inspiratory muscle dysfunction is characterized by a reduction in their ability to generate pressure and force.
In an attempt to reduce respiratory muscle dysfunction in CHF sufferers, several investigations have demonstrated
the effects of Inspiratory Muscle Training (IMT). 8,10,13
A recent study by Chiappa et al 13, recorded a 72% increase in MIP among individuals who underwent IMT and
suffered from CHF related to inspiratory muscle weakness, compared to patients not submitted to training. Using
ultrasound testing, the investigation also found that IMT provoked notable diaphragmatic hypertrophy.
Another clinically significant aspect in CHF sufferers is the presence of cardiomegaly in some patients.
Thus, the present study aims to assess regional lung ventilation distribution in patients with CHF after completing an
inspiratory muscle training program and correlate it with functional capacity and quality of life among these
individuals.
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Ganesha Associates
INSPIRATORY MUSCLE TRAINING IMPROVES REGIONAL LUNG VENTILATION
DISTRIBUTION IN CHRONIC HEART FAILURE PATIENTS: A RANDOMIZED
CONTROLLED CLINICAL TRIAL
Introduction: The main symptoms of chronic heart failure (CHF) are dyspnea and fatigue,3,4 Several
studies suggest that skeletal muscle abnormalities may contribute to these symptoms. 6,7 Diaphragm
biopsies of individuals with CHF show an increase in type I fibers, suggesting a compensatory
mechanism for the ventilation overload of these muscles. 11 Moreover, weakness in these muscles can
also be explained by the reduced diameter of muscular fibers, causing mechanical alterations. 12
Clinically, this dysfunction may lead to limited exercise ability and diminished quality of life, as well as a
less favorable prognosis among individuals affected.10 Some CHF patients have cardiomegaly. Expansion
of the chest wall is limited and extra-pulmonary restriction, caused by competition between the lungs
and heart for space inside the chest, may occur. As the disease advances episodes of dyspnea become
more frequent and muscle fatigue sets in progressively sooner.14-15
In an attempt to increase respiratory muscle function in CHF sufferers, several investigations have
demonstrated the positive effects of Inspiratory Muscle Training (IMT). 8,10,13 IMT improves respiratory
function in daily activities with regard to the type of muscle recruitment pattern required during
exercise or activities of daily living of patients. 15 For example, a recent study by Chiappa et al 13,
recorded a 72% increase in MIP in CHF patients who underwent IMT. Using ultrasound testing, the
investigation also found that IMT provoked notable diaphragmatic hypertrophy.
Here we show that IMT improved muscle strength, functional capacity and quality of life in CHS
patients. We also analyzed the distribution behavior of lung volumes for the thoracoabdominal system
in this population and found that larger abdominal rib cage and abdomen volumes may result in more
effective diaphragmatic contraction.
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Ganesha Associates
INSPIRATORY MUSCLE TRAINING IMPROVES REGIONAL LUNG VENTILATION
DISTRIBUTION IN CHRONIC HEART FAILURE PATIENTS: A RANDOMIZED
CONTROLLED CLINICAL TRIAL
Introduction: The main symptoms of chronic heart failure
(CHF) are dyspnea and fatigue.
Clinically, this dysfunction may lead to limited exercise ability
and diminished quality of life, as well as a less favourable
prognosis among individuals affected.
In an attempt to increase respiratory muscle function in CHF
sufferers, several investigations have demonstrated the
positive effects of Inspiratory Muscle Training (IMT).
Here we show that IMT improved muscle strength, functional
capacity and quality of life in CHS patients.
18/10/2013
Ganesha Associates
Learning points
• Read critically, make notes
• Analyse the structure of articles
• Because each paragraph has a specific function they
should appear in a logical order
• Ditto each sentence within the paragraph.
• Within each sentence, try to move from the general
to the particular
• Punctuation can alter meaning, so use it sparingly
– Example: The panda eats shoots and leaves vs. The panda
eats, shoots and leaves
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Break
Types of scientific writing
– Grant application
– Mestrado or Doutorado proposal
– Published scientific article
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•
•
•
•
•
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Abstract
Brief communication
Primary research article
Review
Methods/Techniques
Supplementary content
Book chapter
Monograph
Patent
Conference proceedings
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Scientific papers have a structure
• A scientific paper is a written report describing original
research results whose format has been defined by centuries
of developing tradition, editorial practice, scientific ethics and
the interplay with printing and digital publishing services.
• The result of this process is that virtually every scientific paper
has a title, abstract, introduction, materials and methods,
results and discussion – the so-called IMRD structure.
• Even so, most publications have their own rules about a
paper's format: So read the Journal’s Instructions for Authors
first!
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Instructions to authors
•
•
•
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•
•
•
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•
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General Information
Types of Articles
Submission Fee
Publication Fee
Policies
Contact Information
Preparing a Manuscript
Regular Manuscripts
Brief Communications
Journal Clubs
Letters to the Editor
Invited Articles
Submitting a Manuscript
Review Process
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•
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•
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Requirements for Submission
Submission Fee
Revising/Finalizing a Manuscript
Revisions
Proofs
Publication Fee
Embargo Policy
Cover Art
NIH Public Access Policy
Correcting Errors in Published
Articles
• Corrections
• Retractions
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Other guides for authors
• CONSORT, which stands for Consolidated
Standards of Reporting Trials, encompasses
various initiatives developed by the CONSORT
Group to alleviate the problems arising from
inadequate reporting of randomized controlled
trials (RCTs).
• Nature has also produced a checklist is used to
ensure good reporting standards and to improve
the reproducibility of published results
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Summary of an article’s main components
•
•
•
•
•
Title
Author details
Keywords
Abstract/Summary
Introduction
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• Materials and Methods
• Results
• Tables
• Figures
• Discussion
• References/Citations
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More on simple rules
Each section has a specific purpose
Research proposals (and research articles) tell a story
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Slides by Susan Ruff Spring 2007
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Title
• A title should be the fewest possible words that
accurately describe the content of the paper.
• Omit all waste words such as "A study of ...",
"Investigations of ...", "Observations on ...", etc.
• Remember, the title appears in the search results –
so make it explicit
• And, indexing and abstracting services depend on
the accuracy of the title, extracting from it keywords
used for cross-referencing and computer searching.
• So, a badly-titled paper may never reach the
audience for which it was intended!
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Titles – some good examples
• Cognitive-behavioral strategies improve dyspnea and related distress in
COPD.
• Reversal of Histone Lysine Trimethylation by the JMJD2 Family of Histone
Demethylases
• Similar Frontal and Distinct Posterior Cortical Regions Mediate Visual and
Auditory Perceptual Awareness.
• Breathing exercises for adults with asthma.
• Wntless is a Conserved Membrane Protein Dedicated to the Secretion of
Wnt Proteins from Signaling Cells
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Titles – some not so good examples
• Cloning and nucleotide sequencing of three heat shock
protein genes (hsp90, hsc70, and hsp19.5) from the
diamondback moth, Plutella xylostella (L.) and their
expression in relation to developmental stage and
temperature. (Result ?, length, abbreviations)
• Effect of docosahexaenoic acid-rich fish oil supplementation
on human leukocyte function. (Result ?)
• Organization and methodology of early rehabilitation of the
patients with cardioembolic stroke complicated by cardiac
insufficiency. (Length)
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Titles – some not so good examples improved
• Diamondback moth heat shock genes are expressed
differentially according to developmental stage and
temperature
• Docosahexaenoic acid-rich fish oil supplementation has a
positive effect on human leukocyte function.
• Early rehabilitation of patients with cardioembolic stroke and
cardiac insufficiency].
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Names: How many do you have?
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Choose, and stick with, a unique author
name. Register with ORCID
André Luiz Cabral Monteiro de Azevedo Santiago
Clarissa Daisy Costa Albuquerque
Eliane Maria Soares-Ventura
Neide Santos
Bethânia de Araújo Silva Amaral
Maria Tereza Cartaxo Muniz
Flávio José da Costa Ramos
Cecília S.C. Melo
Raquel dos Santos Vera Cruz
Vera Lúcia Lins de Morais
Terezinha de Jesus Marques–Salles
Maria Auxiliadora de Queiroz Cavalcanti
Galba Maria de Campos Takaki
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Keywords
• The author keyword list provides the opportunity
to add alternative indexing terms, in addition to
those already present in the title.
• Judicious use of keywords may increase the ease
with which interested readers can locate your
article in a database such as SciELO or
ScienceDirect.
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Keywords
• Title
– Keywords
• BK Channels in Cardiovascular Diseases and Aging
– Calcium-activated potassium channels, BK, vascular
smooth muscle cells, endothelium, aging,
cardiovascular diseases
• Qualitative changes in fetal trabecular meshwork
fibers at the human iridocorneal angle
– Trabecular meshwork, Schlemm's canal, collagen,
silver staining
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Abstract
• The abstract should summarize the results and
principal conclusions.
• A well-prepared abstract enables the reader to identify
the basic content of a document quickly and accurately,
and thus to decide whether to read the document in its
entirety.
• Do not include details of the methods used unless the
study is methodological, i.e. primarily concerned with
methods.
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Abstract
• The abstract, together with the title, must be selfexplanatory as they are published separately from the
paper in abstracting/indexing services
• Omit all references to the literature and to tables or
figures
• Omit obscure abbreviations and acronyms even though
they may be defined in main body of the paper.
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A good abstract always has a well-defined
structure
It is known that white adipose tissue (WAT) serves as the primary energy depot in
the body by storing fat. During development, fat cell precursors (i.e.,
preadipocytes) undergo a hypertrophic response as they mature into lipid-laden
adipocytes. However, the mechanisms that regulate adipocyte size and mass
remain undefined. Herein, we demonstrate that the membrane anchored
metalloproteinase, MT1-MMP, coordinates adipocyte differentiation in vivo. In
the absence of the protease, WAT development is aborted, leaving tissues
populated by mini-adipocytes which render null mice lipodystrophic. Hence, MT1MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyteECM interactions critical to WAT development.
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A good abstract always has a well-defined
structure
It is known that white adipose tissue (WAT) serves as the primary energy depot in
the body by storing fat. During development, fat cell precursors (i.e.,
preadipocytes) undergo a hypertrophic response as they mature into lipid-laden
adipocytes. However, the mechanisms that regulate adipocyte size and mass
remain undefined. Herein, we demonstrate that the membrane anchored
metalloproteinase, MT1-MMP, coordinates adipocyte differentiation in vivo. In
the absence of the protease, WAT development is aborted, leaving tissues
populated by mini-adipocytes which render null mice lipodystrophic. Hence, MT1MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyteECM interactions critical to WAT development.
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Different Abstract styles
– Background: Markers of inflammation such as high sensitivity C-reactive protein (CRP) were shown
to be elevated in patients with hypertension. Small trials using statin therapy showed bloodpressure (BP) reductions, but it is unknown whether this association extends to larger populations.
The objective of this study was to determine whether statin use was associated with better bloodpressure control in adults with hypertension and whether inflammation levels mediated this
relationship.
– Methods: This was a cross-sectional study of 2584 hypertensive adults aged _40 years with no
known cardiovascular disease from the National Health and Nutrition Examination Survey 1999–
2002. Logistic regression models were calculated to determine whether there was an association
between statin use and blood-pressure control. C-reactive protein was added to the full model to
determine its impact on the association.
– Results: Compared with people not using statin medication, significantly more statin users had their
blood pressure under control (52.2% v 38.0%). After adjustment for demographic factors, statin
users were two times (95% confidence interval [CI], 1.46 to 2.72) more likely to have their blood
pressure under control (_140/90 mm Hg) than nonusers. After further adjustment for body mass
index, diabetes, smoking, exercise, low-salt diet, and antihypertensive medications, the likelihood
of having blood pressure under control remained more likely among statin users (odds ratio, 1.46;
95% CI, 1.05 to 2.05). The association between statin use and lower BP was most evident among
participants who used antihypertensive medication as well as statins and was unchanged with the
addition of CRP to the model.
– Conclusions: Statin use was associated with a BP level _140/90 mm Hg in a representative sample
of US adults with hypertension. Levels of CRP did not attenuate the association. Further studies are
needed to explore the effects of statin use on blood pressure and to determine how best to apply
this knowledge in clinical care.
– From the American Journal of Hypertension
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Resource value affects territorial defense by Broadtailed and Rufous hummingbirds
Territorial behavior of Broad-tailed (Selasphorous platycercus) and Rufous (Selasphorous
rufus) hummingbirds in Colorado was measured at sites with feeders containing 10%,
20%, and 30% sucrose solutions, respectively. The presence or absence of territory
holders, number of intruders, and intensity of defense were measured at the three levels
of energy availability. Migrating Rufous Hummingbirds displaced Broad-tailed
Hummingbirds from territories they had defended during the breeding season; Broadtailed Hummingbirds then defended only lower quality sites. Both Broad-tailed and
Rufous hummingbirds employed more energetically expensive behaviors when
defending high quality sites, with longer chases more often supplemented with chip calls
and hovering. Other investigators have suggested that chip calls and hovering are
precursors to a chase. However, I found that chasing was the default response to the
presence of an intruder. Chip calls and hovering were added to intensify a chase. In the
few cases where chip calls were uttered or hovering occurred without a chase, Rufous
Hummingbirds were more likely to exhibit this behavior than Broad-tailed
Hummingbirds.
©2006 Journal of Field Ornithology.
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Introduction
• The Introduction establishes why there was a need to conduct
the study by placing your objectives within the context of the
current literature.
• Thus the need for the new work should clearly flow from that
carried out previously. Each logical step should be fully
supported by appropriate references.
• At the end of the Introduction you should state clearly the
specific scope and objectives of the new research.
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An example of a problem
•
Ectomycorrhizal fungi (EMF) have a fundamental role in nutrient absorption of many plant species.
•
Tree species of ecological and economic relevance in reforestation programs depend on ectomycorrhizal
symbiosis, especially in soils contaminated by mining activities.
•
The ability of EMF to reduce the toxicity of heavy metal ions (e.g. copper) in their host plants is
accompanied by the decrease of metal concentrations in the aerial part of the plant.
•
Due to increased absorption of these metals by the EM roots and the accumulation in the extra radical
mycelium, greater tolerance to such elements is achieved by the host.
•
Research has been conducted to determine the sensitivity of EMF to a variety of potentially toxic metals to
understand the diverse mechanisms through which the fungi may tolerate heavy metals.
•
Enzymatic activity is important for the mobilization and transference of soil nutrients through EM fungi
towards the host plant.
•
In this study we investigate the effects of copper and phosphorus concentrations on mycelial growth and
enzymatic activities of the EM fungi Pisolithus microcarpus, Chondrogaster angustisporus and Suillus sp. in
two growth experiments.
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Materials and Methods
• The main purpose of the 'Materials and Methods' section is to provide
enough detail for a competent worker to repeat your study and reproduce
the results.
• Equipment and materials available off the shelf should be described
briefly (e.g. Licor underwater quantum sensor, Model LI 192SB) and
sources of materials should be given if there is there is likely to be a
variation in quality between suppliers.
• Modifications to equipment or equipment constructed specifically for the
study should be carefully described in detail. The methods used to prepare
unusual reagents, fixatives, and stains should also be described in detail.
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Materials and Methods
• Be precise in describing measurements and include the confidence
intervals associated with your measurements. Ordinary statistical methods
should be used without comment; advanced or unusual methods may
require a literature citation.
• So there is a pattern emerging. Standard techniques can be dealt with
quickly, but modified or new techniques should be described with a view
to enabling replication
• Show your materials and methods section to a colleague. Ask them if they
think they would have difficulty in repeating your study
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Results
• Write this section first!
• Display items (figures and tables) are central in this section.
Get them prepared and complete all of your statistical analysis
before you start writing
• Present your results in the order that makes the overall
significance of your work clearest. Note that this may not
necessarily match the order in which the experiments were
performed.
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Results
• Many readers will start reading your paper by looking at the figures and
tables.
• The conclusions to be drawn from individual figures and tables should be
clear from the titles and captions used, i.e. they should be designed as
self-contained units of information.
• The main text should read logically and be understandable without the
reader initially having to refer back and forth repeatedly to the figures and
tables
• So don’t say ”The relationship between bird species richness and habitat
complexity is clearly evident from Fig. 1". Say instead "Bird species
richness increased with habitat complexity (Fig. 1)".
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Table design example
0%
2%
4%
6%
8%
8.38 (±1.15)
8.49 (±0,90)
9.67 (±1.29)
10,72 (±2,88)
-
Subglobose
9.38 (±1.44) x
8.44 (±1.18)
9.93 (±1.40) x
8.94(±2.8)
10.2 (±2.42)
x 9.19 (±0.97)
10.95 (±0.9) x
9.93 (±1.41)
12.52 (±1.13) x
10.3 (±0.93)
Subglobose
to ellipsoidal
11.4 (±1.5) x
9.60 (±1,.2)
10.87 (±0.64) x
9.30 (±1.15)
11.24 (±1.0) x
8.916 (±0.10)
11.94 (±1.28) x
10.27 (±0.82)
13.32 (±1.92) x
11.25 (±1.12)
10.89 (±0.43) x
9.9 (±2.66)
13.28 (±3.60) x
10.5 (±1.54)
12.45 (±1.51) x
9.12 (±1.14)
12.55 (±1.72) x
9.75 (±1.22)
15.37 (±1.66) x
11.62 (±1.23)
Form/%
NaCl
Globose
Ellipsoidal
Caption - Average size (μm) of C. elegans sporangioles in Hesseltine & Anderson culture
media with 0, 2, 4, 6 and 8% NaCl at 20ºC.
Why is this a bad example?
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Discussion - structure
Don’t repeat the results section
Answer the research question(s) posed
Emphasize the major finding(s) first
What is your major conclusion, based on the results you have presented?
Interpret your results …
Compare with other studies
Same or different?
Possible reasons why?
Unexpected results
Briefly describe any limitations
Sample sizes
How could experiments be improved?
Restate major conclusion(s)
Possible applications and implications
Suggest future work
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References - purpose
• By placing references at strategic points in the text,
the reader is able to retrieve the evidence being used
to support a particular argument or statement
• In this way the reader is able to recreate the logical
train of thought that led the author to a particular
conclusion
• Any mistakes in reference use could result in
rejection of your article
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References - format
• References
• [1] Kotsis V, Stabouli S, Karafillis I, Nilsson P. Early vascular aging and the
role of central blood pressure. J Hypertens. 2011;29(10):1847–53.
[PubMed]
• [2] Barodka VM, Joshi BL, Berkowitz DE, Hogue CW, Jr, Nyhan D. Review
article: implications of vascular aging. Anesth Analg. 2011;112(5):1048–60.
[PMC free article] [PubMed]
• [3] Toro L, Marijic J, Nishimaru K, Tanaka Y, Song M, Stefani E. Aging, ion
channel expression, and vascular function. Vascul Pharmacol.
2002;38(1):73–80. [PubMed]
• [4] Panza F, D’Introno A, Colacicco AM, Capurso C, Parigi AD, Capurso SA,
Caselli RJ, Pilotto A, Scafato E, Capurso A, Solfrizzi V. Cognitive frailty:
Predementia syndrome and vascular risk factors. Neurobiol Aging.
2006;27(7):933–40. [PubMed]
• [5] Jackson WFn. Ion channels and vascular tone. Hypertension. 2000;35(1
Pt 2):173–8. [PMC free article] [PubMed]
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Plagiary and ‘language re-use’
If you use somebody else’s words, make this clear by
using quotation marks and a reference
The act of plagiarizing or appropriating the ideas,
writings, or inventions of another without due
acknowledgment; specifically the stealing of passages
either for word or in substance, from the writings of
another and publishing them as one's own
It is now easy for publishers to detect plagiarism
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Covering letter format
• Address to the editor personally
• State your manuscript title and publication
type
• Give a brief background, rationale and
description of your results
• Explain the importance of your findings and
why they would be of interest to the journal’s
target audience
• Supply details of possible reviewers
The “write” order
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Common manuscript problems
• Failure to state the purpose of the study in the
title, abstract, introduction…
• Failure to keep function of sections clear and
distinct, e.g. merge results and discussion
• Including non-essential data
• Treating the Introduction and/or Discussion as
an opportunity to review the entire field
• Not following Instructions to Authors
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A letter of rejection
Dear Author,
We have received the reports from our advisors on your manuscript
XYZ-D-13-00220 “Title********************************".
With regret, I must inform you that, based on the advice received, I have decided that your manuscript
cannot be accepted for publication in the Journal of Imaginary Microbiology.
Below, please find the comments for your perusal.
You are kindly requested to also check the website for possible reviewer attachment(s).
I would like to thank you very much for forwarding your manuscript to us for consideration and wish you
every success in finding an alternative place of publication.
With kind regards,
Editor
What to do next
• Unconditional rejection
–
–
–
–
Editor offers no opportunity for appeal
Show comments to colleagues
Revise as though the rejection was conditional
Submit to a different journal
• Conditional rejection
– Regard this as an opportunity to improve your paper
– Show comments to colleagues
– Respond to all comments and record your actions in a
covering letter
– Consider submitting to a better journal!
Reviewer comments - example
• The paper needs to be formatted properly for the journal.
• This reviewer was only able to find information for papers
submitted with Introduction, materials and methods,
results and discussion sections while much of this is in the
paper the format appears to be incorrect even for a short
communication.
• It was difficult to find the number of samples taken or to
understand the experimental set-up as written; changing
the style to a more traditional journal format as suggested
above would help with this.
• In addition the most important reference Brown et al 2013
is missing!
Reviewer comments - example
This paper describes clinical and cytogenetic finding in a child with
retinoblastoma who had an aggressive fatal course. The authors postulate
that this may be related to changes in chromosome 6. However, it is
difficult to see how the findings here either promote or negate that
hypothesis. In addition several other problems should be addressed:
a. Abstract, line 9: could (not should)
b. Abstract: define IO
c. Staging details at the time of initial diagnosis are inadequate. Were scans
done of the head? chest? abdomen? pelvis? bone?
d. One assumes that the right eye was normal at initial diagnosis but this is
not stated.
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Referee’s comments can be confusing
Referee response letter
• Respond to all of the reviewers’ comments
• Describe all of the changes you have made in the letter
• Also describe the reasons why you have not made
suggested changes
• Make it easy to see the changes have made in the
manuscript itself
– Refer to line and page numbers
– Different color font
– Highlight the text
Referee response letter
• If you disagree with the reviewer with the reviewer be clear
why:
– Reviewer Comment: In your analysis of the data you have
chosen to use a somewhat obscure fitting function (regression).
In my opinion, a simple Gaussian function would have sufficed.
Moreover, the results would be more instructive and easier to
compare to previous results.
– Author response: We agree with the reviewer that a simple
Gaussian fit would facilitate comparison with the results of
other studies. However, our tailored function allows for the
analysis of the data in terms of the Smith model [Smith et al,
1998]. We have added two sentences to the paper (page 3
paragraph 2) to explain the use of this function and Smith’s
model.
Journal of Voice
Voice problems of future speech-language pathologists.
The impact of phonation mode and vocal technique on vocal fold closure in young females with normal
voice quality
Acoustic voice analysis of prelingually deaf adults before and after cochlear implantation.
Quantifying component parts of indirect and direct voice therapy related to different voice disorders.
Acoustic and electroglottographic analyses of nonpathological, nonmodal phonation.
The effect of experience on classification of voice quality.
The vocal clarity of female speech-language pathology students: an exploratory study.
Obstacles to communication in children with cri du chat syndrome.
Current and emerging concepts in muscle tension dysphonia: a 30-month review.
Journal of Applied Oral Science
2.1 Illustrations and Tables
2.1.1 The illustrations (photographs, graphs, drawings, charts, etc.), regarded as
figures, should be limited to the least amount possible and should be uploaded in
separate files, consecutively numbered with Arabic numbers according to the order
they appear in the text.
2.1.2 Photographs should be sent in original colors and digitized in .jpg or tif formats
with at least 10 cm width and at least 300 dpi. These illustrations should be provided
in supplementary files and not inserted in the Word document.
2.1.3 The corresponding legends for figures should be clear, concise and typed at the
end of the manuscript as a separate list preceded by the corresponding number.
2.1.4 The tables should be logically arranged, consecutively numbered with Arabic
numbers. The legend shall be placed on the top of the tables. Tables should be open in
the right and left laterals.
2.1.5 Footnotes should be indicated by asterisks and restricted to the least amount
possible.
Results section
A total of 60 direct speech sessions were
completed during the 3 phases of the program.
The assessment procedures described above
were performed before and after the intensive
speech therapy and bulb reduction program. As
presented and described in Figure 7 all speech
alterations present before the interventions
were absent after the program (Figure 7).
Figure 7
Journal of Voice
• Legends to figures should be brief, specific,
and explanatory. They should not unduly
repeat information already given in the text
PLoS Medicine
Figure Legends
The aim of the figure legend should be to describe the
key messages of the figure, but the figure should also be
discussed in the text. An enlarged version of the figure
and its full legend will often be viewed in a separate
window online, and it should be possible for a reader to
understand the figure without switching back and forth
between this window and the relevant parts of the text.
Each legend should have a concise title of no more than
15 words. The legend itself should be succinct, while still
explaining all symbols and abbreviations. Avoid lengthy
descriptions of methods.
Alternatives: PLOS ONE
• PLOS ONE is a journal that publishes reports of
original research from all disciplines within science
and medicine.
• PLOS ONE will rigorously peer-review manuscripts
and will publish all papers that are technically sound.
• Judgments about the importance of any particular
paper are made after publication by the readership,
I,e, citations, article downloads.
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