andrew moore, editor-in-chief , wiley researcher academy ... · especially costly, and handicaps...

Andrew Moore, Editor-in-Chief

[email protected]

Ideas that push the boundaries…

, Wiley Researcher Academy

Wiley Researcher Academy


Keeping it simple…


It was previously demonstrated that fibroblasts subjected to hypoxia in the tumor microenvironment manifest behavior resembling subversion by, or collaboration with, the tumor cells [13, 14].

Fibroblasts under hypoxia in the tumor microenvironment seem to be subverted by, or collaborate with, the tumor cells [13, 14].

Oxygen‐starved non‐cancer cells are manipulated by their cancerous neighbours.


…being clear…


A nasty little word: “with”…


Such populations form cooperative structures with the aggressive individuals living at their periphery.

Such populations form cooperative structures, the aggressive individuals living at their periphery.


Finish the abstract with a reminder of thenovel insight in the context of its wider implications and applications.

This means that both the implications and the applications should be wider (than thecore topic of the paper).

But what if the paper is only about basic research, and doesn’t mention any applications yet?... We need, within the same sentence, to distinguish implications from applications…

Finish the abstract with a reminder of thenovel insight in the context of its wider implications, and applications.

Seen in instructions to authors…

Finish the abstract with a reminder of thenovel insight in the context of its wider implications and its applications.


These animals possess heterozygous sex chromosomes, with recombination at sites close to the pseudoautosomal boundary suppressed.

These animals possess heterozygous sex chromosomes in which recombination at sites close to the pseudoautosomal boundary is suppressed.


Commas are not optional pause marks for effect… They separate concepts and clauses, thereby defining semantics (particular

meaning).


The second brood is produced in a new burrow while the first is raised in the original burrow.

What was intended?

The second brood is produced in a new burrow, while the first is raised in the original burrow.

i.e. this is not describing temporal overlap, but a different situation. Clarity is achieved by using “whereas”, in which case, comma sensitivity disappears:

The first second brood is produced in a new burrow whereas the first is raised in the original burrow.


[Blue whales] are a sub-species of baleen whale feeding mainly on krill that can grow to up to 30 metres long and weigh 100-150tonnes.

[Blue whales] are a sub-species of baleen whale feeding mainly on krill, which can grow to up to 30 metres long and weigh 100-150tonnes.

[Blue whales] are a sub-species of baleen whale feeding mainly on krill, that can grow to up to 30 metres long and weigh 100-150tonnes.

[Blue whales] are a sub-species of baleen whale, feeding mainly on krill, that can grow to up to 30 metres long and weigh 100-150tonnes.

[Blue whales] are a sub-species of baleen whale that feed mainly on krill. They can grow to up to 30 metres long and weigh 100-150tonnes.


“Which” and “that”…


The supernatants which contained the protein of interest were aspirated.

The supernatants, which contained the protein of interest were aspirated.

The supernatants that contained the protein of interest were aspirated.


The moon, which orbits at around 384,400 km from the Earth, is covered with craters.

The moon that I saw last night with my telescope is Titan.


…structuring your writing strategically…


Mean sentence length in number of whole words. Sources, respectively: Sherman LA. 1803. Analytics of Literature: A Manual for the Objective Study of English Prose and Poetry. Ginn & Company, Boston; Gunning R. 1964. How To Take The Fog Out Of Writing, Dartnell Corp.; analysis of “Harry Potter and the Sorcerer's Stone” by JK Rowling in The Lexile Framework for as a Framework Reading Measurement and Success; and unpublished analysis, Andrew Moore (2017).

Chaucer 49

(1343 – 1400) Dickens 20

(1812 - 1870)

Rowling 12

(1965 - )

SteinbeckHemingway

Lawrence 15ProustStein

(writings between 1913 - 1952)

(1775 - 1817)

Austen 22

(1973 - )

Meyer 10

(writings between 1966 and

1985)

17 Lessing


Now seen graphically...

Mean number of words per sentence in individual works

23,2

17,1

14,616,3

15,2

11,89,7

http://www.tylervigen.com/literature/statistics


Sentence Lengths in Inaugural Addresses

Source: Liberman M. Real Trends in Word and Sentence Length :http://languagelog.ldc.upenn.edu/nll/?p=3534 (accessed 14.12.2013)


First five sentences:Among the vicissitudes incident to life no event could have filled me with greater anxieties than that of which the notification was transmitted by your order, and received on the 14th day of the present month. On the one hand, I was summoned by my country, whose voice I can never hear but with veneration and love, from a retreat which I had chosen with the fondest predilection, and, in my flattering hopes, with an immutable decision, as the asylum of my declining years — a retreat which was rendered every day more necessary as well as more dear to me by the addition of habit to inclination, and of frequent interruptions in my health to the gradual waste committed on it by time. On the other hand, the magnitude and difficulty of the trust to which the voice of my country called me, being sufficient to awaken in the wisest and most experienced of her citizens a distrustful scrutiny into his qualifications, could not but overwhelm with despondence one who (inheriting inferior endowments from nature and unpracticed in the duties of civil administration) ought to be peculiarly conscious of his own deficiencies. In this conflict of emotions all I dare aver is that it has been my faithful study to collect my duty from a just appreciation of every circumstance by which it might be affected. All I dare hope is that if, in executing this task, I have been too much swayed by a grateful remembrance of former instances, or by an affectionate sensibility to this transcendent proof of the confidence of my fellow-citizens, and have thence too little consulted my incapacity as well as disinclination for the weighty and untried cares before me, my error will be palliated by the motives which mislead me, and its consequences be judged by my country with some share of the partiality in which they originated.

George Washington, 1789My fellow citizens, I stand here today humbled by the task before us, grateful for the trust you have bestowed, mindful of the sacrifices borne by our ancestors. I thank President Bush for his service to our Nation, as well as the generosity and cooperation he has shown throughout this transition. Forty-four Americans have now taken the Presidential oath. The words have been spoken during rising tides of prosperity and the still waters of peace. Yet every so often, the oath is taken amidst gathering clouds and raging storms.

Barack Obama, 2009

Source:Liberman M. Real Trends in Word and Sentence Length :http://languagelog.ldc.upenn.edu/nll/?p=3534 (accessed 14.12.2013)


Most articles probably have mean sentence lengths between 25 and 30 words, but…

A sentence of between 60 and 70 words is not uncommon!

Source: Moore A. 2007. The long sentence: A disservice to science in the Internet age: http://onlinelibrary.wiley.com/doi/10.1002/bies.201190063/full


Although it has been demonstrated that exaggerated traits can have detrimental effects on locomotion and predation rates [26,27], and their growth may occasionally stunt allocation to other structures [28,29], there is growing evidence that many signal traits – even exaggerated traits – are not especially costly, and handicaps may not be necessary to maintain honest signals [27,30]. (52 words)

Exaggerated traits can have detrimental effects on locomotion and predation

rates [26,27]: their growth may occasionally stunt allocation to other

structures [28,29]. However, there is growing evidence that many signal traits – even exaggerated traits – are not especially costly, and handicaps may not be necessary to maintain honest signals [27,30].


Since inhibition of CIC leads to a significant reduction in LPS induced NO, prostaglandins and ROS production, the authors speculate that the citrate exported may be used in synthesizing acetyl-CoA (Figure 1), which in turn is used as a precursor for phospholipid production leading to prostaglandin synthesis. (46 words)

Inhibition of CIC leads to a significant reduction in LPS induced NO, prostaglandins and ROS production. The authors therefore speculate that the citrate exported may be used in synthesizing acetyl-CoA (Figure 1), which in turn is used as a precursor for phospholipid production leading to prostaglandin synthesis.


The signaling adaptor, tumor necrosis factor receptor-associated factor 6 (TRAF6), then translocates to the mitochondria. Here it interacts with Evolutionary Conserved Signaling Intermediate in Toll pathway (ECSIT), leading to an increased production of mitochondrial ROS. The mitochnodrial ROS combines with the cytoplasmic ROS resulting from phagosomal NADPH-oxidase dependent respiratory burst, to aid bacterial killing.

The signaling adaptor tumor necrosis factor receptor-associated factor 6 (TRAF6) subsequently translocates to the mitochondria where it will interact with Evolutionary Conserved Signaling Intermediate in Toll pathway (ECSIT) leading to an increased production of mitochondrial ROS, which together with the cellular ROS resulting from phagosomal NADPH-oxidase dependent respiratory burst, will aid bacterial killing. (53 words)


Serial Position Effect: Deese and Kaufman (1957) Serial effects in recall of unorganized and

sequentially organized verbal material , J Exp Psychol. 1957 Sep; 54(3):180-187; Murdock, B.B.,

Jr. (1962) The Serial Position Effect of Free Recall, Journal of Experimental Psychology, 64,

482-488

recall

primacy recency

t

An important cognitive principle:


• Put something important and new at the beginning.

• Put something important and new at the end.

• Don’t make the middle part longer than necessary as background information for your intended readership.

Therefore, in an abstract:


Sexual reproduction in mammals allows an organism to transfer part of its genes over to the next generation…

Don’t begin like this :-)


Most important insight in context, or intriguing future perspective / question

As much background as necessary, and as little as possible

Most important insight or intriguing question

We show that skt-1 is the key regulatory factor inthe signal transduction pathway that causes boneto grow in response to mechanical forces.

Optimal structure of an abstract

The mechanoreception signaltransduction pathway (MSTP) begins with a G-protein complex that senses forces ofcompression, tension and shearing in the actincytoskeleton of osteoblasts…

The discovery that skt-1 controls theresponse of bone growth to mechanical stress haspotential implications for accelerating bone repairby directly intervening in the MSTP at this point.

Disclaimer: The above example was invented for the sake of illustration; it does not reflect real knowledge


A combination of

and


Apply the principle of “chunking”

throughout your manuscriptSection heading Section heading

Sub-heading

Sub-heading

Sub-heading

This is hard to digest and remember… This is easier to digest and remember…

Keep your lowest level sections below 600 words; better 300, if possible.s


…and being as explicit as possible…


…especially in your article titles.

The involvement of protein X in signal transduction pathway Y

Effect of…Involvement of…Evidence of…Role of…Insights into…Implications of…

✘Protein X does Z in signal transduction pathway Y ✔

✘

Or:Does protein X do Z in signal transduction pathway Y ✔


Combinations of title and abstract that work well

Title:• Statement

Abstract:• (Intriguing) question• Background• Main novel finding with

perspective on implications / applications / future

Title:• Question

Abstract:• Statement of novel finding• Background• Re-statement of novel

finding, and speculation as to significance / application etc.


You can work with editors to optimize your title before

peer review• Submitted title – this doesn’t stand a good chance in peer review :-(

Histone crotonylation and male germ cell gene expression

• Re-written before peer reviewers invited :-)Histone crotonylation specifically marks the haploid male germ cell gene expression program

• Submitted title – this also doesn’t stand a good chance in peer review :-(Chromosomal organization of Drosophila melanogaster genome

• Re-written before peer reviewers invited :-)Banding patterns in Drosophila polytene chromosomes correlate with DNA-binding protein occupancy


• Submitted title – this doesn’t stand a good chance in peer review :-(Integration of two-dimensional difference in gel electrophoresis, quantitative proteomics, and bioinformatics reveals oxidative damage to enzymes of carbohydrate metabolism in Saccharomyces cerevisiae in response to lidocaine

• Suggested alternative:

• Revealing oxidative damage to enzymes of carbohydrate metabolism in yeast: A Integration of 2D gel electrophoresis, quantitative proteomics and bioinformatics

>>Note to author: I know that that leaves out the lidocaine and the yeast species, but you will have that in your abstract, and part of the knack of pairing titles and abstracts is to capture a curious reader first, and then qualify.<<

Another example


And keep your title concise and readable

Prostate Cancer Heterogeneous High-Metastatic Multi-Organ-Colonizing Chemo-Resistant Variants Selected by Serial Metastatic Passage in Nude Mice Are Highly Enriched for Multinucleate Giant Cells


You can apply the principles of statement-like titles and strategic

structuring to all parts of your manuscript – particularly

advisable for thediscussion section!


Why?

And why particularly now?


Image attribution: as published in

https://www.nationalgeographic.com/scienc

e/phenomena/2009/08/24/information-

overload-heavy-multimedia-users-are-more-

easily-distracted-by-irrelevant-information/


https://www.nationalgeographic.com/science/phenomena/2009/08/24/information-overload-heavy-multimedia-users-are-more-easily-distracted-by-irrelevant-information/


In an increasingly distracting online environment.

Readers wantintellectual gratification…


1980s 2010s

Writing

Reading

+ = + =


Analysis of the challenges of reading

electronic media compared with

paper and ink: the implications for authors…


Online text presents challenges

compared with paper…

As reviewed in: Ferris Jabr: http://www.scientificamerican.com/article/reading-paper-screens/

Reading experiences from a screen compared with paper:

• Less intuitive navigation of long texts• Less “satisfying”• Requires more mental energy

Understanding and memory of texts read from a screen compared with paper:

• Less deep understanding• Less long-term memory• Slower recall of facts• Roughly equal short-term memory• Harder to remember where particular elements of an article are


Ease of cognitive map-making

seems to be more

important

than

medium

…The findings implied that it is not the materiality of the presentation medium that influences reading outcomes, rather it is the extent to which the text presentation facilitates, or impedes, the reader's ability to construct a cognitive map that influences the reading process…

Jinghui Ho, Justin Rashis, Kwan Min Lee. Cognitive map or medium materiality? Reading on paper and screen. Computers in Human Behavior 2: 84-94 (2017 )


html pdf paper

Speed of foxesThe quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.The quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.The quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog.

Fur colour in canidsThe brown fox jumped overthe lazy dog. The brown foxjumped over the lazy dog.The quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over the

Lazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.The quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog.

The quick brown fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.

Comparative jumping ability of quadrupedsThe fox jumped over thelazy dog. The fox jumpedover the lazy dog. The quickbrown fox jumped over thelazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.

2

Positional information about mammalsOver the lazy dog. Over thelazy dog. Over the lazy dog.Over the lazy dog. Over thelazy dog. Over the lazy dog.The quick brown fox jumped

brown fox jumped over thelazy dog. The quick brownfox jumped over the lazydog. The quick brown foxjumped over the lazy dog.The quick brown fox jumpedover the lazy dog. The quick

Speed of foxesThe quick brown fox jumped over the lazy dog. The quick brown foxjumped over the lazy dog. The quick brown fox jumped over the lazydog. The quick brown fox jumped over the lazy dog. The quickbrown fox jumped over the lazy dog. The quick brown fox jumpedover the lazy dog. The quick brown fox jumped over the lazy dog.The quick brown fox jumped over the lazy dog. The quick brown foxjumped over the lazy dog. The quick brown fox jumped over the lazydog.

Fur colour in canidsThe brown fox jumped over the lazy dog. The brown fox jumpedover the lazy dog. The quick brown fox jumped over the lazy dog.The quick brown fox jumped over the lazy dog. The quick brown foxjumped over the lazy dog. The quick brown fox jumped over the lazydog. The quick brown fox jumped over the lazy dog. The quickbrown fox jumped over the lazy dog.

The quick brown fox jumped over the lazy dog. The quick brown foxjumped over the lazy dog. The quick brown fox jumped over the lazydog. The quick brown fox jumped over the lazy dog.

Comparative jumping ability of quadrupedsThe fox jumped over the lazy dog. The fox jumped over the lazydog. The quick brown fox jumped over the lazy dog. The quickbrown fox jumped over the lazy dog. The quick brown fox jumpedover the lazy dog. The quick brown fox jumped over the lazy dog.The quick brown fox jumped over the lazy dog. The quick brown foxjumped over the lazy dog. The quick brown fox jumped over the lazydog. The quick brown fox jumped over the lazy dog. The quickbrown fox jumped over the lazy dog. The quick brown fox jumpedover the lazy dog. The quick brown fox jumped over the lazy dog.The quick brown fox jumped over the lazy dog.

Positional information about mammalsOver the lazy dog. Over the lazy dog. Over the lazy dog. Over thelazy dog. Over the lazy dog. Over the lazy dog. Over the lazy dog.Over the lazy dog. Over the lazy dog. Over the lazy dog. Over the lay


People wantintellectual gratification

in an increasingly distracting online environment.


And writers must structure

articles to make it easier for

readers to• identify

• navigate, orient themselves

• read

• understand

• remember

relevant new information.


How do readers find your

paper, and what can we infer?


A little “ ology”

Visits to Wiley Online LibraryJune 2016 – July 2017


Search Engine Optimization


• 200 variables in the Google algorithm: you can only hope to influence 4 or so...

• Use of words in body text (frequency, proximity, context...)

• Terms and position of terms in:

• Title

• Abstract

• Section headings


Choose and place

keywords wisely

Title: Core keywords/key-phrases

Abstract: Repeat core keywords/key-phrases 2 –3 times, and add other field-related ones

Headings and body text: Consistent use of keywords

Make sure the terms you use are consistent:e.g. which one: “dorsoventral”, “dorso-ventral”, “dorsal-ventral”?


Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules

Fossils, development and molecules produce … - Wiley Online Library

Fossils, development and molecules produce a congruent picture of cephalopodorigin and development.

Fossils, development and molecules produce a congruent picture of cephalopod origin and evolution

55 65

, Slayer of Titles


And now, a final quick-draw

question for you!


• Consider your audienceS.

• Write good English in short sentences.

• Apply the principles of clear, concise messages in statement-form or question-form in titles and section headings.

• Don’t undersell with inexplicit titles/abstracts/headings.

• Emphasize principles without interweaving qualification or supporting details: detail obscures the message.

• Chunk longer sections for digestibility and memorability.

• Incorporate structured repetition.

• Write your discussion section as a narrative (story).


Writing Scientific Research Articles: Strategy and Steps, 2nd EditionMargaret Cargill, Patrick O'Connor ISBN: 978-1-118-57070-8236 pagesJune 2013, Wiley-Blackwell

Editorials in BioEssayswww.bioessays-journal.com

14 interactive, multimedia Learning Paths with assessment exams and learning-by-doing activities

1

2

3

4

5

6

7

8

9

11

12

13

14

10

Qualities of a Successful Scientific Researcher

Research and Publication: The Essential Link

Funding the Research Project

Selecting an Appropriate Journal

Best Practices in Writing Scientific Articles

Key Components of a Scientific Article

Manuscript Submission

Peer Review

Open Access to Scientific Literature

Managing Research Data

Ethical Questions in Writing Scientific Papers

Roles of the Publisher and Journal Editors

Post-Publication Activities and Driving Visibility

Becoming a Peer Reviewer


Extra material


You Won’t Finish This ArticleWhy people online don’t read to the end

Farhad Manjoo:

http://www.slate.com/articles/technology/technology/2013/06/how_people_read_online_why_

you_won_t_finish_this_article.html


Since inhibition of CIC leads to a significant reduction in LPS induced NO, prostaglandins and ROS production, the authors speculate that the citrate exported may be used in synthesizing acetyl-CoA (Figure 1), which in turn is used as a precursor for phospholipid production, leading to prostaglandin synthesis. (46 words)

Inhibition of CIC leads to a significant reduction in LPS induced NO, prostaglandins and ROS production. The authors therefore speculate that the citrate exported may be used in synthesizing acetyl-CoA (Figure 1). This in turn is used as a precursor for phospholipid production, leading to prostaglandin synthesis.


The signaling adaptor, tumor necrosis factor receptor-associated factor 6 (TRAF6), then translocates to the mitochondria. Here it interacts with Evolutionary Conserved Signaling Intermediate in Toll pathway (ECSIT), leading to an increased production of mitochondrial ROS. The mitochnodrial ROS combines with the cytoplasmic ROS resulting from phagosomal NADPH-oxidase dependent respiratory burst, to aid bacterial killing.

The signaling adaptor tumor necrosis factor receptor-associated factor 6 (TRAF6) subsequently translocates to the mitochondria where it will interact with Evolutionary Conserved Signaling Intermediate in Toll pathway (ECSIT) leading to an increased production of mitochondrial ROS, which together with the cellular ROS resulting from phagosomal NADPH-oxidase dependent respiratory burst, will aid bacterial killing. (53 words)


Communicate your finding(s) in

the title… not like this…


Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4,

target human Cdt1 for proteolysis


…technically complicated

titles restrict the potential

readership.

but


Subtitle: SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis

Preventing over-replication of DNA in the cell

cycle: Two E3 ubiquitin ligases regulate licensing

factor Cdt1


Niehuis, O., Judson, A. K. and Gadau, J. 2008. Cytonuclear genicincompatibilities cause increased mortality in male F2 hybrids of Nasoniagiraulti and N. vitripennis. Genetics. 178: 413–426.

Niehus, O., Judson, A. K. and Gadau, J. 2008. Cytonuclear geneticincompatibilities cause increased mortality in male F2 hybrids of Nasoniagiraulti and N. vitripennis. Genetics. 178: 413–425.

* **

*


Title optimization: not a one-off

exercise…• “Pseudotitle” for the Editor:

We are investigating what prevents over-replication of DNA in the cell

cycle, and have discovered multiple pathways.

• For the reviewers:

Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1

for proteolysis

• For the final readership:

Limiting DNA replication to one round: two E3 ubiquitin ligases regulate

Cdt1 in the cell cycle

or

Control of replication licensing: Two E3 ubiquitin ligases regulate Cdt1

to limit DNA replication


Work with editors to optimize

your title before peer review

• Submitted title – this doesn’t stand a good chance in peer review :-(

Histone crotonylation and male germ cell gene expression

• Re-written before peer reviewers invited :-)

Histone crotonylation specifically marks the haploid male germ cell

gene expression program


Specific guidelines for good titles

• Keywords up front, and optimised (N.B. Google et al.)

• State a key finding, or frame a question

• Short – typically up to 15 words

• Punctuation to split into main message and qualifier, e.g.:

• Returning to the stem state: Epigenetics of recapitulating pre-differentiation chromatin structure

• Consider a subtitle, if permitted (search engine output!)

For editorial “What’s in a title” see: http://onlinelibrary.wiley.com/doi/10.1002/bies.201190063/full


Titleology for (sub)headings, and

structuring of longer sections


• Apply titleology to the section-headings and sections in your paper to help create a scientific narrative that leads readers through the ideas logically.

• Introduce sections with a summary of what the section communicates.

• End sections with another very brief summary, this time adding implications.

Basic scientific narrative


xyzxyzxyzxyz

abc abc abcBox 1


Evolution is the key phenomenon that cuts across diverse biological systems. However, understanding remains patchy of how evolution acts on biological networks, and how that action is best identified, modelled and understood. Starting with graph theory and the evolution of protein-protein interaction networks…

Don’t begin like this:


Motile cilia are evolutionarily conserved cellular organelles whose periodic beating provides propulsive force for movement of fluid. In vertebrates, the activity of motile cilia has been associated with…

…nor like this:

andrew moore, editor-in-chief , wiley researcher academy ... · especially costly, and handicaps...

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