12 August 2013Ganesha Associates1 Competências Básicas de Investigação Científica e de Publicação Lecture 5: Writing a scientific article.

12 August 2013 Ganesha Associates 1

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

• Abstract• Brief communication• Primary research article• Review• Methods/Techniques• Supplementary content

– Book chapter– Monograph– Patent– Conference proceedings

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Styles of communication

– 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• 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

• 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

• Materials and Methods• Results• Tables• Figures

• Discussion• References/Citations

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More on simple rulesResearch proposals (and research articles) tell a story

Slides by Susan Ruff Spring 2007

Each section has a specific purpose

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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 SantiagoClarissa Daisy Costa AlbuquerqueEliane Maria Soares-VenturaNeide SantosBethânia de Araújo Silva AmaralMaria Tereza Cartaxo MunizFlávio José da Costa RamosCecília S.C. MeloRaquel dos Santos Vera CruzVera Lúcia Lins de MoraisTerezinha de Jesus Marques–SallesMaria Auxiliadora de Queiroz CavalcantiGalba 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 self-

explanatory 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, MT1-MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyte-ECM 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, MT1-MMP acts as a 3-D-specific adipogenic factor that directs the dynamic adipocyte-ECM 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 blood-pressure (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 blood-pressure 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” person-reported 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 Dystrophy12 August 2013

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Resource value affects territorial defense by Broad-tailed 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; Broad-tailed 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 problemsToo 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• 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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Caffeine-induced endothelial cell death and the inhibition of angiogenesis

• 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 anti-angiogenic 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 anti-angiogenic factor TSP-1, and sought to identify the molecular mechanism responsible for its activities.

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• 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 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].

• 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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Caffeine-induced endothelial cell death and the inhibition of angiogenesis

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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

Form/%NaCl

0% 2% 4% 6% 8%

Globose 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)

Ellipsoidal 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)

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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• 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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Figures – instructions to authors

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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 12 August 2013

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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