Month: January 2007

UK PubMed Central

A UK version of the free biomedical research server PubMed Central will provide free access to a permanent online archive of peer-reviewed research papers in medicine and the life sciences.

UK research funders, led by the Wellcome Trust, awarded the contract to develop UKPMC to a partnership between the British Library, The University of Manchester and the European Bioinformatics Institute (EMBL-EBI).

Members of this group now require that articles describing the results of research they support are made available in UKPMC with the aim of maximising its impact. The UKPMC service will ensure that articles resulting from research paid for by any member of the funding consortium will be freely available, fully searchable and extensively linked to other online resources.

The UKPMC essentially mirrors the US PubMed Central database but as of 8th January 2007, UK scientists will also be able to submit their research outputs for inclusion in UKPMC.

Mark Walport, Director of the Wellcome Trust commented: “Medical research is not complete until the results have been communicated. The development of UKPMC provides a great opportunity for this research to be made freely available, and I am very pleased that a first class partnership of the British Library, the University of Manchester, and the European Bioinformatics Institute will be running it.”

The British Library will run the service, promote it to researchers, as well as offering support for those who want to include their research papers in UKPMC. The University of Manchester hosts the service — on servers based at MIMAS (Manchester Information and Associated Services) — and will support the process of engaging with higher-education users. EBI, which is part of the European Molecular Biology Laboratory (EMBL), will contribute its biomedical domain knowledge and state-of-the-art text-mining tools to integrate the research literature with the underlying bioinformatics databases.

The launch of UKPMC brings into sharp relief once again the ethical debate surrounding scholarly publication. The Wellcome Trust has insisted that authors publish research arising from its funding in open access repositories since 1st October 2006.

Writing in PLoS Biology in 2005, Robert Terry (Senior Policy Adviser at the Wellcome Trust, Cambridge, United Kingdom), discussing the plans for UKPMC at the time said, “For a funder, having all its research in one format, ‘under one roof’, and searchable will improve the efficiency of strategy setting–for example, setting funding priorities–assessing the outputs of the funded research, and even gaining an insight into the impact of the work. As grants management becomes more electronic, there can be a direct link between original research proposals and the research outputs.”

According to AJ Cann on MicrobiologyBytes recently, this widely adopted funding-body policy already means “publishers are over a barrel – sign up or sign out.”

Blu-ray and HD DVD

If you’ve been worrying that either one of the high-definition video technologies – Blu-Ray or HD DVD could become the next Betamax, then worry no further. It seems that Korean company LG Electronics has come to the rescue with a dual format system that will cope with both.

It seems like an obvious idea – combine both capabilities in one machine. Why not? My DVD recorder can read and write positively and negatively and it’s not as if the new formats suffer from the differing form factor and mutually exclusivity issues as VHS tapes and Betamax tapes.

“We’ve developed the Super Multi Blue Player to end the confusion caused by the current competition between Blu-ray Disc and HD DVD. Customers are no longer forced to choose between the two formats,” explains Hee Gook Lee, president and chief technology officer of LG Electronics in a press release disseminated on January 7. “As Full HD TV is already gaining ground, we are hoping that the Super Multi Blue Player will play the trigger role in expanding and advancing both Full HD TV and high- definition DVD market volume together.”

You can read more techie details in that press release and I won’t bore you with them here, suffice to say that it’s pretty unlikely these machines will appear in the UK in the very near future, but early adopters Stateside will be able to go dual blue some time in the next couple of months.

Both high-def DVD formats were introduced in 2006 and 2007 is expected to see film studios release more of their output in these formats as more players become available. With the advent of dual-format players, the studios will not be forced to opt for an either-or scenario nor have to offer both formats in a single product package.

Knights of the chemical realm

Right royal honours were bestowed on two of my very oldest contacts in the field of chemistry this week. Royal Society of Chemistry president Professor Jim Feast was awarded the CBE in the New Year Honours List for ‘services to polymer chemistry.’ And, supramolecular ex-pat Fraser Stoddart was given a Knighthood for to ‘services to chemistry and molecular nanotechnology.’

Congratulations to them both. With such accolades under their belts, it’s surely only a matter of time before either one of them gets that phone call from Stockholm too.

Pluto is a planet

Well, no, it is, and it isn’t. It all depends on your perspective and what you feel about there being more than 20 planets in the Solar System rather than the more usually seen 9.

David Weintraub takes us on a cosmic tour through the history books from Aristotle’s logical fallacies of aether and perfect spheres moving in perfect circles to the discovery of dozens upon dozens of shapely and shapeless objects littering the once perfect heavens.

On 24th August 2006, as reported on Sciencebase (and everywhere else, admittedly), the International Astronomical Union decreed that Pluto should be demoted to the status of dwarf planet. After all, it’s discovery was a pure accident, it shouldn’t really have been spotted where it was in the 1930s at all, and it’s just so small, and really just the biggest of what we now refer to as the Kuiper Belt Objects.

However, there is no scientific reason to label Pluto as “not a planet”.

In one sense, Weintraub’s argument hinges on the fact that we cannot define what is and what is not a planet on the basis of a mnemonic taught to science students – My Very Earthly Mother Just Served Us Nasty Pizza.

Space is far more messy than that. Between Mars and Jupiter, where earlier astronomers hoped to find a planet that fit the now debunked Titius-Bode rule (which never quite became law), we find some startlingly large asteroids instead, among them Ceres. Then there is Eris (formerly known as UB313 and colloquially as Xena), and a myriad swarm of Kuiper belt objects, trans-Neptunian object, Oort cloud objects…

The list goes on. But, in the final reckoning is it for us to draw lines and say such and such an icy rock whirling around the sun billions of miles from earth is any more planet than the next chunk of ice and rock.

Pluto looks like a planet, moves like a planet, and quacks like a planet. Obviously that last one isn’t quite right. But, it’s not a planet like the inner planets, it’s not a gas giant, and it’s not like an asteroid, which would have been much more appropriately named planetoids rather than being labelled literally as “star-like”.

Weintraub anticipates that there will be no problem for the young, upcoming astronomers to simply add qualifiers to all the different kinds of planet we find. Nothing will be less alien than terms such as giant, terrestrial, icy, pulsar, belt-embedded prefixing the word planet and allowing is to create a sophisticated taxonomy that allows us to understand the nature of the universe around us.

It will make for an unwieldy mnemonic with our Earthly Mother having to add all kinds of toppings to that Nasty Pizza to make it stick. But then planets are intrinsically unwieldy.

RFID for chemicals

RFID for moleculesA new type of radio frequency identification (RFID) sensor for gaseous molecules has been created based on a standard RFID tag coated with a chemically sensitive film at low cost. The use of multivariate analysis allows these new RFID sensors to be used to identify and quantify vapours important to industrial, in health, law enforcement, and of security applications.

Radislav Potyrailo and William Morris of the Materials Analysis and Chemical Sciences Technology at General Electric Global Research Center, in Niskayuna, New York, explain the benefits of their new technology in a forthcoming issue of the journal Analytical Chemistry. “Distributed sensor networks are critical for numerous applications such as monitoring of transport of pollution plumes across the perimeters of industrial plants, leak detection from storage tanks, health monitoring of buildings, large-area tracking of contamination sources in natural water supplies, and spatially resolved combinatorial screening of materials,” they explain.

More…

Scratchy and itchy

Researchers are only just begin to scratch the surface of the brain with functional MRI. Now, a study of perception in both allergen- and histamine-induced itch has revealed how different parts of the brain are activated in response to stimulation from each type.

Allergens, such as pollen and dust, and histamine released by allergy cells as a result of activation by foods, drugs, or infection often lead to a vicious itch?scratch cycle as any allergy sufferer will tell you. However, researchers at Oxford University have demonstrated that the brain responds differently to itchiness caused by allergens and histamine.

Siri Leknes, Susanna Bantick, Richard Wise, and Irene Tracey at Oxford have worked with Carolyn Willis and John Wilkinson of the Department of Dermatology, at Amersham Hospital to try to understand the nature of itch? cycle with a view to improving outcomes for allergy sufferers and people with certain chronic skin conditions.

Read on in the latest science news round-up from David Bradley on spectroscopynow.com

Being particular about DNA

Surface-enhanced Raman spectra (SERS) of DNA and RNA mononucleotides can be detected with high sensitivity, according to UK researchers. Using citrate-reduced silver colloidal nanoparticles aggregated with magnesium sulfate instead of the more common halide ions, reduces inappropriate enhancements and produces spectra that are sufficiently different to allow each to be distinguished.

“The main advantage of our SERS approach is that it allows direct label-free identification of mononucleotides in aqueous solution,” Steven Bell, Director of the Innovative Molecular Materials Group, at Queen’s University Belfast, explains, “There is no requirement for labels because the Raman signals of each of the mononucleotides are intrinsically different due to the differences in their chemical structures.” He adds that spectra can be obtained at ten nanograms per millilitre. “We were working with large samples but reducing the sampling volume to a few microlitres would move the sample down to tens of picograms,” he says.

More…

Nervous scoop

An action shot of the protein Scp1, which plays a crucial role in the development of the nervous system has been obtained using crystallography by researchers in the US. Their structure could provide drug designers with a template for creating small molecule inhibitors of this protein that would be useful in neurological research.

Joseph Noel and Samuel Pfaff of the Salk Institute for Biological Studies and colleagues there and at the University of California, San Diego (UCSD) and The Scripps Research Institute, La Jolla explain that a network of signalling molecules controls embryonic stem cell differentiation. Controlling the controllers might allow scientists to nudge embryonic stem cells into becoming specific cell types, which would be useful in basic research and for potential therapies.

Read on…

PLoS ONE Impact Factor

UPDATE: June 21, 2010: At last, PLoS ONE has now been given an impact factor of 4.351, which puts it into the 25th percentile of the “Biology” category.

UPDATE: June 19, 2009: ISI will publish its latest stash of impact factors on the evening of the 19th. We will hopefully find out then whether or not a PLoS ONE impact factor will be made public, and just how well it is rating relative to the traditional journals.

Until recently, online scientific journals were really just e-versions of the printed copy. Of course, we had advance publication online and ToC alerts etc, but now Public Library of Science will publish a general science journal to rival Science and Nature that covers primary research results from all areas of science. Unique to the new format is the use of both pre- and post-publication peer review, which are set to revolutionize the way the scientific literature evolves.

PLoS co-founder Harold Varmus says, ‘For those of us who have been engaged with PLoS from its conception, the launch of PLoS ONE is tremendously exciting–this is the moment when we seize the full potential of the Internet to make communication of research findings an interactive and fully accessible process that gives greater value to what we do as scientists.’

It has launched with publication of 100 peer-reviewed research articles peer-reviewed under the guidance of an extensive academic editorial board, and covering molecular science and clinical studies with topics including the evolution of language, the control of rabies, mimicry of jumping spiders, and Alzheimer’s disease.

Every article published is under an open access license, which means everyone is free to read, reuse, and build upon these research papers.

One of the key selling points is the possibility of almost instantaneous publication with virtually zero delay between submission and publication. As soon as a paper is published a dialog between author and reader is opened.

PLoS launched in “beta” in December, 2007 could see big changes in the way the scientific literature evolves.

UPDATE: 2009-06-16 Recent headlines added:

Open access news
  • Open Access Publisher Under Scrutiny for Taking Sham Paper
  • Science publishing also suffers from its curmudgeons
  • What’s wrong with scholarly publishing today?
  • Merck’s Ghostwriters, Haunted Papers and Fake Elsevier Journals
  • Scholarly community gives feedback regarding Wikipedia
  • Scitable is a Social Network for Science
  • The Impact Factor Game
  • Scitable is a Social Network for Science
  • Guestimating PLoS ONE impact factor