Category Archives: Format

Format

Difference between Nature Articles and Letters

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Q. I plan to submit a research article to Nature, but I am not sure what is difference between Nature article and letter. I notice there is usually only one article per issue of Nature, but several letters. I do not know how to decide to submit a manuscript as an article format or as a letter format. Would you please explain this to me?

A. Articles are original reports whose conclusions represent a substantial advance in understanding of an important problem and have immediate, far-reaching implications.

Letters are short reports of original research focused on an outstanding finding whose importance means that it will be of interest to scientists in other fields.

More details are available at the journal’s guide to authors and at the Nature Publishing Group author and reviewers’ website, where there is a description of the article types published in all the Nature journals.

Short is sweet, says EMBO reports

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Scientific publishing seems to be moving in several contradictory directions. Against these conflicting trends, EMBO reports seeks to re-assert the importance of the short-format article, carrying a single key message of ground-breaking significance. So writes the journal’s Editor, Howie Jacobs (EMBO reports 10, 935; 2009). Against a background of screeds of scientific articles, blogs and other commentary available on the internet, and vast mountains of supplementary information and data, the short-format of EMBO reports is increasingly popular. From the Editorial:

“Our philosophy is that science proceeds in steps. Each major conceptual advance towards a complete understanding—whether of a macromolecule, an organelle, the cell or the organism—should be documented properly, judged on its merits and made rapidly available for the community. In a fast-moving field such as molecular biology, erroneous findings inevitably make their way into print; however, any resulting damage is minimized if knowledge is parcelled into manageable chunks. When too many different findings are bundled together, valid results can be ‘contaminated’ by their association with those that prove to be flawed, and significant errors might be overlooked. More importantly, crucial discoveries should not require sophisticated data-mining tools to be accessible.”

The Editorial goes on to define the key features the editors look for in a “short report” – encapsulation of the key message in a single sentence, novelty, significance for the field, and broad interest to the molecular biology community. Those who think their work fits these criteria and are considering submitting to EMBO reports will find the Editorial a helpful guide.

EMBO reports guide to authors.

New rules for presentation of statistics in cell biology

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New rules for the presentation of statistics in the Nature journals are described in the June Editorial of Nature Cell Biology (11, 667; 2009). From the Editorial:

Thanks to advanced imaging technologies and better integration with molecular and systems approaches, cell biology is undergoing something of a renaissance as a quantitative science. Robust conclusions from quantitative data require a measure of their variability. Cell biology experiments are often intricate and measure complex processes. Consequently the number of independent repeats of a measurement can be limited for practical reasons, yet the variability of the measurements can be rather high. Cell biologists have developed good intuition to guide their analysis of such constrained datasets. Biological complexity and the reliance on intuition can cause culture shock to physical scientists crossing over into cell biology (a kind of extension of the celebrated ‘two cultures’ concept of C. P. Snow).

With the arrival of quantitative information and ‘-omic’ datasets, statistical analysis becomes a necessity to complement instinct. The problem is that statistical tools are built on basic assumptions such as the independence of replicate measurements and the normality of data distribution. Usually, sizeable datasets are prerequisite for statistical analysis. Alas, these can be as hard come by as a biostatistician (n is typically well below 5). The result is that all too often statistics (frequently undefined ‘error bars’) are applied to data where they are simply not warranted.

There are no easy solutions to rectify the prevalence of poor statistics in cell biology studies. However, an obvious recommendation is to consult a statistician when planning quantitative experiments. Consider whether n represents independent experiments (you may actually be publishing a measure of the quality of your pipette!) and whether it is large enough for the test applied. Avoid showing statistics when they are not justified; instead, show ‘typical’ data or, better still, all the measurements. Importantly, displaying unwarranted statistics attributes a misleading level of significance to the data. Always describe and justify any statistical analysis applied. We have updated our guidelines to reflect these recommendations. One key rule: if the number of independent repeats is less than the fingers of one hand, show the actual measurements rather than error bars. If you wish to present error bars, include the actual measurements alongside them.

Finally, please remember that you are interrogating a complex system — be careful not to discard ‘outlier’ data points on a whim, as they may well be as relevant as clustered measurements. One is naturally inclined to ignore data that does not match the hypothesis tested, but biology is rarely as black and white as we would like. Do not make ‘hypothesis driven’ research become ‘hypothesis forced’!

Nature Methods announces online methods

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Nature Methods follows in the footsteps of Nature by ushering in an online methods section, fully integrated with the paper, for all original research articles. Details of the service described in the journal’s current (May) Editorial (Nature Methods 6, 313; 2009), and the editors welcome comments on the service at Methagora, the Nature Methods blog.

Daniel Evanko, Chief Editor of Nature Methods, writes: “We are relieved that we will no longer have to relegate important methodological details to Supplementary Information and we expect our authors will appreciate being able to include more citations in their papers. A potential downside of this change is that the print and online versions of papers have quite different levels of methodological detail. What do you think? Those of you who are online readers may not have very strong opinions on this, but what about our print readers? If anyone who regularly receives a print copy of the journal is reading this, we would ”https://blogs.nature.com/nmeth/methagora/2009/04/methods_section_remake.html">like your feedback as well."

From the Editorial: “We expect that our readers and authors will appreciate the advantages that Online Methods bring to Nature Methods. With this change effectively increasing the length of Nature Methods papers—and more than doubling the length of Brief Communications—our authors will have far more space to communicate their new methodologies and cite previous work. But by limiting the increase in length to the methods section we continue to emphasize the value of succinct scientific reports. The body of the paper will remain short enough that casual readers can easily obtain the important information. The details required for more in-depth understanding or reproduction of the work will be easily accessible if needed. We hope our authors and readers are as excited by this change as we are.”

Nature Methods journal website.

Nature Methods guide to authors.

Nature‘s formats for methods.

Methods in full, the Editorial announcing Nature’s introduction of this service (Nature 445, 684; 2007).

Nature Methods on “big data” and the scientific method

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The rise of ‘omics’ methods and data-driven research presents new possibilities for discovery but also stimulates disagreement over how science should be conducted and even how it should be defined. Is the ability of these methods to amass extraordinary amounts of data altering the nature of scientific inquiry? These are the issues dicussed in the April Editorial of Nature Methods (6, 237; 2009).

“Methodological developments are now making it possible to obtain massive amounts of ‘omics’ data on a variety of biological constituents. These immense datasets allow biologists to generate useful predictions (for example, gene-finding and function or protein structure and function) using machine learning and statistics that do not take into account the underlying mechanisms that dictate design and function—considerations that would form the basis of a traditional hypothesis.

Now that the bias against data-driven investigation has weakened, the desire to simplify ‘omics’ data reuse has led to the establishment of minimal information requirements for different types of primary data. The hope is that this will allow new analyses and predictions using aggregated data from disparate experiments.”

The Editorial goes on to ask whether the generation of parts lists and correlations in the absence of functional models is, in fact, science? “Based on the often accepted definition of the scientific method, the answer would be a qualified no. But the rise of methodologies that generate massive amounts of data does not dictate that biology should be data-driven. In a return to hypothesis-driven research, systems biologists are attempting to use the same ‘omics’ methods to generate data for use in quantitative biological models. Hypotheses are needed before data collection because model-driven quantitative analyses require rich dynamic data collected under defined conditions and stimuli.

Correlations in large datasets may be able to provide some useful answers, but not all of them: ‘omics’ data can provide information on the size and composition of biological entities and thus determine the boundaries of the problem at hand. Biologists can then proceed to investigate function using classical hypothesis-driven experiments. It is still unclear whether even this marriage of the two methods will deliver a complete understanding of biology, but it arguably has a better chance than either method on its own.”

Comment on this Editorial at Nature Methods’ Methagora blog.

Media for reading research papers

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“Would you like to be able to read research papers on a support like Kindle?”, asks Thomas Lemberger, at FriendFeed via Twitter.

Here’s a selection of the answers he received:

Yes, if it had a larger screen and the PDF formating was OK. Reading research papers and reference books would be the main reason I would consider buying an e-reader – Pedro Beltrao

As near as I can determine, the stumbling block is the volume of tables and similar graphics in journal articles. But short forms (such as articles, periodical materials, etc) are ideal for e-readers- Jill O’Neill

Both Kindle and Sony E-Reader are a bit too small for PDFs formatted for approx A4 page in my experience – Cameron Neylon

If you are worried about rendering and screen size, Papers for iPhone is really quite acceptable – Daniel Swan

Reading a paper with Papers for iPhone works mainly for looking up specific information, rather than reading the full paper – Martin Fenner [See here for earlier posts about Papers by Martin, at Nature Network.]

Papers for iPhone is great, though you still wouldn’t want to read an entire thesis on it – Chris Cotsapas.

Do you read articles on e-readers or mobile devices? What is your experience? Let us know, either here or at Friend Feed.

European Commission survey on Internet resources for research

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Via e-mail from Arnaud Berghmans of Deloitte Belgium on behalf of Augusto Burgueño of the Research Directorate-General of the European Commission:

Deloitte is conducting, on behalf of the European Commission, a survey on Internet-based services in support of the research process. So far, responses have been received from more than 3,500 EU researchers. As a benchmark, Deloitte would like to get the opinion of researchers already using the Internet for research and is asking readers of this website for their help by taking the survey.

About the survey

With this survey, the European Commission would like to find out which Internet-based resources (such as websites, wikis, social networks, mailing lists, bulleting boards, chat rooms, etc) the research community at large currently uses when carrying out research, and which ones it would be willing to use in the future.

The survey has six sections corresponding to the following phases of a research project: (1) Generate, elaborate and refine ideas; (2) Find partners; (3) Set up the research project; (4) Seek funding; (5) Run the research project; and (6) Exploit results. Each section has 3 questions.

The results of this survey will help the European Commission better understand what Internet-based services could in the future facilitate the participation of the research community in the European research and innovation programmes.

The questionnaire is anonymous and responses are aggregated for analysis. It takes ten minutes to complete.

Upon request, the survey results can be shared.

Link to the survey is here

Video journal to be indexed in Medline and PubMed

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The Journal of Visualized Experiments (JoVE) has announced that its online video protocols will be indexed in the popular US National Library of Medicine repositories MEDLINE and PubMed.

Founder and chief executive Moshe Pritsker views the MEDLINE–PubMed listing as a sign that the scientific community has accepted video-based publications. “It was a very important decision for us, and for scientific publishing,” he says.

Since JoVE was founded in 2006 with support from an angel investor, the journal has published more than 200 videos, most produced by professional videographers. It aims to improve the reproducibility of scientific results by using videos to clarify subtle experimental details. The journal was itself an experiment in video publishing and remains the only video-based scientific journal.

From Nature 455, 13 (2008).

Due credit for Asian authors

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Chinese authors are publishing more and more papers, but are they receiving due credit and recognition for their work? Not if their names get confused along the way. Jane Qiu investigates these, and other questions, in a Nature news feature in the current issue of the journal (Nature 451, 766-767; 2008). The article covers the huge problem of how to distinguish between Asian researchers, given the vast numbers of people sharing relatively few surnames. The problem is particularly challenging in the publishing sphere, not only in identifying an author correctly in citation databases and other indeces, but for editors in choosing appropriate peer-reviewers. Asian researchers suffer in being hampered from full participation in the international scientific community, for example they are less likely to be invited to contribute to conferences, to be successful in grant applications or to win awards.

The news feature provides a clear overview of these issues, and more, from a range of perspectives. Some journals have begun to provide author names in original (not Latin) characters, and there are various initiatives to provide unique author identifiers. At this stage, however, there is no consensus as to the best way to proceed: there are problems of technical compatibility between publishing, database and indexing systems, of agreement on universal standards, and other challenges, such as the high mobility of scientists, making it difficult to track the author of several publications.

Nature Network has a forum “”https://network.nature.com/forums/nnano/939">What’s in an Asian name?“, in which several Asian and other researchers provide their perspective of this challenging issue for publishers and database curators. ”https://blogs.nature.com/nautilus/2006/12/web_visibility.html">A Nautilus post last year highlighted the efforts of the Human Frontiers Program to help Japanese and other Asian scientists to improve their international visibility.

Language and languages of science

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Martin Fenner, on his Nature Network blog Gobbledygook, notes that The Deutsche Ärzteblatt , the official journal of the German Medical Association, will from this month be publishing an English version. The reason? So that the journal is more clearly indexed in databases such as PubMed, hence available to more readers, leading to more citations of journal articles, a better Impact Factor, and enhanced reputation of the journal. Martin’s opinion is that although German was once an important scientific language, today only 2 per cent of articles indexed in Medline are in the language. “In the end”, he writes, " it makes the exchange of ideas between scientists much easier if we can all use the same language. And Nature Network is a good example for this."

In the stimulating discussion arising from the post, Nicolau Werneck comments that “to this day there are a bunch of interesting words and expressions from German that came into the international scientific jargon in the last 2 centuries, such as gedankenexperiment, eigenvector and gestalt…We must fight. But not to forbid people from talking in english, or other imperialistic arrogant language, and certainly not to make them speak only in English. We must fight for the plurality of languages.”

Nicholas Wigginton’s view is that of someone considering a postdoc in a country where English is not an official language. “Although the science that the groups I am looking into publish everything in English, some operate their labs in the national language whereas others prefer their science to be done exclusively in science. I find this very interesting.”