10 August 2012Copyright: Ganesha Associates 2012 1 Basic reading, writing and informatics skills for biomedical research Segment 7. The structure of a

10 August 2012 Copyright: Ganesha Associates 2012

1

Basic reading, writing and informatics skills for biomedical

researchSegment 7. The structure of a

scientific article


2

Types of scientific writing

– Grant application– Mestrado or Doutorado proposal– Research article

• Abstract• Brief communication• Research article• Review• Methods/Techniques• Supplementary content

– Book chapter– Monograph– Patent– Conference proceedings


3

You are writing for the readers

– “In order to understand how best to improve writing, we would do well to understand better how readers go about reading. It does not matter how pleased an author might be to have converted all the right data into sentences and paragraphs; it matters only whether a large majority of the reading audience accurately perceives what the author had in mind.”• George D. Gopen and Judith A. Swan in “The Science of

Scientific Writing” – available on the web site.– Clarity, relevance, believability, repeatability– Back to Bishop Spratt “…bringing all things as near

the Mathematical plainness…”


4

Language styles and communication

– Conversation– Meeting minutes– Chemical patent– Legal document– Car owner manual– Yellow pages– Computer software– Newspaper article

– Which styles are similar to a scientific journal article ?


5

“…Mathematical plainness…”

• Structure– Article sections, paragraphs– Individual sentences, number of clauses– Word order in sentences

• Order– General to specific– Lists

• Links– “Tokens” provide landmarks within body text

• Translation


6

Some simple rules - word order

• Por 37 votos a favor e 11 abstenções (deputados ausentes), foi aprovado, ontem, na Assembléia Legislativa, a 2a versão do Projeto de Lei Antinepotismo que prevê a proibição de contratação de parentes até terceiro grau no Poder Executivo.

• A 2a versão do Projeto de Lei Antinepotismo, que prevê a proibição de contratação de parentes até terceiro grau no Poder Executivo, foi aprovado ontem por 37 votos a favor e 11 abstenções (deputados ausentes) na Assembléia Legislativa

• Diario de Pernambuco 20 Set 2007


7

Example – 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.


8

• The smallest of the URF's, URFA6L, has been identified as the animal 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.

Example – sentence order


10

The structure of a scientific paper

• 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 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.

• Most publications have rules about a paper's format: So read the Journal’s Instructions for Authors first!


11

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

Slides by Susan Ruff Spring 2007

Each section has a specific purpose


12

Summary of main components

• Title• Author• Keywords• Abstract/Summary• Introduction

• Materials and Methods• Results• Tables• Figures

• Discussion• References


13

Summary of main components - comments

– Each section has a specific purpose – try not to mix them !

– Some journals publish supplementary data sets

– Some journals/fields require deposition of certain data in a public database prior to reviewing the manuscript

– ALWAYS read the journal’s Instructions to Authors before starting to write


14

Instructions to authors

Brazilian Journal of Medical and Biological ResearchScope and policy Page charges Manuscript criteria and information Manuscript Submission Paper format Cell Biology Biological activity of natural products Authorship information Editorial review and processing Manuscript preparation Writing a good abstract Tables Figures References Manuscript check list Related Links


15

Naming authors

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


16

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• And, indexing and abstracting services depend

on the accuracy of the title, extracting from it keywords used for cross-referencing and computer searching.

• So, an improperly titled paper may never reach the audience for which it was intended, so be specific.


17

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


18

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)

• 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)


19

Keywords

• The 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.


20

Abstract• 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.

• The abstract should summarize the results and principal conclusions.

• Do not include details of the methods used unless

the study is methodological, i.e. primarily concerned with methods.


21

Abstract• Do not repeat information contained in the title. The

abstract, together with the title, must be self-contained as it is 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.


22

The abstract has a well-defined structure

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.


23

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.


24

A different Abstract style– 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


25

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 containing10%, 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.


26

Introduction

• The most important function of the introduction is to establish the significance of your current work: Why was there a need to conduct the study?

• The introduction begins by introducing the reader to the pertinent literature, leading from the general to the particular

• The most important function of the introduction is to establish the significance of your current work: Why was there a need to conduct the study?

• Having introduced the pertinent literature and

demonstrated the need for the current study, you should state clearly the scope and objectives.


27

Introduction

• Introduce references so they do not interfere with the flow of your argument: first write the text without references so that it reads smoothly, then add in the references at the end of sentences or phrases so they do not interrupt your flow.

• Avoid a list of points or bullets; use prose • The introduction can finish with the statement of

objectives or, with a brief statement of the principal findings. Either way, the reader must have an idea of where the paper is heading to follow the development of the evidence.


28


29


30

Introduction – common problems

Far 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


31

An example• 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.


32

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 variation in quality among supplies.

• Modifications to equipment or equipment constructed specifically for the study should be carefully described in detail. The method used to prepare unusual reagents, fixatives, and stains should be stated exactly, though reference to standard recipes in other works will suffice.


33

Materials and Methods

• The usual order of presentation of methods is chronological. However, related methods may need to be described together and strict chronological order cannot always be followed.

• If your methods are new (i.e. unpublished), you must provide all the detail required to repeat them. However, if a method has been previously published, only the name of the method and a literature reference need be given.

• Be precise in describing measurements and include errors of measurement. Ordinary statistical methods should be used without comment; advanced or unusual methods may require a literature citation.

• Show your materials and methods section to a colleague. Ask if they would have difficulty in repeating your study


35

Results• In the results section you present your findings: display

items (figures and tables) are central in this section.

• Present the data, digested and condensed, with important trends extracted and described.

• 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.

• Because the results comprise the new knowledge that you are contributing to the world, it is important that your findings be clearly and simply stated.


36

Results

• Do not say "It is clearly evident from Fig. 1 that bird species richness increased with habitat complexity". Say instead "Bird species richness increased with habitat complexity (Fig. 1)".

• However, don't be too concise. Readers cannot be expected to extract important trends from the data unaided. Few will bother.

• Combine the use of text, tables and figures to condense data and highlight trends. In doing so be sure to refer to the guidelines for preparing tables and figures.


37

Tables and Figures

– All tables and figures should be put into a contextual framework in the corresponding text, e.g. a table of strains used should be mentioned in the Materials and Methods

– A good rule of thumb is that it should be possible to figure out the meaning of a Table or Figure without referring to the text. Tables and figures should typically summarize results, not present large amounts of raw data.

– When possible, the results should provide some way of evaluating the reproducibility or statistical significance of any numbers presented


38

Constructing tables

• DO include a caption and column headings that contain enough information for the reader to understand the table without reference to the text. The caption should be at the head of the table.

• DO organize the table so that like elements read down, not across.

• DO present the data in a table or in the text, but never present the same data in both forms.

• DO choose units of measurement so as to avoid the use of an excessive number of digits.


39

Constructing tables

• DON'T include tables that are not referred to in the text. • DON'T be tempted to 'dress up' your report by

presenting data in the form of tables or figures that could easily be replaced by a sentence or two of text. Whenever a table or columns within a table can be readily put into words, do it.

• DON'T include columns of data that contain the same value throughout. If the value is important to the table include it in the caption or as a footnote to the table.

• DON'T use vertical lines to separate columns unless absolutely necessary.


40

Constructing Figures

• DO include a legend describing the figure. It should be succinct yet provide sufficient information for the reader to interpret the figure without reference to the text. The legend should be below the figure.

• DO provide each axis with a brief but informative title (including units of measurement).


41

Constructing Figures

• DON'T include figures that are not referred to in the text, usually in the text of the results section.

• DON'T be tempted to 'dress up' your report by presenting data in the form of figures that could easily be replaced by a sentence or two of text.

• DON'T fill the entire A4 page with the graph leaving little room for axis numeration, axis titles and the caption. The entire figure should lie within reasonable margins (say 3 cm margin on the left side, 2 cm margins on the top, bottom and right side of the page).

• DON'T extend the axes very far beyond the range of the data. For example, if the data range between 0 and 78, the axis should extend no further than a value of 80.

• DON'T use colour, unless absolutely necessary. It is very expensive, and the costs are usually passed on to the author. Colour in figures may look good in an assignment or thesis, but it means redrawing in preparation for publication.


42

Table design

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)

Table 1 - Average size (μm) of C. elegans sporangioles in Hesseltine & Anderson culture media with 0, 2, 4, 6 and 8% NaCl at 20ºC.


43

Figure design


44

Figure design


45

Discussion• In the discussion you should discuss what

principles have been established or reinforced; what generalizations can be drawn; how your findings compare to the findings of others or to expectations based on previous work; and whether there any theoretical/practical implications of your work.

• When you address these questions, it is crucial that your discussion rests firmly on the evidence presented in the results section.

• Refer briefly to your results to support your discussion statements.

• Do not extend your conclusions beyond those that are directly supported by your results.


46

Discussion

• A brief paragraph of speculation about what your results may mean in a general sense is usually acceptable, but should not form the bulk of the discussion.

• Be sure to address the objectives of the study in the discussion and to discuss the significance of the results.

• Don't leave the reader thinking "So what?". • End the discussion with a short summary or

conclusion regarding the significance of the work.


47

Discussion

• What are the main conclusions of your study ?

• How do these results advance our understanding of the field ?

• What new questions do they raise ?


48

ReferencesThe HH morphogen controls many key development processes, with different thresholds specifying distinct outcomes1, 2, 3, 4. In Drosophila wing discs, HH proteins secreted by posterior (P) compartment cells move into the anterior (A) compartment to form a local concentration gradient5, 6. Low levels of HH suffice to induce the expression of decapentaplegic (dpp), whereas high levels are required to induce patched (ptc) and engrailed (en) (Supplementary Fig. 1)7, 8, 9.

Nature 450, 252-258 (8 November 2007)

The HH morphogen controls many key development processes, with different thresholds specifying distinct outcomes1, 2, 3, 4.

In Drosophila wing discs, HH proteins secreted by posterior (P) compartment cells move into the anterior (A) compartment to form a local concentration gradient5, 6.

Low levels of HH suffice to induce the expression of decapentaplegic (dpp), whereas high levels are required to induce patched (ptc) and engrailed (en) (Supplementary Fig. 1)7, 8, 9.

http://www.nature.com/nature/journal/v450/n7167/suppinfo/nature06225.html

http://www.nature.com/nature/journal/v450/n7167/suppinfo/nature06225.html


49

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


50

References - format

• A list of references ordered alphabetically by author's surname, or by number, depending on the publication, must be provided at the end of your paper.

• The reference list should contain all references cited in the text but no more.

• Include with each reference details of the author, year of publication, title of article, name of journal or book and place of publication of books, volume and page numbers.

• Different journals may have a different referencing styles, so read the Instructions to Authors first


51

There are several possible causes of mis-citation.

• First, some younger researchers simply do not know the rules. • Second, they may know the rules but are unable to locate the literature,

because it does not exist online and/or because the idea of visiting the library and taking a journal off the shelf is anathema.

• Third, the original source may somehow appear "old- fashioned" and therefore inappropriate. It is probably true that researchers have always been biased towards citing research done during their own career, but ignoring research done in previous generations misrepresents history.

• Fourth, young researchers often say that there is too much literature and they cannot be expected to know it all. This is no excuse. It is hard keeping up with the literature, but knowing the literature is what being a researcher is all about. For well-known discoveries such as natural selection or the structure of DNA, the relevant references are also well known. But for many other areas, the most appropriate references are less obvious and may require effort to locate. Indolence is no excuse for mis- citation.

• Fifth, and perhaps most insidiously of all, some researchers deliberately fail to cite competitors' work to enhance the (apparent) novelty of their own work. All five of these causes seem to be part of a general erosion of scholarship in schools and universities.


52

Where are the rules of citation set out?

• I looked at three books I had to hand: an undergraduate study guide to science, a book on what science is and another on communicating science, all published in the past six years. Not one of them stated the rules for citation.

• So what are they? The rule is that you cite the first reference to report a particular fact or concept, giving credit where credit is due. Sometimes, of course, it is not absolutely clear when a particular discovery was made, and the ludicrous extreme in biology (and much else) would be to trace everything back to Aristotle. The best strategy is to cite the original source, probably followed by a reference to a more recent review of the topic. What is neither appropriate nor acceptable is to cite a recent paper (not a review) that simply mentions the topic.

• How are today's researchers supposed to know the rules? The obvious answer to this is through their undergraduate training, and if not, then through their postgraduate years. The fact that mis-citation is so widespread suggests that as university teachers we are failing to do this properly. This may be true, but what is perhaps worse is the widespread rewarding of mediocrity in education that allows undergraduates to get away without absorbing many of the attributes of being a good researcher.


53

Does it matter that researchers mis-cite the literature?

• Yes, it does. • First, appropriate citation is the foundation of science. As the Nobel

laureate Peter Medawar said, being first is what matters; there are no prizes for being the second person to discover something. Priority rules in science are written in stone; they form the bedrock of the entire enterprise.

• Verification by second and later "discoverers" is important, but being first is what matters. Researchers who make important discoveries should get due credit for their work, and it is those citations that determine a scientist's standing in the field.

• Mis-citation undermines the very process of scientific endeavour. Not citing the literature appropriately is poor scholarship and perverts history.


54

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.

• Reference incorrect


55

Deposition of data in public repositories

– Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

– Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

– Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

http://www.ddbj.nig.ac.jp/

http://www.ebi.ac.uk/

http://www.ebi.ac.uk/

http://www.ncbi.nlm.nih.gov/

http://www.expasy.org/sprot/

http://pir.georgetown.edu/

http://www.wwpdb.org/

http://ndbserver.rutgers.edu/

http://www.ccdc.cam.ac.uk/products/csd/deposit/


56

Plagiary and ‘language re-use’

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

If you use somebody else’s words, make this clear by using quotation marks and a reference


57

Summary

• Each section of the manuscript has a specific function

• Each paragraph has a specific function and should be presented in a logical order

• Ditto each sentence within the paragraph.• Within each sentence, try to move from the

general to the particular• Punctuation alters meaning, so use it sparingly


58

Common manuscript problems

• Failure to state the purpose of the study• Failure to keep function of sections clear

and distinct• Including non-essential data• Treating the Introduction and/or

Discussion as an opportunity to review the entire field


59

Practical activity 7a - The Structure of a Scientific Article

• The Case of the Ivory-billed Woodpecker

• At approximately 1:30 in the afternoon on February 11, 2004, Gene Sparling spotted a large black and white woodpecker while kayaking on a rural bayou in Monroe County, Arkansas. The notes he posted to his website about the sighting caught the attention of Tim Gallagher and Bobby Harrison, two university researchers, and triggered a year-long research effort that resulted in the publication of a peer-reviewed paper in the journal Science. The link below gives free access to this research article. To learn more about scientific writing, including how research papers are organized, how they are reviewed, and how they contribute to our understanding of the scientific world, read the article and then try the exercise below.

• See original paper by Fitzpatrick et al. (2005) "Ivory-billed Woodpecker (Campephilus principalis) Persists in Continental North America" Science 308:1460-1462. See also this site for further discussion about the issues raised by this paper.

• Questions about the article's format:

• Indicate where in the article the Introduction section ends and the Materials and Methods section begins and explain why you choose this point in the article.

• Indicate where in the article the Materials and Methods section ends and the Results section begins and explain why you choose this point in the article.

• Indicate where in the article the Results section ends and the Discussion section begins and explain why you choose this point in the article.

• Questions about the article's content:

• When testing a research hypothesis, which the researcher has good reason to believe is true, it is customary to use a first test a null hypothesis. This is typically a hypothesis that there is no difference or no association between variables being tested. What is the null hypothesis in this article with respect to the data discussed?

• What evidence do the researchers present disprove their null hypothesis ? • Why is the data presented graphically and how do these visual representations help the interpretation of the article? • Based on the evidence presented, is the hypothesis that the ivory-billed woodpecker still exists now a proven fact ? • What happened subsequently ?


60

Practical 7 – cont’d• Practical activity 7b - Reconstructing abstracts• Download the Word document which contains four article abstracts

deconstructed as a random series of sentences. Now put the sentences back in their original order.

• Practical activity 7c - Identifying key reference points• Download the Word document which contains

introductions to scientific articles which have been stripped of references. Indicate which sentences contain statements that should be supported by references.

• Practical activity 7d - Identifying problems with a document's logical structure.

• This document is an edited version of an introduction to a research article about copper toxicity in plants. Identify places where there are rapid jumps or breaks in the logical structure of the document and discuss

Documents

10 August 2012Copyright: Ganesha Associates 2012 1 Basic reading, writing and informatics skills for biomedical research Segment 7. The structure of a