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Archive by date: January 2007

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Footprint, weight, or is there a better term?

In his Nature Correspondence "Time to give due weight to the 'carbon footprint' issue", Geoffrey Hammond writes: "The media are increasingly using the term 'carbon footprint' in articles about the need to mitigate climate change by reducing our carbon dioxide emissions. Footprints are spatial indicators, measured in hectares or square metres. The property that is often referred to as a carbon footprint is actually a 'carbon weight' of kilograms or tonnes per person or activity.
To improve public understanding of the issues surrounding climate change, it is necessary to be precise. Other 'footprints', such as the ecological or environmental footprint, convert resource consumption and waste production into spatial units. The term 'ecological footprint' was coined by William E. Rees, a planner at the University of British Columbia — who had previously used the term 'appropriated carrying capacity' — after a computer delivery man told him that the new machine, which took up less space than his old model, had a 'smaller footprint'.
As well as the media, many government agencies and environmental groups now use the expression 'carbon footprint'. Those who favour precision in such matters should perhaps campaign for it to be called 'carbon weight', or some similar term. That would avoid lasting confusion. Losing weight might even take on a whole new meaning."
Nature 445, 256 (18 January 2007) | doi:10.1038/445256b; Published online 17 January 2007.
We welcome suggestions from readers.

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Who is reading what at your institution

As part of an institutional site licence, Nature Publishing Group provides monthly reports that measure visits to all content on nature.com licenced to that institution. These reports are uploaded to the site licence administration account before the 15th of every month for the preceding month. The registered site license administrator is alerted by e-mail. For more details of the reports provided, please see the statistics page in the NPG Librarian gateway.

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Q&As about Q&As, from Nature's News and Views Editor

The Question & Answer (Q&A) is a new format in Nature's popular News & Views section, the first outing being "Chromosome territories" by Karen J. Meaburn and Tom Misteli, published in the current (25 January 2007) issue (subscription or site licence required). Tim Lincoln, Nature's News and Views editor, provides some of his own questions and answers about this venture:

What is it? Q&As come in different guises in different publications, including Nature’s own News and News features sections. For News & Views, the Q&A approach involves a collaboration between an expert author and an editor in formulating questions and answers to illuminate some aspect of ‘happening’ science. It does not constitute an interview as such, and the expert author (or authors; two maximum) is the named source of the piece. Like everything in News & Views, Q&A pieces deal with science itself, not matters of policy, funding and so on.

Do these items require a news peg in the form of a new paper? No, which is one of the distinguishing characteristics of the Q&A approach from the conventional type of News & Views article. The latter format will remain the mainstay of News & Views, but it restricts the topics we can cover, and the breadth in which we do so.

Isn’t the object of Q&A the same as that of the long News & Views features that appear from time to time? Yes it is, but there are various reasons for trying a different approach. One is that, unlike News & Views features, the appearance of Q&A items is very different to that of Reviews/Progress articles, emphasizing the intent to appeal to non-specialists. Another is that the Q&A format looks less intimidating not only in print but -- crucially -- also on the web, and will be more browsable in both media.

Will potential authors see the Q&A approach as trivializing their subject? Not if we can persuade them that this is a way to reach a very large audience -- one well beyond that which would tackle an article in more usual form. Although we want these pieces to be readable and lively, they won’t be frivolous. At about 2,000 words they’ll actually be pretty substantial. They just won’t look it.

What does one of these Q&A pieces look like? See for yourself via the article in the current issue on chromosome territories. It’s the fruit of collaboration between Karen Meaburn and Tom Misteli as the expert authors, and Helen Dell as the editor. More generally the rules are that these pieces should take around 2 or (maximum) 3 pages, with 2 or 3 display items (illustrations or tables). On the practical front, the Qs and As both need to vary in length to provide changes of pace (but with an absolute maximum of 110 characters for the Qs and of 180 words for the As). There’s no reference list as such; instead a maximum of six review articles/book chapters/websites are cited at the end.

How often will they appear? We’ll test the water by publishing a few in 2007. What follows will depend on how they are received by readers.

What kind of topics will be covered? Areas of science that are lively or that are seeing progress (not necessarily the same thing), or that are ripe for expansion. Put another way, Q&A pieces can answer the question of “What’s all this about?” in the mind of the general reader -- “this” being a topic that is coming to prominence or enjoying a revival. They will offer the opportunity to visit comparatively specialist areas. Whatever the topic, they should offer a balanced view, which is not to say they will be bland, or that authors won’t be encouraged to provide their own views about disputes and sticking-points as long as they are flagged as such.

Cell biology: Chromosome territories by Karen J. Meaburn and Tom Misteli. Nature 445, 379-781 (25 January 2007) | doi:10.1038/445379a; Published online 24 January 2007.

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Call for papers for The ISME Journal

Nature Publishing Group (NPG), in partnership with the International Society for Microbial Ecology (ISME) is delighted to announce the launch of a new international publication: The ISME Journal: Multidisciplinary Journal of Microbial Ecology. The journal will be available in print and online from May, and is welcoming submissions for the first issues. Submit now at the journal's website.
The ISME Journal is a cooperative effort between ISME and NPG, and will join NPG's stable of highly respected journals in the discipline, including Nature Reviews Microbiology, Nature Immunology and EMBO Journal. All research published will receive high exposure through online hosting on nature.com, extensive press coverage and rapid publication. The editorial team is led by George Kowalchuk, Mark Bailey and John Heidelberg, and will include a highly respected international editorial board.

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Question of the year for genetics researchers

The question of the year for genetics researchers is: what would you do if it became possible to sequence the equivalent of a full human genome for $1,000?
The sequencing of the equivalent of an entire human genome for $1,000 has been announced as a goal for the genetics community, and new technologies suggest that reaching this goal is a matter of when, rather than if. What then? In celebration of its upcoming 15th anniversary, Nature Genetics is asking prominent geneticists to weigh in on this question: what would you do if this sequencing capacity were available immediately? The Nature Genetics 'Question of the Year' website, updated monthly, reveals the answers -- in the process offering a glimpse of the future of genetics. Answers so far posted on the site include Francis S. Collins, George Church, Stephen J. O'Brien, Evan Eichler and Jonathan Pritchard.
Also for genetics researchers and those interested in the subject, the February issue of Nature Reviews Genetics is free access for the whole month. With an impact factor of 19.211, Nature Reviews Genetics is the world's top-rated genetics journal.

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Breakaway journals improve quality but need subscriptions

Rebels hold their own in journal price war : Article : Nature (Subscription or site licence required.)

In a News story in the current issue of Nature, "Rebels hold their own in journal price war", Declan Butler looks at what has happened since last August, when the entire editorial board of the Elsevier journal Topology quit in a row over pricing. Now the board is setting up a non-profit competitor to be published by the London Mathematical Society. The Journal of Topology, announced last week, will launch next January and will cost US$570 per year, compared with Topology's $1,665.

Over the past eight years, continues the News story, around a dozen cheap or open-access journals have been created to compete directly with an expensive commercial journal, many by editorial boards that had quit the original publication in protest. (See the News story for a table of these journals.) But do the cheaper journals fare better than their rivals?

As far as scientific credibility is concerned, the answer is often yes — many of the challengers have obtained impact factors (a measure of the citations its papers receive) higher than their competitor. Nevertheless, the rebel journals often get poor support from libraries, with subscriptions being an uphill battle for them.

Source: Nature 445, 351 (25 January 2007) | doi:10.1038/445351a; Published online 24 January 2007.

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Community consultation at Nature Biotechnology

Following the MIAME (minimal information about microarray experiments) standards for reporting microarray data, various scientific communities are engaged in producing similar guidelines. Some of these standards papers are under consideration for publication in Nature Biotechnology. Because data-reporting standards are only as useful as the community finds them, we want to know what you think. The papers are freely available for at least a month, and your comments are welcome. New papers are added to the list on the Nature Biotechnology website as they become available, with a commenting facility for each one. The papers cover standards for 'minimum information about a genome sequence', proteomics, protein modification data, mass spectrometry, mass spectrometry informatics, gel electrophoresis, functional genomics, molecular interactions, and in situ hybridization and immunofluorescence experiments.

The Nature journals' policy on data availability, including MIAME standards, is available at the author and referees' website.

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Scopus adds older citation data and abstracts

Scopus, Elsevier’s abstract and citation database, has now added citation data, including abstracts, for many older papers, making it ever-closer to the rival Thomson’s Web of Science service. Nature Publishing Group titles are indexed by both databases, as well as by many other abstract&indexing services.

Since its launch two years ago, Scopus is now attracting publishers who want their older journals to be listed, including Springer, Nature Publishing Group, the American Physical Society, and the American Institute of Physics. Most of these publishers have digitized their content themselves back to the first issues of their journals. Older journals, such as Nature (first issue published on 4 November 1869, and freely available online), are still in the process of digitizing their very old content. Nature's digital archive currently goes back to 1950, with the issues back to 1869 to be added later this year. Nature New Biology and Nature Physical Sciences archives are also being digitized.

Scopus already contains 15 million pre-1996 records, and the new deal will add around seven million more. The new records will include full abstracts, traditionally a strength of Thomson’s Web of Science. Scopus does not necessarily intend to index older content in all areas, believing that 11 years of citation data is enough for some purposes - for example, to provide an overview of a publication for a grant or tenure application, so is prioritzing the digitization of older content accordingly.

In some cases, researchers may be interested in older content to see the citations that their own research has received over the years, or may use it to study historical trends. Whatever the needs of the reader, the addition of more search features and functions as the two organizations compete for customers can only be of benefit, especially taking into account features being introduced by the free-to-use service Google Scholar, also driving innovation and introduction of more reader services by the commercial providers.
See Nature Publishing Group abstracting and indexing page.

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Active is better than passive or neutral

Q. Dear Nature Editorial Staff,

I run a research team, and for my sins, I also give lectures to undergraduates and graduates. One series of lectures that I give is entitled "Scientific Writing", the series being aimed at providing some general pointers regarding the layout of scientific papers and the style of scientific writing. The primary audience are PhD students and undergraduates doing lab projects.
On the question of the use of active versus passive voice, my advice to the students is to always use the active voice (where possible) since it is clearer and, most important, shorter. However, most of the students find it almost impossible to make a simple declarative statement along the lines of "I found that", preferring the passive "we found that", or more often, the neutral "it was found that".
I have always attributed this tendency towards the use of "we" or "it" in place of "I" down to a subconscious desire to avoid taking direct responsibility for a piece of research. Recently though, this malaise has spread to certain supervisors, who have taken to correcting dissertations written by undergraduates such that they are entirely written in the passive or neutral voice.
I wonder whether you might tell me the view of the Nature editors on the use of active and passive voices? I realize that you must receive relatively few single author manuscripts, but when you do, do you prefer the active voice? I'd be happy to be wrong in my own assumptions/asserttions about this (and will modify my lecture recommendations accordingly if required), but some up-to-date advice from the top journal would be appreciated.

A. Dear Dr Lecturer

Thanks for your interesting query. Yes, we agree with you that the active voice ("I" or "We" in the case of multi-author papers) is better and makes papers far clearer and more comprehesible, as described in our guidelines.
Unfortunately, many books and courses advise the opposite. An example is when one of my daughters was doing a practice science SATs test in primary school, in which a mark was given for saying that scientific papers/writing should be in the passive -- answering "active voice" did not get you the mark. What can one do under these entrenched, embedded circumstances?
Active voice has been Nature policy for as long as I can remember; it is enshrined in our style manual and is specifically recommended to all authors as part of our standard acceptance procedure. However, if an author insists on the passive, we would probably allow it, as at the end of the day it is the author's paper. We'd only make a rule ironclad if it affected the scientific content, I think. So you will see papers in Nature in the passive voice, but you can be assured that this is at the author's insistence rather than Nature policy.

best wishes
Maxine Clarke
NATURE
www.nature.com/authors

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Citing submitted but not published papers

Q. Dear Editor,

We want to submit a letter to Nature. Is it allowed to cite papers that are submitted but not yet accepted?

Best regards,

Prof. Author


A. Dear Prof. Author

Thank you for your enquiry. Yes, it is allowed to cite such papers. If the paper is submitted to a journal and likely to be in the press or published by the time your paper is published (say within a couple of months of your submission), then include the paper in the reference list, with a number. If the work you are citing is less advanced, you should cite it in the text of your paper, in brackets, in the style of (manuscript in preparation) or (personal communication) or similar. These informal refereneces do not go into the reference list of the paper and do not have numbers.

For futher details, please see the guide to authors.

Yours sincerely
NATURE
www.nature.com/authors

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Connections: a series of Nature essays

There are times in the development of science when a shift in approach is sufficiently extensive that only a collection of thoughts and perspectives from many different practitioners can do justice to it. This issue of Nature sees the launch of a themed series of essays, called Connections, which take such an approach to the interdisciplinary study of complex, dynamic systems

The series begins just a few weeks after the popular Essay page returned to Nature. It will reiterate the tradition of this format as a forum for scientists to reflect on new ideas, or re-evaluate old ones. The Connections essays is being collated into a Nature web focus, where access to the first four will be free. We hope that, week by week, a greater story develops than could be told by a single article — and that over the coming year, the Essay page will continue to provide scientists with a valuable opportunity to say exactly what they think.

In the first Connections essay, "Biology's next revolution", Nigel Goldenfeld and Carl Woese argue that the emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself.

The Nature editorial introducing the Connections series is at this link.

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Planning a productive (and long) academic career

In this month's (February) Nature Chemical Biology, the Editorial "The ivory tower grays" (subscription or site licence required) discusses how the aging of the professoriate has raised questions about how to support productive faculty members late in their careers, while integrating the vitality of youthful scientists.

Arguing strongly for an abolition of a mandatory retirment age, the Editorial concludes: "Although forward-looking universities have been planning for the effects of an aging professoriate for many years, recent trends suggest that the issue deserves much greater attention among today's faculty and university leaders. These decision makers must provide answers to the major questions facing academia's future, including: what retirement options are appropriate and reasonable for research universities? What are the appropriate space and funding levels for scientists at different career stages? How does the changing face of the professoriate affect the current tenure system? Though the challenges and answers will likely be different for each country, there is a global need to reevaluate how we sustain and nurture academic faculty—one of science's greatest resources."

From Nature Chemical Biology 3, 69 (2007) ; doi:10.1038/nchembio0207-69

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Free online access to Palgrave journals

Free online access to all Palgrave journals: 15 Jan - 14 Feb 2007 � Update

Palgrave are offering FREE online access to the complete Palgrave Macmillan Journals Portfolio from 15 January to 14 February 2007. Palgrave Macmillan publishes journals in information systems and technology, education and economics, among other areas. It is also the publisher for the UK national statistical office. More information about Palgrave Macmillan is available at this link.

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The figure police

Juan-Carlos Lopez, Chief Editor of Nature Medicine, discusses the question of data integrity of figures in his post on Spoonful of Medicine: The figure police.

Juan-Carlos discusses an editorial in the Journal of Cell Biology, which takes the line that "the progress of science depends on the reliability of the entire published record, and journal editors must do their part to ensure that reliability", urging editors to "participate in this dialogue with the scientific community, to help devise effective and practical standards that can be applied to the published literature".

Should scientific journals screen every image in every paper, as the Journal of Cell Biology editorial recommends? Or is a spot-checking system, such as used by the Nature journals, preferable, on the grounds that the vast majority of the papers published are not fraudulent, and that the journal could invest more usefully in other author and publication services? (This last point is particularly critical for small, society-owned journals that have limited resources.) Or is the responsibility that all research work is honest, and that the papers produced accurately reflect the work done, that of the scientific institution and/or the funder?

The Nature journals' policies on image integrity can be found at our Author and Referees' website.

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Increasing public awareness

The editorial in the February issue of Nature Immunology, "Increasing public awareness" (subscription required) discusses ways in which scientists and universities can benefit from mobilizing the power of public support.

"In the academic scientific community, a furor rages over the ever-tightening National Institutes of Health (NIH) budget that funds non-bioterrorism-related biomedical research. This past year, the topic was a fixture among the headlines of science journals and magazines, but it was buried deep in the 'issues' sections of most political candidates' websites and was rarely featured in mainstream news periodicals."

Scientists need to communicate to the US public so it is more aware of the situation and the role it can play in demanding more support for research. The editorial discusses several examples of how scientists have raised public consciousness, and provides some suggestions for more of the same. As the editorial concludes: "Whether the NIH budget will rebound anytime soon is not known. It therefore is up to scientists and universities to tap every available resource, particularly one as powerful as the American public".

From: Nature Immunology 8, 109 (2007); doi:10.1038/ni0207-109.


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EMBO journal picture competition

The EMBO Journal is running a competition to find cover images for the journal in 2007. The closing date is 31 January. There will be two winners for the prize of a year's print and online subscription, one for "the prettiest and most thought-provoking contribution depicting a piece of molecular biology research"; and one for "the most beautiful or interesting image that was made outside of the lab". An array of each type of picture, and further explanation (including an entry form), can be found at this PDF at the journal's website.

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Banned words in titles

The always stimulating Language Log blog features a post on hated words in titles. Current suggestions for a world ban are whither, revisited, status, role and (lower-case n) nature.

These words may crop up more frequently in the linguistics literature than they do as part of titles in the scientific literature. A favourite phrase that is usually edited out of titles on Nature journals is "Evidence for". "New" is an over-used word in titles, and indeed in the body of the paper. Any other pet hates that cause the reader's eyes hastily to move on to the next item in the table of contents?

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Nature special feature on scientific misconduct

Today's issue of Nature (vol 445, pp 229 and 240-246; 2007) contains an Editorial and several news stories about scientific misconduct. These articles, with links to the journal content (subscription required) are listed at Nature's newsblog so that readers can comment.
From the Editorial: ...."most important of all, as the first scientific studies of the factors behind good conduct confirm, is the example set by senior researchers themselves. It is here in the laboratory — not in the law courts or the offices of a university administrator — that the trajectory of research conduct for the twenty-first century is being set."

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Writing advice for non-native-English speakers

In commenting on the post "Web visibility", José J. Lunazzi writes: "The title of the article mentioning "speaking" english concerns in fact to a smaller but not small problem, that of "writing" english. It is good to read that people whose native language is english need to be conscious and willing in some way to reduce the problem for the whole science. A good and simple way is to learn esperanto and start communicating with the world through it. Seeing the broad spectrum the "delta" strictly selective function of english can be understood. I had beeing at Korea, China and Japan using esperanto and english, same as in USA, and am sure that esperanto performs much better in every field of activity, coloquial, domestic or in physics."

I replied along these lines: the Esperanto solution is sensible "on paper" but realistically it is unlikely to occur, given the length of time since Esperanto was devised as a universal language.

International science journals can provide help in various ways for authors whose first language is not English. The Nature journals provide advice before the author submits -- see our webpage on the author and referee site for this purpose. This page provides a link to similar useful advice at SciDev.Net.

We'd be happy to link to other examples of writing advice for scientists in our "writing a paper" guidelines -- whether research papers, review articles or other types of scientific or technical article. Please let us know if you are aware of good guidelines, and we'll link to it to help future authors maximize clarity in preparing their manuscripts.

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Practice Points and Napoleon Bonaparte

The Nature Clinical Practice journals are now publishing their “Practice Point” articles in NPG’s advance online publication (AOP) programme. Practice Points put original research articles into context and offer expert opinion on best practice for clinical researchers and clinicians. They are available in each of the eight journals in the Nature Clinical Practice series. With the addition of this AOP feature, the definitive versions of these articles will now be available online before the print issues of the journals appear.

More information about the Nature Clinical Practice journals is available here. You may have heard about a current article in NCP Gastroenterology and Hepatology on the death of Napoleon Bonaparte. It seems that rather than being poisoned, as is often suggested in history books, the emperor was suffering from gastric cancer. The article is currently free access, so read the fascinating, if gory, details at the link.

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Call for seminar and lecture listings

Nature Network London, a free new website for science and scientists in London, will be launching in March 2007. We hope to make the Nature Network London scientific event listings, which will be regularly updated after Network London is launched, comprehensive. We are currently collecting a database of all scientific lecture and seminar listings, especially those at academic institutions, both in London and at those within a day's return journey to or from the city.

Please can you let us know about any lecture and seminar series you attend, and/or of which you are aware? You can contact us via email if you wish to include an attachment with calendars and topic lists, or drop a URL, together with any other relevant diary and contact information, in the comments to this post. You can also enquire further about Network London using this email address.

Many thanks for your help.

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Generating enthusiasm for outreach

Nobel Intent: How do we get scientists to do outreach?

John Timmer at Nobel Intent (link above) promotes the idea of "outreach faculty": people in an academic institution who could, proposes Dr Timmer, work in the institution's public affairs office to improve the quality of press releases and other often-muddled output; who would visit schools and other local community organizations; help to train graduate students so that they themselves will be better able to interact with the public, and so on.

The end result, writes Dr Timmer, would "provide benefits for the two most important constituencies—the institutions, which receive better outreach, and the departments that provide the faculty, which receive better-trained graduate students. Provided [ he adds, cynically but probably with reason ] that the academic community does not attach stigma to these positions, it can provide a rewarding experience for those inclined to become outreach faculty."

There is a discussion of these proposals in the comments section at Nobel Intent. We also welcome your views in the comments here. How can journals such as those published by Nature Publishing Group help in this process?

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Allconversions for units

Music of the Spheres: Converting Scientific Units

Bruce Irving, writing on his blog Music of the Spheres (link above) notes: "Orbiter is completely metric, so when I was writing yesterday's post about force vector visualization, I wanted to mention the conversion from meganewtons (MN) to pounds-force (lbf) for those more familiar with "English units" (i.e., pounds of thrust for rocket engines). There are probably a billion web sites with information on converting units, but I especially like AllConversions.com, because it has a simple format and includes a huge number of units in its drop-down lists."

Let us know your favourite, unit-conversion websites.

Allconversions.com can be accessed directly here.

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Author and referee website launched

Nature Publishing Group has this week launched a website dedicated to authors and peer-reviwers. Authors & Referees @ npg (http://www.nature.com/authors) provides links to and information about the Nature journals' publication policies for primary research papers; author and referee services; and author benefits. We also provide feedback links so potential authors, peer-reviewers, scientists and other readers can ask questions about these topics. This blog (Nautilus) and our peer-reviwers' blog (Peer to Peer) are integrated into the site.

Find out more about the site here or via the links in the vertical column to the left of this page. We hope to be hearing from you about what you'd like us to include in this site, and receiving your questions and comments about our policies, services and benefits for authors and reviwers.

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Measures for measures

Citation analysis can loom large in a scientist's career. On pages 1003-1004 of the 21-28 December 2006 issue of Nature, Sune Lehmann, Andrew Jackson and Benny Lautrup compare commonly used measures of author quality. The mean number of citations per paper emerges as a better indicator than the more complex Hirsch index; a third method, the number of papers published per year, measures industry rather than ability. Careful citation analyses are useful, but Lehmann et al. caution that institutions often place too much faith in decisions reached by algorithm, use poor methodology or rely on inferior data sets.

Read the full text of the Commentary here (subscription or site licence required).

We welcome comments on this Commentary and on citation-based quality measures in general.

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Nature Photonics is launched

Nature Publishing Group has just launched a monthly journal called Nature Photonics , dedicated to publishing the most significant photonics research from academia and industry.

This first issue can be seen at the link in the previous sentence, and reflects the journal's broad scope by including research papers on topics as diverse as lasers, microphotonic circuitry, near-field imaging and slow light. The inaugural issue also contains a Technology Focus on LEDs , the first of a series of regular supplements on important photonics technologies that are enabling new applications or transforming existing ones. The aims and scope of the journal are available here; information for authors is at this link; and to submit your work to this new journal, please visit this link.

Nature Photonics is NPG's first monthly research journal to have its core editorial base in the Asia-Pacific region, reflecting the strength of the Asia-Pacific region, and Japan in particular, in photonics research.