Writing Course Belgrade Handout Jan11 2

8/3/2019 Writing Course Belgrade Handout Jan11 2

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I was on the editorial advisory board of the Journal of Experimental

Botany for over 10 years.

As well as publishing over 50 papers in international refereed journals, Ihave a lot of experience reviewing other peoples work.

2. Publishing yourresults

1. Good quality research

5. Presenting yourresults

3. Writing project

proposals4. How to manage

everything

6. Good qualitysupervision

I was/still am a regular reviewer of manuscripts submitted toJournal of Experimental Botany.My last review request was for Journal of Experimental Biology inNovember, and already the review reminder emails are coming in!

Over the years I have also reviewed manuscripts regularly forPlant, Cell and EnvironmentPlant Physiology

Plant Growth RegulationTheoretical and Applied GeneticsJournal of Agricultural Sciences, and so on .


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Scientific publications

This is your starting point:

So, first you need to know whether what you actually did isworth a paper in an international journal.

What youactually did

A publication in

a good journal

Therefore, your starting point was the research itself.

The tale of the lost traveller and the Irish cowherd.

Irish cowherds are very wise people!

OK, so whats the story all about?

Heres the lost traveller, and .

A typical wise Irish cowherd:

From your experiences, what are (or what would be) your biggestchallenges in publishing your research in an international journal?


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As director of a bureau helping Serbian scientists write successfulresearch proposals for FP7*, I have to know whether their research issuitable for writing into a proposal.

I need to know whether it is good enough quality to succeed in FP7.So, I need to have the wisdom of an Irish cowherd: like the one shownin the previous slide.

So, here was the truth.**

Ah, to be sure, my young man, if I were you, I wouldnt bestarting from here!

You cant write good quality scientific papers if youre not alreadydoing - good quality research, with good quality experimental design, to achieve good quality data to analyse and interpret!

[The Irish are very wise, like the railway level crossing keeper who leftone gate open because he was half-expecting a train!]

We have an expression you cant make a silk purse from a sowsear!

Another way to say you cant make a good quality paper if youdidnt do good quality experiments!

i.e. you cant make something wonderful from poor qualitystarting materials.

* FP7 is EU Framework Programme 7 - over52 billion for research, training andsupport actions from 2007 to 2013.

Good research:

Good research was described in the previous module:Identifying all thefactors to get to the truth.

If your research wasnt good quality then your manuscript isunlikely to be accepted.

But it needs more than this -It needsinternationalinterest and appeal

- more on this in a moment

International journals give you more impact!


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Choose a journal that is suitable for the research you want topublish.

This is not as straightforward as it might seem!

Decide who is most likely to want to read about your work.

Whatever the subject of your research decide what type ofpaper you want it to be:- progress in studying a particular process.- important for a particular species/substance.

- about a particular technique.- reviewing other peoples results.

Where to publish:

The higher you aim with impact factors, the more difficult it isin general to publish.

Two journals with very high impact factors are Nature (IF ~34)

and Science (IF ~30).

Most M21 journals are in the range for- medical sciences journals up to 50!- biological/life sciences from 2 to 10,

- physical sciences from 1 to 12

- social sciences 1 to 3- agricultural sciences from 0.5 to 4- material/computer sciences from 0.5 to 4

Impact factors**:

** Journal impact factor is calculated over a three-year period, andcan be considered to be the mean number of times published papersare cited up to two years after publication.

The impact factor of a journal determines its Ministry M factor(M21, M22, M23, and so on)

For example: vrednost M21 = 8, M22 = 5, M23 = 3.

Your total M factor vrednost is important for your promotion, takingpart in Ministry projects, etc. Mine is around 475.


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Typical journal impact factors (1):

2007 data for M21 journals

Journal of Immunology - 6.07Journal of General Physiology - 4.83Journal of Physiology-London - 4.58

Journal of Neurophysiology - 3.68Journal of Cellular Physiology - 3.64Journal of Applied Physiology - 3.63

Experimental Physiology - 3.01Journal of Vascular Research - 2.46

Regulatory Peptides - 2.42Physiological and Biochemical Zoology - 2.23

Cell and animal sciences

http://kobson.nb.rs


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Chemistry/chemical engineering

Journal of the American Chemical Society - 7.89Progress in Surface Science - 6.52Chemical Communications - 5.14Journal of Medicinal Chemistry - 4.89Journal of Catalysis - 4.74

Carbon - 4.26Organometallics - 3.83Journal of Membrane Science - 2.43Chemical Engineering Science - 1.77Journal of Process Control - 1.32

Environmental Microbiology - 4.93Applied and Environmental Microbiology - 4.00European Journal of Soil Science - 2.73

Agriculture and soil sciences

Journal of Hydrology - 2.16Plant and Soil - 1.82Irrigation Science - 1.74European Journal of Agronomy - 1.50

Food Policy - 1.06Land Economics - 1.04

Journal of Agricultural Economics - 1.00


2007 data for M21 journalsSocial sciences and economics

Future of Children - 4.76Evolutionary Anthropology - 3.14British Journal of Sociology - 2.45

Human Relations - 1.10Critical Social Policy - 0.87Human Organisation - 0.79


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Do not worry about the differences of impact factor across subjects!This is just reflects how popular a particular subject is:- medical and molecular biological sciences very popular- economics, agriculture and engineering not very popular!

[For example, I could find hardly any M21/M22 agriculturaleconomics journals with an impact factor over 1!]

It is where the journal ranks in Kobson that matters!

So, within your subject area, aim for an M21 journal (an impact factor inthe top 30% of journals).

Nature and Science have very high impact factors because they bothcover every science subject

Scientific publications:

There are basically four types of paper:

1. A research paper which will set up a hypothesis and then test it.

2. A purely descriptive paper that is describing something new.

3. A techniques paper on developing a new/improved technique forsomething.

4. A review paper describing and discussing what other peoplehave done.

OK, so lets focus on how you should write a good-qualitymanuscript of your own with some general comments ...

First, what type of manuscript is it going to be?

http://www.kobson.nb.rs.proxy.kobson.nb.rs:2048/servisi/pretrazivanje_casopisa.84.html


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2) a purely descriptive paper needs:

a clearly-defined reason explaining whythe work needed to be done, a reason why it is of internationalimportance

to know about this, interpretation of the findings to put them

into the context of similar work doneelsewhere.

3) a techniques paper needs:

a clearly-defined reason saying why thenew technique was necessary,

a sufficiently detailed description of thetechnique (including validation) forothers to use it as a protocol,

detailed comparison with existingtechniques to show how the new

technique is better/differs.


1) a research paper needs:

one or more hypotheses to be tested, clearly-defined aims, saying why the

research needs to be done, replicated experiments (with exceptions) results that match the aims interpretation to test the hypotheses.

To be suitable for publishing in an international journal -

short communications( c , , .)


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Journal of General PhysiologyThe Journal of General Physiology publishes original articles that

elucidate basic biological, chemical, or physical mechanisms of broadphysiological significance. Four types of articles will be considered:

Scientific publications (4):

4) a review paper needs:

a clearly-defined subject area thathasnt been reviewed recently,

a comparison of findings of others,usually including your own work,

including the latest research findings,plus where possible papers in press,

an opportunity for you to publish dataotherwise not suitable for publication!

To be suitable for publishing in an international journal -

Scientific review publications:

Annual Review of Immunology - 37.9Chemical Reviews - 36.0Nature Reviews: Cancer - 29.5Annual Review of Microbiology - 12.8Annual Review of Fluid Mechanics - 9.4ACM Computing Surveys - 7.7Annual Review of Sociology - 3.7Review of Economic Studies - 2.9

Note that review papers in review journals will usually give you ahigh impact factor!

i.e. M21 journals (osam poena)!!

Instructions for authors:

Always start by reading the journals Instructions for Authors -either inside the journal cover or on the journal web-site.


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No substantial part of an article may have been, or may be, publishedelsewhere.

Except in special circumstances, manuscripts that fall within thefollowing categories are unlikely to be accepted: Purely methodological or theoretical developments (except as noted

in Scope of Publication). Descriptive reports,in which no specific hypothesis is tested. Manuscripts that primarily confirm results already established

for other species, . Manuscripts which merely amplify a previous brief publication andcontain no substantial new information.



Annals of Botany publishes experimental, theoretical and appliedpapers on all aspects of plant science.

Submission of manuscripts that report small incremental advancesor are ofgeographically local interest only is discouragedunlessthe implications of the findings are wide-reaching. In general, a paper

is unlikely to be accepted unless referees and editors involved inits evaluation are enthusiastic about the science.

The submitted manuscript or its essential content must not have beenpublished previously or be under consideration for publicationelsewhere. To merit publication , contributions should be

substantial, written in clear English and combine originality of contentwith potential general interest.

Journal of General Physiology continued -

Regular articleswhich should be as concise as possible, but with nolower or upper page limit;Tutorial Research Articles,..., presented in a more pedagogical(lengthy) manner;Communications, short articles that are no longer than six printedpages (and cannot include online supplemental material);Letters to the Editorthat comment upon, criticize, or interpret findingspublished in the Journal.


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Human Relations is an international peer reviewed journal, whichpublishes the highest quality original research to advance ourunderstanding of social relationships around work through theoretical

development/empirical investigation.

Authors should use clear English comprehensible to readers outside oftheir area of specialism, and should ensure that their methodology is nottoo long, avoiding overly long explanations of why particular norms andstandards have been chosen.

Papers must advance knowledge, and make a strong theoretical andempirical contribution to the literature on work relationships andorganisational work processes.

Papers must be original research and must not have already beenpublished or be under consideration for publication elsewhere.


Human Relations (cont.)does not publish studies based on laboratoryexperiments unless there is confirmatory field data. Studies referring tosimulation exercises involving students or others without experientialknowledge of the simulated context are discouraged.

Papers containing a poor standard of English language are less likely tobe considered for review.

Field-study results are more likely to be accepted if they use more than asingle technique of data collection and analysis. You should strengthenthe validity of, for example, questionnaire scales or constructs byconsidering multiple influences in the context of the field study.


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Youve had (I hope!) a read through the manuscript I gave you ondrought responses in maize.

What suggestions do you have on ways in which this could beimproved?

Ill give you my comments later ...

Time for an exercise and then a break.

So, having sorted out the drought manuscript, now lets startwriting your manuscript ...

But first, once youve decided which journal you will submit thepaper to, make sure you read carefully allthe journals

Instructions to Authors for writing the text!

These will tell you how to format the manuscript correctly.

Journal of Biological Chemistry

Instructions for Authors:

Manuscript preparation

All of the text should be single spaced with one-inch [2.54 cm] marginson the left and right sides.

Once the text of the manuscript is completed in Word, convert theSummary through Discussion sections from a single column format todouble column format.Select these sections of the text, click on Format heading, thenColumns from the drop-down menu. Select two columns and equalcolumn width and then change spacing to 0.25 inches [0.63 cm]. Title and running title sections as well as references, footnotes, figurelegends and tables should remain in single column format. Use Times New Roman font and select size and bolding to mimic theappearance shown above for the title section; use 11 point for theremaining text.


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Annals of Botany


Manuscript preparation (Always consult a recent issue of Annals of Botanyfor layout andstyle) Text should be typed using size 12 Times New Roman or Courier,double-spaced throughout and with an approx. 25 mm margin. All pages should be numbered sequentially. Each line of the text should also be numbered, with the top line ofeach page being line 1 [FormatDocumentLayout].

The article file should be in PC-compatible Microsoft Word - file typeDOC

[please make sure the "Language" is "English (U.K)" via ToolsLanguage Set Language].

Human Relations


Manuscript preparationMANUSCRIPTS SHOULD BE ANONYMOUS. Please do not putyour name anywhere on the manuscript. Please do not includeacknowledgements, which might indicate your identity.Acknowledgements can be added to papers after acceptance.

Manuscripts may be of any length consistent with their content.However, most papers can be presented effectively WITHOUTEXCEEDING 8000 words, including tables and references.

Articles should be preceded by an ABSTRACT of between 100-150words, summarising the aims and main empirical contribution of thepaper.

Please indicate the position of figures and tables in the text as

follows: INSERT TABLE 1 ABOUT HERE


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This is your starting point:

Once upona time

and they all

lived happilyever after

and this is your target end point.


Journal of Biological Chemistry

Advice on units:

Abbreviations of units of measurement and of physical and chemicalquantities(These abbreviations may be used without definition. They are not followedby full stops. The same form is used in the plural.)

Not bothering to prepare your manuscript in the correct formatcreates a bad impression at the start, even before anyone has

read what you have written!


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The first page:

For example, instead of A new assay for abscisic acid, which says

nothing about the method, I used the titleA rapid and sensitive assay for abscisic acid using ethyl abscisate as an

internal standard

Think carefully about the author list and their order of presentation - theone doing the research usually comes first. Authors should have contributed in some way to the science or themanuscript!

Should you include your technicians as authors?

Choose a title that gives clear information about the content of theresearch.

So, lets assume that you have a good story to tell - thoughtfullydesigned experiments, carefully carried out.

The secrets to making a good quality paper are to be logical,unambiguousand consistentin the way that you present and

discuss information:- points should go clearlyfrom one to another.

If not, reviewers wont be able to follow what is going on and yourisk comments that the work is not focused or has unclear

objectives.

Ill describe here a typical research paper.

Ill use the format usual for life sciences Introduction

Materials and methods Results

Discussion

to say a few words about putting together what is needed for a goodquality paper - whatever the subject of the research.


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Before you start the main text:

Have a go at a draft of the Abstract, just to help you organise yourthoughts for the paper itself - come back to it later.

Provide a list of Key words - think carefully about these: who do youwant to read your paper? What aspects of your paper should beidentified by a search engine?

Provide a list of abbreviation definitions (to be added to as you goalong).

Introduction

subject area background information research area background information your previous work leading you to this research clear statement of objectives and hypotheses to be tested sometimes objectives change during the paper!

By the end of this the reader should have a clear impression of why theresearch needs to be done and what sort of conclusions will be reachedat the end.

Typical length no more than 2-3 double-spaced pages, depending on theresearch complexity.


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Results

Present results in a logical order Design tables and graphs to have the most visual impact (theymust make points clearly and unambiguously)

Say something in the text about all the points made in tables orgraphs

Leave interpretations to the Discussion

Now a few words on how to show data:

Materials and methods

Sufficient detail to allow others to repeat your workInclude onlyparameters/measurements and treatments that youwill present later on

State clearly the research methods/experimental design and howmany replicates are being analysed*(needs very careful thought to be unambiguous)

Give details of analytical methods and assays (briefly if previouslypublished)

Give details of statistical methods that have been used.

* both biological and analytical replicates.

Heres the sugar experiment example from the previous module.

So, in the case of the sugar experiment, to test the (primary)hypothesis that sugar types dissolve at different rates:

When showing results graphically, you should always put the mostimportant comparisons nearest to each other.

Not this ...

H C H C H C H C H C

Timetodissolve

1 2 3 4 5SugarTemp.

... but this

Hot Cold51 2 3 4 1 23 4 5

Timetodissolve

SugarTemp.

Key: 1 = large crystals, 2 = cubes, 3 = raw sugar, 4 = ordinary, 5 = icing,H = hot water, C = cold water


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Here are examples of problems with graphs from an actual manuscript:

Relative

watercontent (%)

Water Loss(gh-1g-1DW)

Proline(moles/g FW)

Hours of stress

Variety CVariety B Variety DVariety A

0

20

40

60

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100

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1,2

1,6

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1,6

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0 2 4 6 8

a

b

c

RESISTANT

The authors wanted to compare and contrasttwo groups of varietiesdiffering in drought resistance (otpornost prema sui) and theypresented two graphs - one for 4 resistant varieties, and the next for 4susceptible varieties.

Present your data in graphs in a logical order.For example, many of my PhD students showed data like this:

Why are 50% hot/50% cold samples on the right hand side?This order may be in real time, but is not logical to a reader.


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Variety E Variety F Variety G Variety H

Relativewatercontent (%)

Water Loss(gh-1g-1DW)

Proline(moles/g FW )

Hours of stress

0

20

40

60

80

100

0

20

40

60

80

100

0

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100

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0,4

0,8

1,2

1,6

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0,4

0,8

1,2

1,6

0

0,4

0,8

1,2

1,6

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0,8

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0 2 4 6 8

a

b

c

SUSCEPTIBLE

How easy is it for you to compare differences in drought responsesbetween the resistant and susceptible varieties?

Therefore, remember to put the most important comparisonsyouwant the reader to see or appreciate close to each other in figures.

So, in this example it would be much better to compare resistant andsusceptible varieties in the same graph, using a separate set of graphsfor each trait/parameter.

Dont make a table too dense with numbers.Dont use more decimal points than are justified by the precisionneeded (3 significant figures?).

Remember to include all the units (cm, h, mmol).Dont repeat data shown in figures.

Points to note on tables:


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Table 1: Phenotypic analysis of shoot number and plant height in the population.

s

hoot

No units for height Far too many decimal places! Judging by the size of s.ds., only 1 is justified.

How easy is it to assimilate and understand the data in this table?!!! KEEP IT SIMPLE!


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These are a bit like Appendices for a PhD thesis- such as individual replicate or analytical data.

You can add extra graphics using colour, as these shouldnot add much to the publication costs.

You can add animations and movies here.

Most, if not all, good quality journals now allow Electronic

Supplementary Material to be added to a paper, accessiblethrough the journals web site.

Electronic Supplementary Material

JBC On-line provides the opportunity for authors to include dataimpossible or impractical to include in the printed JOURNAL.

Heres an example of instructions on ESM:

These are for Journal of Biological Chemistry.

Only data that substantially contribute to the manuscript will beaccepted. We encourage authors to include data such as videos, 3-Dstructures/images, sequence alignments, and data sets that are very largesuch as those obtained with microarray hybridization experiments.

These data will be reviewed as a part of the normal manuscript reviewprocess and will be judged by the same criteria.

Data files can be prepared in Plain Text, MS Word, HTML Page, MSExcel, TIFF, JPEG or GIF. When practical supplemental data files shouldbe converted and submitted as PDF files.

Movies and large excel files should be submitted in their native formats.

Fraud involves deliberate deception, including the invention of data,and the omission from analysis and publication of inconvenient data.

Presenting Fraudulent Results

Scientific ethics must always be respected, and great care must beexercised when deciding that data may be ignored or changed forsome reason.

Think of the example in module 1 (this morning) on how data mayjustifiably be rejected from an analysis when searching for the truth:


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Remember this example justifying the omission of data:Could there still be mistakes in our dataset? - module 1 handout.

Yield in wheat is derived by multiplying the following components:

spikelets/ear x ears/plant x grains/spikelet x weight/grain

(klasica/klasu x klasa/biljci x zrna/klasicu x teina/zrnu)

Components are determined at different stages of development

- essentially in the order shown above.

Ozone treatment started on 20th May.Spikelet production was already completed by 20th May.Therefore spikelets/ear should be the samein both treatments.

But for several genotypes there were somesmall spikelets/ear, particularly for controlplants, as shown here:

Genotype Spikelets Spike lets

Nu mb er Co ntr ol O zo ne

21 17 18

21 17 17

21 14 17

21 11 17

21 16 17

21 17 17

Discussion

Do not repeat the results in the Discussion!! Discuss results in the order that they were presented Interpret how your results fit in with your stated objectives/hypotheses

Interpret how your results fit in with other published work What happens next?Give a take-home message at the end.

It has been suggested that under water stress soluble sugars can function as

osmotic agents and as osmoprotectants47,48. The results obtained in this

experiment showed that after D3 treatment sugar concentration was higher in

comparison to Control, D1 and D2 treatments. This indicates that soluble

sugars are significant contributors to metabolism under water stress.

Make sure your Discussion is genuine discussion and not justdescriptive - restating parts of your Introduction and Results:

Discussion (2)


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Give a little background (one sentence) describing the subject areaof the research Say what the research objectives are.

Describe briefly the materials (information sources/species/substances) used, how they were maintained/grown, treatments givenand what was measured.

If you cant squeeze a summary of the essential results andinterpretations into 250 words then you are trying to put too much into asingle publication!

Identify which of your results are most important. Identify the most important interpretation of your results. Maybe, say what this means for the future.

Try to save words wherever possible, for example as follows:Short sentences save words:

Replace and with a full stop whenever possible.

Never waste words by repeating information.

Rearrange or change words when possible. Instead of:, and exploitation of the variety sizes in order to improve ...use this shorter version: Exploiting variety sizes to improve (5 words less)

Dont use redundant words:To do this, .. and not In order to do this,

On the next page are two contrasting abstracts of the same article ..

Complete this once the paper is written

Abstract

Remember that most readers of your paper willnever get beyond the abstract. So, ensure the abstract says in 250 words all the reasons for doing theexperiments and the main conclusions.

It should have an immediate impact on the reader, so needs to be writtenin as concise (short) a sentence construction as possible and must givereaders a take-home message.

Writing a good Abstract is an art and isnt easy for most scientists, so

think carefully about what to put in it.


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ABSTRACTMicroorganisms participating in the self-heating phase of compostingmaterial, which consisted of marker gene tagged corn (Zea mays), horsedung and wood chips, were characterized by DNA finger-printing(ARDRA) of cells cultured at 50C and by analyzing DNA that wasdirectly extracted from compost samples. Cultivation-dependentmethods detected five major groups at the end of the self-heating phase(after 18 d). Three groups showed high homology to bacteria from thegenus Bacillus at the 16S rRNA gene level. Straightforward PCRamplification of bacterial target genes from compost extracted DNA wasinhibited because of the high background of plant DNA and presence of

humic acid-like compounds. By use of humic acid resistant, heat-stableDNA polymerases in combination with single strand, DNA binding, T4gene 32 protein, PCR inhibition could be completely overcome. After 6 dof composting, the marker gene of the corn plants was degraded belowthe threshold of detection (< 102.6 copies per g of compost). Thediversity of bacterial and fungal communities in the compost wasanalyzed by single-strand conformation polymorphism (SSCP) ofapprox. 400 bp PCR products, which were amplified with universalprimers for 16S rRNA (bacteria) and 18S rRNA genes (fungi), withcompost DNA as a template. The generated patterns showed a

succession of different members of the microbial community during theself-heating phase.

ABSTRACTNucleic acid based genetic fingerprinting techniques provide new andvaluable tools to characterize diversity of microbial communities duringthe self-heating phase of compost material without the need of microbialcultivation. The present study introduces our compost DNA extractionprotocol and new protocol based on separation of single stranded DNA

molecules obtained from 16S or 18S rRNA gene targeted sequences.DNA extracted from composting material was used as a template forPCR amplification and detection of specific microorganisms. We usedtwo corn (Zea mays) plant types in two piles: wild typeand geneticallyengineered with chromosomal insertion of the phosphinothricin acetyltransferase (pat) gene, which confers resistance to the herbicide(BASTA). We showed indications of DNA degradation as decrease ingeneral DNA yield and patand 18S gene of corn. DNA sequencing of the16S rRNA genes showed that three groups of isolates had highestsimilarities (> 98 %) to bacteria of the genus Bacillus. One group,

detectable on BASTA amended medium, was related to Pseudomonasstutzeri(similarities, 96 to 97.3 %). We found that profiles of 16S rRNAamplified genes from compost DNA increased in their complexity duringthe composting process demonstrated that community memberschanged during composting (succession). Analysis of fungal 18S rRNAgenes confirmed general knowledge and recent experimental evidencethat during the hot composting stage fungal biomass is reduced. Theseresults have relevance for recommendations for a waste recyclingprocess for genetically engineered plants. However, the patterns needmore detailed analysis, to understand their ecological relevance.

Green is background,blue is methods, red is results, yellow isconclusions. Which do you prefer?


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Writing style (1)

So may 'It is significant to note the fact that', 'It should be borne inmind in this connection that', and other phrases that correspond to nomore than spoken 'errrs, ummms and ovajs'.

This is the time to tighten up the text and remove unnecessary words -

Serbian scientists like to use unnecessary words!

At the end, put aside your draft and come back to it later. Youll be

surprised how much you want to change!

Such phrases as 'It is worth pointing out in this context that' may bedeleted without affecting the meaning.

For 'It is plainly demonstrable from the data presented in Table 2' write'Table 2 shows'.

Quotations should be kept to a minimum. Where possible, keep

quotations to 100 words or less. Where quotations exceed 400 words,the permission of the publisher (or copyright holder) must be obtainedand acknowledged.

Guidelines on quotations from Human Relations:

Diagrams and tables reproduced from already published work requirepermission from the original publisher (or copyright holder).

It should be stated in the relevant legend that permission forreproduction has been granted, giving the reference and name of the

copyright holder who has given the permission.

Quotations from published work, including any author's own previouswork, must be acknowledged as such and fully cited.

Plagiarism is becoming an increasing problem.

The first was written by one of my Biology Faculty PhD students.The second was the original written by the papers authors!


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Some closing remarks 1:

Can you write up negative results for a publication(ie no significant differences betweentreatments or genotypes)?

- maybe, provided previous encouraging results justify the experiments

you have now done:- for example it worked in the laboratory, but not in the natural

environment!

Writing style (2)

should be advantageous for the avoidance of .becomes should be advantageous to avoid

A comparison of mean values of evaluated traits for becomes A comparison of trait means for .

Diversity in the evaluated traits amongst the . becomes:Diversity in traits amongst the .

The findings in this section imply that studied organisms .becomes These findings show that the organisms .

the main limitation of the studied organisms is .

becomes the main limitation of these organisms is .

tabulated all the abovementioned traits in order to present the .becomes tabulated all these traits to present the .

How to Write & Publish a Scientific Paper

5th EditionRobert A. Day- ORYX PRESS1998ISBN 1-57356-164-9 Hardback 1-57356-165-7 Paper

Appendix 4: Words and expressions to avoidReplace witha considerable amount of mucha considerable number of manya decreased amount of lessa decreased number of fewera majority of mosta number of manya small number of a fewabsolutely essential essentialaccounted for by the fact because

adjacent to nearalong the lines of like


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Your written English needs to be sufficiently good for it to beunambiguous/obvious what you are trying to say. If in doubt, whenpossible get a native English speaker to check your manuscriptbefore you send it.

Referees will not bother to struggle reading very bad English!However, if the English is acceptable, they will often be willing tocorrect for you any subtleties in the use of words (eg prepositions,and when to use a and the).

Dont assume referees are always right! Just like us, they sometimes make mistakes, not reading textcarefully enough or jumping to the wrong conclusions.

So, you dont have to accept everything a referee says! If you can provide a good counter-argument to a referees commentin your reply to the journals editor, then do so.

The review process:

This example for Journal of Experimental Botany is typical.The Editor makes the initial evaluation of the manuscript. If the topic isimportant and relevant to the journal readership, he/she assigns themanuscript to an Associate Editor, who oversees the review process.

Manuscripts are reviewed by two independent experts in the particulararea. The reviewers will make a scientific assessment andrecommendation to Editors.

If reviewers reports are contradictory, the Editor will either send themanuscript for a third opinion and accept the majority view, or decideto reject the manuscript.

A frequent reason for rejecting a manuscript is that theresults/conclusions of your research are not thought to be

sufficiently novel or not substantial enough or of local interest only.

If the referees say your manuscript is too long and needs reducing,a good way to do this is to combine the Results and Discussionsections so you say everything only once!

- for example just repeating someone elses work with differentvarieties/species.

Some closing remarks (cont):


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The review process:

Referee Assessment

Please complete the following assessment and use these criteria in writing your report.

Yes No See comments

The reported results are novel

The experiments are well designed and executed

The manuscript is well written, clear, concise and in the third person

The subject area is important and relevant to experimental botany

Figures and tables are clear, non-repetitive and necessary

Titles and abstracts are representative and concise

References are adequate without being excessive

Colour plates are essential to understanding the science

Please score the paper on a scale of 1 to 5 with 5 the highest quality or most important:

Importance of the topic

Quality of the science

Overall Recommendation

Please tick the appropriate box

Acceptable with minor revision

Acceptable with revision

Unacceptable as major revision required

Unacceptable

Note: J. Exp. Bot. rejects over 60%of manuscripts submitted!

Quality of science has to be 4 or 5 for manuscripts to succeed.

So, if youve carried out carefully-designed research testinghypotheses, the advice given here should allow you to prepare a good

quality manuscript for an M21 international journal describing yourresearch.

Remember:your research should be looking for the truththe reader of your paper needs to see clearlythat you are presenting the truth!

Conclusion:

Finally, for complementary advice on writing a scientific papersee: http://vivovoco.astronet.ru/VV/E_LESSON/WRITING.HTM


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Examples of review comments - cont.:

Review of MS 010643 by M. and R.

A few minor errors and stylistic improvements have been noted on thetext.

A couple of specific points from the text that the authors should address inany new manuscript are listed here:

1 P7 It is not clear in the Materials and Methods (lines 16 et seq)how many replicate samples of each genotype were analysed for Cd

complexes. Was it just one per genotype or more? With appropriateexperimental design it would have been possible to carry out a paired t-test with each isoline pair to test whether any consistent trend existedbetween H and L lines - for example Table 2 shows that L linesconsistently had lower means for Cd peak I than H lines for each tissuetype, though any significance of differences is lost in the noise generatedby pooling data for all the lines within a phenotype.

2 P10 L12 Cd concentration in seedling leaves was NOT lower forTL-L, according to Table 1.

3 P10 L22 It is not clear what the 'expectation' is from Table 1!

Review of MS 010643 by M. and R.

At first sight this looks a carefully carried out and written up piece ofresearch to study aspects of the mechanism of Cd uptake andcomplexing in durum wheat. There is some very good science in this; it'sjust a shame that the hydroponics experiment didn't work!

The authors need to repeat this aspect of the work with much lower levelsof Cd in the hydroponics to be able to test the association between Cduptake and sequestering in relation to seed levels of Cd. This may revealdifferential expression of Cd-complexing polypeptides.

Nevertheless, much of the biochemistry presented here is probablypublishable in its own right, though not in relation to any genetic variationin seed Cd contents. The authors should be encouraged to consider this,while at the same time repeating the hydroponics experiment with morerealistic Cd treatments to test for genetic variation in Cd complexes.

If it is any consolation, it is nice to see a manuscript so well presentedwith so few unnecessary errors.

Examples of review comments 1:


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Review of Manuscript by F et al. for J Exp Bot This paper describes agronomic properties of several annual ryegrassaccessions under drought stress. Although the paper more-or-less comeswithin the remit of the journal's subject matter, it might be more suited toanother journal such as European J of Agronomy or Euphytica.In anycase, the present version of the manuscript is flawed, and could not beaccepted for publication.The major problem with the present version isthat the authors have not adequately addressed the apparent objectivesof their work. They talk about high seed production being necessary forgood drought adaptation, yet their data do not include seed number perunit area. They present data only for seed yield, which is not the samething, and none of the data for other traits studied and presented in themanuscript allow seed number per unit area to be assessed.

They present an unclear picture of the sort of traits that areassociated with drought resistance. They also confuse adaptation interms of an active response of the plant to a drought and traits that areconstitutively present, such as earliness. They claim a drought resistantmorphotype should have an erect habit, yet the seed yield was not

significantly correlated with plant habit! Or is drought resistancesomething else?


Report on MS 000937 by H. et al.

This manuscript describes a QTL analysis of physiological traits in

sunflower that could potentially be very interesting for publication in JEB.However, at present the manuscript has major deficiencies that placeserious doubt on the validity of the QTL analysis. These need to beaddressed before the manuscript could be considered for publication. Inconsequence, the manuscript has been reviewed only as far as the startof the Results section.The essential problem is caused by attempting to analyse traits that aretemporally and environmentally highly variable in a large population ofplants and believing that the measurements reflect genetic variation.

For example, to measure leaf water potential with a pressure chamber islikely to take at least 2 min per leaf - a conservative estimate as the SoilMoisture Equipment Corp. chambers are rather slow to seal and unseal.Therefore, with a single leaf chamber only about 30 samples could becollected per hour, which means 90 genotypes in 3 h and if all threereplicates were sampled (not stated in the text), that is 9 h. So, how longa period was regarded as representative of 'pre-dawn' water potential?What is the dynamics of rehydration of sunflower leaves during the night?


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An example of comments I made on a manuscript I reviewedrecently .

Writing Course Belgrade Handout Jan11 2

Documents

Transcript of Writing Course Belgrade Handout Jan11 2