Monday, January 25, 2010

N - ArXiv seeks cash

ArXiv, the e-print repository that transformed the scholarly communication infrastructure of multiple fields of physics and plays an increasingly prominent role in a unified set of global resources for physics, mathematics, computer science, and related disciplines, is seeking donations to keep it running. Cornell University Library say that it can no longer afford the annual operating costs of the preprint server--expected to increase to $500,000 by 2012-–and will ask the top 200 institutional users to make voluntary contributions. ArXiv itself says that it remains committed to keeping its content free for researchers. (Nature 2010;423:275; http://arxiv.org/help/support/whitepaper)
Thanks to Margaret Cooter

N - Open access call

The Scholarly Publishing Roundtable, a group of representatives from university administration, libraries, information science departments, and the publishing industry, has called for US federally funded research papers to be made open access. One key recommendation of their 12 January report is the establishment of specific embargo periods between publication and public access, allowing for some variation across fields of science. It also advocated common standards to ensure searchability and collaboration across fields and databases, and suggested that international cooperation on standards would also be critical. (http://science.house.gov/press/PRArticle.aspx?NewsID=2712)
Thanks to Margaret Cooter

N - Present information agreeably

People experience scientific debates as contests between warring cultural factions, and endorse whichever position reinforces their connection to other with whom they share important commitments, says an opinion piece in Nature (2010;463:296-7, 21 January). The process of "cultural cognition" accounts for this distinctive form of polarisation-–it also causes people to interpret new evidence in a biased way that reinforces their predispositions. "We need to larn more about how to present information in forms that are agreeable to culturally diverse groups, and how to structure debate so that it avoids cultural polarization," says Dan Kahan, a law professor.
Thanks to Margaret Cooter

Wednesday, January 20, 2010

B - The health illiteracy problem in the USA

Editorial. The health illiteracy problem in the USA. The Lancet 2009;9707 (374):2028
(doi:10.1016/S0140-6736(09)62137-1)



Health illiteracy is the inability to comprehend and use medical information, affecting access to and use of health-care systems. Most individuals with low health literacy are elderly people, poor people and minorities. They are more prone to visit emergency rooms, stay longer in hospitals and use fewer preventive services, with consequent high costs for the health-care systems. A reliable US national health literacy measurement tool is not available at the moment but it should be developed and assessed.

B - Limitations on the publishing of scientific research

Meadows J. Limitations on the publishing of scientific research. In: de Leeuw K, Bergstra J (Ed.). The History of Information Security. A Comprehensive Handbook. Elsevier; 2007. p. 29-51
(doi:10.1016/B978-044451608-4/50003-1)


Journals have played an important part in encouraging greater openness to scientific research but they also impose restrictions on publication since editors and referees decide what research should be published. Restrictions are also on journal access and use due to financial limitations and copyright. Books and report literature are often difficult to access as well. Developments in electronic communication should improve access to research information.

Saturday, January 16, 2010

B - Onwards and upwards: science needs governing

Onwards and upwards. The Economist 2009 December 19:35-38.

Examines scientific, economic, and moral progress. "From the
perspective of human progress, science needs governing. Scientific
progress needs to be hitched to what you might call 'moral progress'.
It can yield untold benefits, but only if people use it wisely. They
need to understand how to stop science from being abused. And to do
that they must look outside science to the way people behave."


Thanks to Margaret Cooter

Tuesday, January 12, 2010

B - University Public-Access Mandates Are Good for Science

Shulenburger D. University Public-Access Mandates are Good for Science

PLoS Biol 2009; 7(11): e1000237.

doi:10.1371/journal.pbio.1000237

The ArXiv online digital version of physic articles preprints and post-prints in August of 1991 had the objective of simplify access to and sharing of scientific papers among the scientific community. Since then many have forwarded the example of ArXiv, to such and extent that if u visit the DOAR home page (last update in Sept 2008) the site advertise over 1500 listings. The author of this article finds that accessibility has some disadvantages when researchers have to face such a well of information retrieval. Whatsmore, open access and public access pose the question of immediate access to a work or in the case of public access of a limitation period in order to weight the cogency of a paper. For instance, ArXiv has no peer review but since 2004 has introduced the endorsement that is the authorization to publication of a paper from another ArXiv author. However, there authors who are not interested in having their work peer-reviewed. The policy of Harvard, MIT and the University of Kansas and other universities to display over the web their scholar literature, the economy benefits and potentials of such an initiative, the request to “ expand the NIH mandate to all federal funding agencies” and other aspects regarding the issue are taken into consideration.

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000237

Monday, January 11, 2010

N - Journals lack policies on animals

Journal editors need to revisit their editorial policies concerning research on animals, a study in the American Journal of Bioethics has concluded (2009;9:55-9, doi:10.1080/15265160903318343). Researchers assessed the policies of a random sample of 288 English language peer reviewed journals that published original research between July 2005 and June 2006 involving the use of animals. They scored editorial policies, with a top total score of 12. No relevant information could be found for 52 of the journals, and 83 did not have any relevant editorial policies. The highest score achieved was 9, and this was achieved by only one journal.

B - the Article of the Future

Emilie Marcus (Editor-in-Chief)Cell. A Publishing Odyssey. 2010

Cell Press has been working for some time on a project they call "the Article of the Future" to rejigger the format of research articles to better use the capabilities of the internet.
The publisher is now releasing the fruits of its labors with articles in the new issue sporting the new format.

http://beta.cell.com/index.php/2010/01/cell-launches-article-of-the-future-format

Thanks to Renata Solimini

N - Retracted papers and attempted extortion

Two papers recently retracted by Science (2004;303:371-3) and the Journal of the American Chemical Society (2004;126:15654-5) have been linked to an extortion attempt, Nature reports (2009;462:969, doi:10.1038/462969a). Documents seen by Nature show that in 2007, police in San Diego considered a former postdoctoral fellow as a possible suspect after another received an anonymous email demanding a $4000 payment and threatening to reveal alleged fraud. The author, Zhiwen Zhan, received an email that read, “You have fraud on at least 3 papers and you stole library material.” Zhang decided not to press charges and says that he stands by his work.

N - Arab world far from knowledge society

Arab states have made progress in technology and research, but there is still a long way to go before the region becomes a knowledge society, according to a report described in a scidev.net article. Arab Knowledge Report 2009: Towards Productive Intercommunication for Knowledge (www.mbrfoundation.ae/English/Documents/AKR-2009-En/AKR-English.pdf), proposes ways of filling what it says are numerous gaps in the Arab knowledge landscape. Many Arab countries now understand the importance of science and technology in promoting development, and some Arab institutions, such as the Qatar Foundation, are pioneers in this knowledge revolution. But Arab countries still have some of the lowest levels of research funding in the world (www.scidev.net/en/science-and-innovation-policy/science-in-the-islamic-world/news/arab-world-long-way-from-knowledge-society-1.html).

N - Open access good for Africa

"The open access movement removes barriers to academic literature and offers opportunities to participate in the wider research and teaching community, ensuring that Africa does not end up on the wrong side of the 'digital divide,'" writes Joseph Juma Musakali, in an article on www.scidev.net. There are also many open access journals, including those in the Public Library of Science (PLoS), as well as others listed in the Directory of Open Access Journals (DOAJ), a project set up by Lund University Libraries in Sweden. To encourage the use of open access resources, faculty and students need training, especially in information search and retrieval (www.scidev.net/en/opinions/bridging-the-digital-divide-through-open-access.html).

Friday, January 08, 2010

B - The GPP2 guidelines

Graf C, Battisti WP, Bridges D, Bruce-Winkler V, Conaty JM, Ellison JM, Field EA, Gurr JA, Marx ME, Patel M, Sanes-Miller C, Yarker YE; International Society for Medical Publication Professionals. Research Methods & Reporting. Good publication practice for communicating company sponsored medical research: the GPP2 guidelines. BMJ 2009 Nov 27;339:b4330. doi: 10.1136/bmj.b4330

Good Publication Practice 2 (GPP2) represents an useful document for the publication of company-sponsored medical research. Commissioned by the International Society for Medical Publication Professionals (ISMPP) and developed by a recruited steering committee, GPP2 is an update of the original GPP guidelines published in 2003. The document is mostly based on the recommendations of codes of practice developed by international associations, like COPE, WAME or CSE, but it takes into account also the publisher’s prospective (Elsevier and Wiley-Blackwell) and the prospective of Pharmaceutical Companies. From authorship to conflicts of interest, the document provides recommendation for both articles and presentations. An interesting section concerns publication planning, to ensure that clinical trials results are communicated to the medical and scientific community in an effective and timely manner.

Thursday, January 07, 2010

N - Uniform form for competing interests

The International Committee of Medical Journal Editors has agreed a standardised format for the reporting of competing interests in biomedical research papers, to better help readers understand the relationship between authors and commercial entities that may have an interest in the information reported. The goal is to make the process of disclosure uniform and easy; a new form should eliminate the need to reformat disclosure information for specific journals. The form also asks for non-financial associations that may be relevant. The form is at www.icmje.org/coi_disclosure.pdf, including instructions to help authors provide the information, and a sample completed form is at www.icmje.org/sample_disclosure.pdf.

N - Rap about physics

On 30 November experiments resumed at the Large Hadron Collider, and although the LHC Rap has been around for some time, it seems apt to flag it up now. The rap is the brainchild of Katherine McAlpine, at the time working in the CERN press office. When Michigan State University announced that it would be building a new particle accelerator, the physicists there asked McAlpine to mark the occasion with a rap. Since then she’s written the Black Hole Rap. See www.katemcalpine.com/scirap.html for the videos and links to other science rappers.

N - Backslash backslash a mistake

Sir Tim Berners-Lee, the UK scientist who created the World Wide Web, has admitted that two slashes at the front of a web addresses is pointless, the Telegraph reports. Sir Tim, now director of the World Wide Web Consortium, which oversees the web’s development, said that if he had his time again he would leave them out. “Look at all the paper and trees that could have been saved if people had not had to write or type out those slashes on paper over the years—not to mention the human labour and time spent typing those two keystrokes countless millions of times.”

N - The end of impact factors . . . and journals?

"Something has just happened that will almost certainly end the tyranny of impact factors and may well mark another step towards the extinction of most scientific journals," the former editor of the BMJ Richard Smith has blogged on bmj.com. He thinks that "article level metrics," information attached to each article in the publications of the Public Library of Science, shift attention from journals to articles, particularly for those anxious to find a convenient and cheap way of ranking academics. "The metrics give a … much broader measure of the influence of an article," he says (http://blogs.bmj.com/bmj/2009/11/02/richard-smith-the-beginning-of-the-end-for-impact-factors-and-journals/).

N - Scientific American gets female editor

Scientific American, the 164 year old magazine, appointed Mariette DiChristina, its first female editor in chief, in December, the Guardian reports. She is the eighth editor in chief at the magazine, which has published articles by more than 140 Nobel laureate authors, including Albert Einstein and Francis Crick, and was acquired by Nature Publishing Group last year. DiChristina joined the magazine in 2001 as executive editor, after nearly 14 years at its rival Popular Science, and launched its spin-off title Scientific American Mind. She is also president of the 2500 member National Association of Science Writers (www.guardian.co.uk/media/2009/dec/03/scientific-american-woman-editor-chief).

N - Living in a world of euphemism

Pre-emptive editing by lawyers "forces us to live in a world of euphemism," said Tracey Brown, managing director of Sense About Science, at a recent panel discussion about English libel law. "Even if you win you could still lose £100 000 and a year or two of your career," said the science writer Simon Singh, who is embroiled in a case brought against him by the British Chiropractic Association (http://www.bmj.com/cgi/content/full/339/oct28_2/b4429). The Index on Censorship has published a report on the current situation, with recommendations for reform (www.libelreform.org). The UK home secretary Jack Straw has pledged to end libel tourism, the Times reports (http://business.timesonline.co.uk/tol/business/law/article6926997.ece).

Wednesday, January 06, 2010

N - Tweeter satirises top stylebook

A user of Twitter, the microblogging site (www.twitter.com), has amassed more than 80000 followers, amused by it’s satirising of the AP Stylebook, dubbed “the journalist’s bible” by Associated Press (www.apstylebook.com). The user @FakeAPStylebook has amused followers with tweets such as “While it’s tempting to call them ‘baristi’ because of the Italian roots, the plural of ‘barista’ is ‘journalism majors’” and “Robots should only be referred to by gender-neutral pronouns, no matter how sexy they may be.” The Twitter presence of the real stylebook has only 30000 followers. See www.wired.com/epicenter/2009/11/how-i-exposed-fakeapstylebook/

N - New words are not awesome

"The stickler-advocated rules of spelling, grammar and punctuation slow the speed of change and allow the language to remain united,” writes David Mitchell in the Guardian, dismissing the annual list of new words that have entered the Oxford English Dictionary (3 Jan, www.guardian.co.uk/commentisfree/2010/jan/03/david-mitchell-english-language-grammar). “Staycation,” “tweetup,” “bossnapping,” and “unfriend” are some of the new entries. But Mitchell argues for conservatism: “If you start describing everything as ‘rambunctious’ or ‘celestial,’ you end up with sentences like meals in expensive ethnic restaurants—all flavoursome sharing plates and no bloody chips. Slagging people off for saying ‘nice’ and ‘good’ is what leads to their resorting to ‘awesome.’” See www.telegraph.co.uk/news/newstopics/howaboutthat/6905776/Tweetups-and-unfriend-among-Oxford-English-Dictionarys-words-of-the-year.html

N - Write for peer reviewers

"The real readers that matter are the peer reviewers. Peer reviewers are specialists and for them to get excited, you’re going to be speaking a language that is not necessarily accessible to the average reader," Judith Swan tells Bob Grant, in the Scientist (2009;23:65). Other tips include starting with the results section, and getting the tables and figures perfect first before moving onto the discussion section and the introduction. "You can do the methods anytime, really," says the communications consultant Margaret Cargill. Grant also recommends writing every day for 15 to 30 minutes, logging your time, and reading your manuscript out loud. (www.the-scientist.com/article/display/56104/)

N - UK libel law risks patient harm

A Danish radiologist says that the lives of patients are being put at risk because libel laws are preventing doctors and scientists from speaking in public about their clinical experiences, writes Zosia Kmietowicz in the BMJ (2009;339:b5615). Henrik Thomsen, professor at the University of Copenhagen, is being pursued in the High Court in London by GE Healthcare over allegations that he defamed the company at a conference in Oxford in 2007. Professor Thomsen told the Sunday Times, “I believe that the lawsuit is an attempt to silence me . . . It’s dangerous for the patient if we can’t frankly exchange views” (20 Dec, http://business.timesonline.co.uk/tol/business/law/article6962816.ece).

B - The textual characteristics of traditional and Open Access scientific journals are similar

Verspoor K, Cohen KB, Hunter L. The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics 2009,10:183

doi:10.1186/1471-2105-10-183

http://www.biomedcentral.com/1471-2105/10/183

The authors collected two sets of documents, one consisting only of Open Access publications and the other consisting only of traditional journal publications. Surface linguistic structures were examined (incidence of conjunctions, negation, passives, pronominal anaphora), and found that the two collections did not differ. The distribution of sentence lengths in both collections were characterized by the same mode. Small differences did exist, but the conclusion is that no structural or semantic differences appeared between the Open Access and traditional journal collections.

Tuesday, January 05, 2010

N - European university presses fold

University presses in Europe are facing funding cuts, with one press having closed and others cutting back on the number of titles they’re publishing, and a European university press association is being planned, reports Kent Anderson in the blog The Scholarly Kitchen (http://scholarlykitchen.sspnet.org/2009/11/11/european-university-presses-fold-consolidate-in-economic-downturn/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+ScholarlyKitchen+%28The+Scholarly+Kitchen%29). Middlesex University Press closed at the end of last year (www.mupress.co.uk). Forty academic presses, including 12 from the United Kingdom, are to create a Europe-wide association. Twelve countries are represented. Andrew Peden Smith, at Northumbria University Press, said, "As part of this focused European approach we will also be looking at possible funding from the EU."

N - Cell highlights proteins and genes

The journal Cell has piloted technology that highlights proteins, genes, and small molecules in research articles. Clicking on these entities opens pop-up windows that contain relevant contextual information, with additional links (http://beta.cell.com/index.php/2009/11/reflect). The project was developed at the European Molecular Biology Laboratory, Heidelberg, Germany. Sean O’Donoghue, coordinator, said, “We wanted to design a system that would enhance the reading of scientific papers on the web.” This follows Elsevier’s recent launch of an “article of the future” prototype with Cell, where the traditional linear journal article is displayed in a more useful format (http://beta.cell.com/index.php/2009/07/article-of-the-future).
Thanks to Emma Campbell

Monday, January 04, 2010

B - On the need to distinguish between author and journal self-citations.

Hartley J. On the need to distinguish betwen author and journal self-citations.
Scientometrics 2009;81(3):787-788.


Prof. James Hartley, on this 'letter to the Editor', with regard to his book on Academic Writing & Publishing tries to make clear the ambiguity of a term he used to indicate those concurring elements that, put together, determine the impact factor of a journal. By reading a recent article - by Loet Leydesdorff - on the subject, he found out that what himself meant by “self-citation” was interpreted not as the “authors (who) cites their own works” instead as “journal self-citation”. Different usages of the term are shown on a table taken from Google Scholars. A problem of interpretation arises.

B - Never mind the impact factor: colleagues know better!

Hartley J. Never mind the impact factor: colleagues know better!
Publication databases disc 77
Keele University


In this article Prof. James Hartley, points the finger to the present system and standards of evaluation narrowly based on publication metrics (impact factors, citation rates etc.); his view is that the authors themselves are better judges of their own work rather than - as he put it – “automated bean counters”. He addresses weaknesses and inconsistencies of evaluation metrics currently used (by the two well-known databases called Web of Science and PubMed) with examples of publications of his own.