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Nature Publishing Group (NPG) is pleased to announce the initiation of a free service, launching in 2008, to help authors fulfil funder and institutional mandates. NPG has encouraged self-archiving, including in PubMed Central, since 2005. Later in 2008, NPG will begin depositing authors’ accepted manuscripts with PubMed Central (PMC) and UK PubMed Central (UKPMC), meeting the requirements for authors funded by the Howard Hughes Medical Institute (HHMI), the National Institutes of Health (NIH), The Wellcome Trust, the Medical Research Council and a number of other major funders in the US, the UK and Canada who mandate deposition in either PMC or UKPMC. NPG hopes to extend the service to other archives and repositories in future.

Nature Publishing Group will begin depositing manuscripts into PubMed Central six months after publication on behalf of authors, starting later this summer, according to a release. But some open access publishing advocates say this is just a way for the publisher to maintain an embargo period, rather than making content immediately available.

Motivation: Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organising, and analysing such textual knowledge. There are numerous efforts that attempt to exploit this information by using text mining and machine learning techniques. We developed a novel approach, called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL and relevant resources from PubMed. Methods: PuReD-MCL avoids using natural language processing (NLP) techniques directly; instead, it takes advantage of existing resources, available from PubMed. PuReD-MCL then clusters documents efficiently using the MCL graph clustering algorithm, which is based on graph flow simulation. This process allows users to analyse the results by highlighting important clues, and finally to visualise the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express 3D. Results: The methodology was applied to two different datasets, previously used for the validation of the document clustering tool TextQuest. The first dataset involves the organisms E. coli and yeast, whereas the second is related to Drosophila development. PuReD-MCL successfully reproduces the annotated results obtained from TextQuest, while at the same time provides additional insights into the clusters and the corresponding documents. Availability: Source code in perl and R are available from http://tartara.csd.auth.gr/~theodos/

pubmed central review article on connotea

Exposure to airborne nanoparticles contributes to many chronic pulmonary diseases. Nanoparticles, classified as anthropogenic and natural particles, and fibers of diameters less than 100 nm, have unrestricted access to most areas of the lung due to their size. Size relates to the deposition efficiency of the particle, with particles in the nano-range having the highest efficiencies. The deposition of nanoparticles in the lung can lead to chronic inflammation, epithelial injury, and further to pulmonary fibrosis. Cases of particle-induced pulmonary fibrosis, namely pneumoconiosis, are mostly occupationally influenced, and continue to be documented around the world. The tremendous growth of nanotechnology, however, has spurred fears of increased rates of pulmonary diseases, especially fibrosis. The severity of toxicological consequences warrants further examination of the effects of nanoparticles in humans, possible treatments and increased regulatory measures.