Competências Básicas de Investigação
Científica e de Publicação
Lecture 5: Writing a scientific article
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Types of scientific writing
– Grant application
– Mestrado or Doutorado proposal
– Published scientific article
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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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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 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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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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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
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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
• The Transcriptional Coactivator CAMTA2 Stimulates Cardiac Growth by
Opposing Class II Histone Deacetylases
• 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.
• Circadian Regulator CLOCK Is a Histone Acetyltransferase
• 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 ?)
• Effects of repetitive TMS on visually evoked potentials and
EEG in the anesthetized cat: dependence on stimulus
frequency and train duration. (Acronyms, order and 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.
• Frequency and train duration of repetitive transcranial
magnetic stimulation affects visually evoked potentials and
EEG in the anesthetized cat.
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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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Possible autosomal origin of macro B
chromosomes in two grasshopper species
The acrocentric macro B chromosomes of Rhammatocerus brasiliensis
(Acrididae, Gomphocerinae) and Xyleus discoideus angulatus (Romaleidae,
Romaleinae) are highly similar to the X chromosome in each species in terms of
morphology, size and pycnosis. However, the results of FISH experiments using
45S and 5S rDNA probes suggest that in both species the B chromosomes are
most likely of autosomal origin. In R. brasiliensis, B chromosome 5S rDNA is
similar to that of L2, L3, M5 and S11 autosomes, whereas the X chromosome
lacks both rDNA families. In X. d. angulatus 45S rDNA is absent in B
chromosomes, whereas the X chromosome contains one of the two 45S rDNA
clusters in the genome. B chromosomes were found in all nine R. brasiliensis
populations analyzed, indicating that they are widely distributed in Northeastern
Brazil. This absence of any significant variation suggests high inter-population
gene flow presumably due to the abundance of the species on several types of
vegetation and its relatively high flight capability.
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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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The 6-Minute Walk Test and Person-Reported Outcomes in Boys with Duchenne
Muscular Dystrophy and Typically Developing Controls: Longitudinal Comparisons
and Clinically- Meaningful Changes Over One Year
Introduction: Data is currently lacking anchoring a 30-meter longitudinal change in
walking ability by 6-minute walk test (6MWT) in Duchenne muscular dystrophy as
a minimal clinically important difference and “clinically meaningful” personreported outcomes (PROs) at differing levels of ambulatory ability. Methods: We
describe correlation between measures, 1-year change in measures, and
correlation of 1-year changes between measures for the six-minute walk test
(6MWT), 10-meter run/walk velocity, PedsQL and POSNA Pediatric Outcomes Data
Collection Instrument (PODCI) in 24 4-12 year old. ambulatory DMD and 36 typical
controls, and determine if minimal clinically important differences (MCID) of PROs
contribute to different estimates of 6-minute walk distance (6MWD) change at
differing levels of ability. Results: PedsQL total and physical function and PODCI
global, transfer/mobility and sports/physical function PROs demonstrated
significant differences between DMD and controls (p<0.05) Discussion: At lower
levels of function, smaller increases in 6MWD result in meaningful change in
quality of life (QoL) instrument scores. At higher levels of function, larger increases
may be necessary to achieve the same QoL change score.
From PLoS Currents in Muscular Dystrophy
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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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Introduction – common problems
Too long, too much time spent on lofty and noble intentions
Little or no time spent linking proposed study to current state of the field
General-to-particular structure lacking
Purpose of study not clear
No or few references
‘Because so little is known…’
References incomplete and out-of-date
Note: these problems apply just as well to manuscripts in Portuguese
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An example of a problem
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Ectomycorrhizal fungi (EMF) have a fundamental role in nutrient absorption of many plant species.
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Tree species of ecological and economic relevance in reforestation programs depend on ectomycorrhizal
symbiosis, especially in soils contaminated by mining activities.
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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.
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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.
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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.
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Enzymatic activity is important for the mobilization and transference of soil nutrients through EM fungi
towards the host plant.
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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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Caffeine-induced endothelial cell death and the
inhibition of angiogenesis
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Angiogenesis is a process whereby new capillary blood vessels are produced from preexisting vessels. This process
is controlled by interplay between growth factors, which either stimulate or inhibit blood vessel growth.
Furthermore, some molecules, such as, vascular endothelial growth factor, basic fibroblast growth factor, and
thymidine phosphorylase, have been reported to have angiogenic activities. Angiogenesis is crucial for normal
processes, such as, fetal development, tissue repair, and the female reproductive cycle, and for abnormal
processes, such as, tumor growth, arthritis, stroke, ulcer development, and diabetic retinopathy [1].
In view of the widespread use of caffeine in food and beverages, and in over-the-counter medications, such as,
cold and flu remedies, any effect on angiogenesis could be of substantial importance [2, 3]. Furthermore, the
caffeine molecule is structurally similar to adenosine, and it has been well established that caffeine acts as an
adenosine receptor antagonist. Adenosine receptors belong to the G-protein-coupled 7 transmembrane super
family of cell surface receptors, which are composed of A1, A2A, A2B, and A3 subtypes [4-8]. Adenosine, a potent
endogenous physiological mediator, regulates many physiological processes, and it has been reported that
adenosine and adenosine agonists up-regulate the expressions of angiogenic factors, down-regulate antiangiogenic factor thrombospondin-1 (TSP-1) via adenosine receptors, and induce angiogenesis [9-15]. In addition
to studies performed in vitro, numerous in vivo studies have shown that adenosine and adenosine agonists induce
blood vessel growth in the corneas of amphibian, avian, and mammalian embryos and in skeletal muscle, the
body, and chick chorioallantoic membrane (CAM) [15-24]. However, somewhat surprisingly, the effects of caffeine
(a known adenosine receptor antagonist) on angiogenesis and on the expressions of anti-angiogenic factors have
not been previously investigated.
TSP-1 is a naturally occurring inhibitor of angiogenesis that is synthesized and secreted by fibroblasts, endothelial
cells, tumor cells, and others [25, 26]. TSP-1 has been shown to play a critical role in the inhibition of angiogenesis
[27], and thereby, to inhibit tumor growth and experimental metastasis [25-31]. Furthermore, an inverse
correlation has been reported between TSP-1 expression and microvessel density in vivo [32-34], and in another
study, TSP-1 was found to mediate endothelial cell apoptosis [35, 36] and inhibit angiogenesis in association with
the expressional down-regulation of Bcl-2 and the processing of caspase-3 into smaller proapoptotic forms [28].
In the present study, we examined the effects of caffeine on angiogenesis and on the expression of the antiangiogenic factor TSP-1, and sought to identify the molecular mechanism responsible for its activities.
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Caffeine-induced endothelial cell death and the
inhibition of angiogenesis
• Angiogenesis is a process whereby new capillary blood vessels are
produced from pre-existing vessels.
• In view of the widespread use of caffeine in food and beverages,
and in over-the-counter medications, such as, cold and flu
remedies, any effect on angiogenesis could be of substantial
importance [2, 3].
• However, the effects of caffeine (a known adenosine receptor
antagonist) on angiogenesis and on the expressions of antiangiogenic factors have not been previously investigated.
• TSP-1 is a naturally occurring inhibitor of angiogenesis that is
synthesized and secreted by fibroblasts, endothelial cells, tumor
cells, and others [25, 26].
• In the present study, we examined the effects of caffeine on
angiogenesis and on the expression of the anti-angiogenic factor
TSP-1, and sought to identify the molecular mechanism responsible
for its activities.
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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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Materials and Methods: Example
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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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Figures – instructions to authors
• Images submitted with a manuscript for
review should be minimally processed (for
instance, to add arrows to a micrograph).
• Authors should retain their unprocessed data
and metadata files, as editors may request
them to aid in manuscript evaluation.
• If unprocessed data are unavailable,
manuscript evaluation may be stalled until the
issue is resolved.
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Results: 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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References – common problems
• Few or no references given !
• References not up-to-date
• Multiple references used in place of reasoning to
support complex key assumptions, e.g. A?>B and
B?>C, therefore A>C.
• References incorrect
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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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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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