BioMed Central Blog

Visit BioMed Central at ISMB 2010

 Conference activities include:

* Gulliver - There will be a limited number of Gullivers, our turtley cool open access turtle, waiting for a fan of open access to adopt him – don’t let him go homeless! 
                                                                                             
 We hope to see you there!

Posted by Sara Eve at 16:52    Comments (0)

Elucidating genetic susceptibility to lupus – credit where credit’s due

“We have way more data than we can possibly analyse”, said Arthritis Research & Therapy Editorial Board member Prof Edward Wakeland, in concluding his keynote address to the 9th International Congress on Systemic Lupus Erythematosus in Vancouver.

The Wakeland Laboratory are generating data that should help elucidate the genetic basis for human susceptibility to lupus. They aim to sequence the genome of 600 patients with systemic lupus erythematosus (SLE) – a disease thought to affect more than 250,000 US citizens  – in the next 16 months. They have sequenced 107 patients so far and are on track to achieve their goal, facilitated by modern ‘deep sequencing’ technology. Control data for the project are being provided by the 1000 Genomes Project.

But generating terabytes of sequence data is just the beginning.  Prof Wakeland explained that there are 89 genomic segments of potential interest but this is more than one lab is able to analyse, and on the second day of the congress he offered the data out to the community to collaborate with his group.

The web-based interface by which the Wakeland lab will make its data available to collaborators is not yet completed, but the proposal seems to be another example of genomic researchers being ahead of the curve in scientific data sharing.

Indeed, collaboration on – and driving – future research is one of the many benefits of openly sharing research data, and the potential for collaboration with large genomic datasets is vast. And where researchers must publish or perish, offering co-authorship on articles to collaborators might seem logical. However, by contributing data alone researchers will not meet the authorship criteria of the ICMJE, which are endorsed by many journals including BioMed Central’s. Moreover, researchers might not want to endorse the findings of every article resulting from their data.

So is it time for a rethink? Authorship criteria offer protection as well as a means of giving academic credit, so ambitious projects such as the Wakeland group’s instead add to the urgent need for data sharing to be recognised by academic institutions and the broader scientific community, particularly as plans for sharing data are increasingly a requirement of research funding agencies, such as the NIH and Wellcome Trust.

Prof Wakeland explained that his group have had a policy for sharing data from the outset. “All of the sequencing data was generated in my laboratory, using samples predominantly obtained from the OMRF. The size of the data set is mammoth already and we are unable to analyze all of the gene segments that are available,” he said.

Posted by Iain Hrynaszkiewicz at 13:01    Comments (0)

Uncovering the role of proteases in neurodegeneration

Alzheimer’s disease (AD) is associated with a progressive accumulation of senile plaques (containing β-amyloid (Aβ)) and neurofibrillary tangles, but the underlying pathology is still, to a large extent, a mystery. Nevertheless, there is growing evidence that matrix metalloproteinases (MMPs), molecules produced by neurons and glial cells, may play an important, but complex, role. 

In an article published last week in Alzheimer’s Research & Therapy, Stomrud and colleagues examined MMP, tissue inhibitor of metalloproteinase-1 (TIMP-1), Aβ and tau protein levels in the cerebrospinal fluid (CSF) of Alzheimer’s patients and found that compared to individuals with no cognitive dysfunction, AD patients had higher CSF levels of certain MMPs. Interestingly, cognitively healthy individuals with risk markers for the future, such as the presence of the APOE-ε4 allele, also had higher MMP levels when compared to healthy individuals with no risk markers.

The results indicate that MMPs could be associated with neuronal degeneration, even in individuals who are yet to develop any evident cognitive dysfunction.

Posted by Alexander Kroll at 09:28    Comments (2)

Welcoming SpringerOpen - a new series of open access journals

Springer Science+Business Media, BioMed Central's parent company and one of the world's largest Scientific, Technical and Medical (STM) publishers, today announced a significant expansion of its open access publishing activity with the launch of SpringerOpen (www.springeropen.com), a new series of open access journals that will span all STM disciplines. Articles published in SpringerOpen journals will be freely and immediately accessible online, licensed under the Creative Commons Attribution License.

BioMed Central became part of Springer in 2008, and BioMed Central’s open access publishing expertise and technology is helping Springer to launch this new series of titles, which will extend the benefits of open access publishing to authors and readers across all disciplines. BioMed Central’s Open Access Membership scheme, offered to institutions, societies, funders and corporations, will be extended to include the SpringerOpen titles. Articles published in SpringerOpen journals will also be sent automatically to participating institutional repositories via BioMed Central's automated SWORD deposit mechanism.

The SpringerOpen journals will complement Springer's existing titles and BioMed Central’s growing portfolio of 200+ open access journals in medicine and life science. The first SpringerOpen journals, which will open for submissions shortly, are:

• Planetary Science
• Global Energy
• Journal of Mathematical Neuroscience
• Health Economics Review
• Journal of Mathematics in Industry
• Journal of Remanufacturing
• Environmental Sciences Europe
• Security and Intelligence Informatics
• Applied Microbiology and Biotechnology Express
• Bulletin of Mathematical Sciences
• Gold Bulletin
• Psychology and Well-Being Research

It was also announced today that Springer has become a member of the Open Access Scholarly Publisher's Association (OASPA).

For the latest news about SpringerOpen, sign up for email updates via the SpringerOpen website or follow @SpringerOpen on Twitter.

BioMed Central is hugely excited by this collaboration with our Springer colleagues, which has potential to greatly extend the success of the open access publishing model, and we look forward to supporting the ongoing development of the SpringerOpen portfolio with continued evolution and improvement of our open access publishing platform, which is rapidly becoming the preferred choice for a wide range of scholarly and society journals.

Posted by Matthew Cockerill at 20:20    Comments (1)

BioMed Central launches two new gateways

BioMed Central has recently launched two new gateways in the fields of Endocrinology and Gastroenterology, providing a useful resource to researchers in these disciplines where up-to-the minute information including relevant research, recent news and research highlights can easily be accessed.

Each gateway features an item about a renowned author in the field who has chosen to publish with us, as well as a "News from around the web" section displaying updates on the latest advances or discoveries in the relevant field.

Springer's Author Mapper, which can be used to view the location of BioMed Central authors around the globe, can also be accessed via the gateways, giving a picture of the geographical spread of specialists in these fields.

To view these new resources or to access any of our other 19 research gateways, please visit BioMed Central’s gateways page.

Posted by Sally Robertson at 11:14    Comments (1)

Family-centred services for children affected by HIV and AIDS - a new supplement

The Journal of the International AIDS Society, under the leadership of guest editor Linda Richter, is proud to introduce its supplement on ‘Family-centred services for children affected by HIV and AIDS’.

The HIV epidemic continues to place a great burden on children, and the importance that treatment and care for children are integrated into the broader context of family-support schemes is becoming increasingly recognized. In this month’s supplement, Journal of the International AIDS Society has brought together a wide range of articles by leading researchers in the field discussing the rationale for family-centred services and some of the available evidence for the effectiveness of doing so.

The articles presented have been solicited from the ‘The Road to Vienna’ initiative, led by the Coalition on Children Affected by AIDS. The Journal of the International AIDS Society hopes the supplement constitutes a beginning of what could be a groundswell of interest in family-centred services for children affected by HIV and AIDS. Readers are invited to participate in a dialogue on this important and timely issue, by using the ‘comment’ option below each individual article.

Posted by Srimathy Sriskantharajah at 16:12    Comments (0)

Planning financing for open access

Last week, Universities UK and JISC held a conference to educate senior university managers about the importance of open access to institutions, how to develop policies and plan financing.
 
A report presented at the conference demonstrates that a single large university could contribute around £3 million each year to the UK research community as a whole simply by sharing knowledge through a more open route.

Indeed, many UK universities and higher education colleges are already exploring open access, but the report suggests more could and should be done in the next five years to make open access the preferred route for publishing research. In turn, it is expected this will increase the competitiveness and creativity of the UK.

However the costs and benefits of an open access policy may well fall unequally across individual institutions. There may also be implications for institutional repository use, open access publication funds and open access policies.

To this end the Research Communications Strategy (University of Nottingham) is hosting a series of free workshops this summer. The series, led by consultant Alma Swan, is aimed at institutions' research support officers, financial modellers and repository managers or administrators. These events will take place in Glasgow, London, Birmingham and Leeds from 15-29 July.

More information about open access and central funds can be found on our website. We have also published case studies of institutions which have successfully implemented central funds, including the University of Nottingham. 

Posted by Charlotte Webber at 10:35    Comments (0)

Transcriptional regulation of miRNA-21

According to research recently published in Genome Medicine, a complex of transcription factors which includes p53, NF-kappa-B and STAT3 is responsible for regulation of miRNA-21 expression. This microRNA is significantly upregulated in stressed heart muscle and has previously been suggested as a therapeutic target in a mouse model of heart failure.  

Roger Foo and colleagues used chromatin immunoprecipitation assays and high-throughput sequencing to examine transcription factor binding at the miRNA-21 locus.  They found that p53 acts as a cofactor, forming a protein complex with NF-kappa-B (RELA), and that STAT3 is also required for the complex to associate with the cis-element controlling mir-21 expression.  This may be a more general mechanism of control in other genes whose promoters lack a p53 consensus sequence.

The authors suggest that understanding the interactions of DNA binding proteins and regulatory elements in miRNA-21 expression will further inform future drug design.

Posted by Rebecca Furlong at 10:53    Comments (0)

New and improved Impact Factors for BioMed Central journals in 2009 Journal Citation Report

The newly released 2009 edition of Thomson Reuters' Journal Citation Report includes official Impact Factors for 77 BioMed Central journals, 54 of which are new or improved. [See full list of new Impact Factors]

Some highlights:

• Genome Biology (IF 6.63) increased its Impact Factor and remains BioMed Central's most highly cited journal.
• BMC Biology (IF 5.64) is now ranked #4 of 73 in the BIOLOGY category.
• BMC Medicine (IF 3.99) climbs to #18 of 132 in MEDICINE, GENERAL & INTERNAL. 
• Five more medical journals in the BMC series received their first Impact Factors:
  • BMC Family Practice (IF 1.71)
  • BMC Medical Genomics (IF 2.66)
  • BMC Medical Informatics and Decision Making (IF 1.90)
  • BMC Medical Research Methodology (IF 2.3)
  • BMC Psychiatry (IF 1.83)
• BMC Plant Biology (IF 3.77) remains in the top 10% of the PLANT SCIENCES category, while Plant Methods (IF 2.98) joins the category in the top 15%.
• Biotechnology for Biofuels (IF 4.12) received an impressive first Impact Factor.
• Breast Cancer Research (IF 5.33) has overtaken its closed-access rival to become the highest ranked breast cancer journal.
• Malaria Journal increased its Impact Factor to 3.00, maintaining its position at #2 in the TROPICAL MEDICINE category.
• Orphanet Journal of Rare Diseases (IF 5.84) experienced a significant gain, taking it to #7 of 92 in the MEDICINE, RESEARCH & EXPERIMENTAL category.
• Parasites & Vectors (IF 2.05) made its debut in the JCR, ranked #11 of 28 in the PARASITOLOGY category.
• Acta Veterinaria Scandinavica (IF 1.00) saw an increased Impact Factor for the 3rd successive year.
• Journal of Neuroinflammation (IF 4.68) and Molecular Neurodegeneration (IF 5.09) both appeared in the top 20% of titles in the NEUROSCIENCES category.

Posted by Matthew Cockerill at 10:02    Comments (4)

Active DNA demethylation

In an article recently published in Genome Biology, Michael Rehli and colleagues of the University Hospital Regensburg have identified novel examples of active DNA demethylation that are coupled to the appearance of ‘activating’ histone modifications.

Until now, the majority of evidence for active, replication-independent DNA demethylation in mammalian systems has relied upon inhibiting cell division using pharmacological inhibitors and monitoring any subsequent DNA methylation. Here, the authors avoid the use of inhibitors by investigating DNA demethylation in a differentiation system; that of human peripheral blood monocytes into macrophages or dendritic cells in which differentiation proceeds without cell division. By monitoring genome-wide methylation levels during a time course of differentiation, the authors were able to identify novel sites of active demethylation. By analysing histone modifications at these sites, they also found that active DNA demethylation correlated with the increase in ‘activating’ histone modifications.

While the enzymes involved in this active DNA demethylation process remain unknown, the characterisation of active demethylation sites and their associated histone modifications is an important step toward identifying these enzymes.

Posted by Andrew Cosgrove at 16:02    Comments (0)

Time to put biomarkers to the test in myocardial infarction?

Have you ever asked yourself exactly what a biomarker is, and what this term really means?  It can be confusing, since biomarkers themselves are discussed in a number of different contexts including: aiding diagnosis, predicting response and monitoring response to therapy, or helping to identify candidates that will benefit from therapy.

In a new review published this month in BMC Medicine, Daniel Chan and Leong Ng from the University of Leicester (UK), outline what makes a good biomarker in the context of myocardial infarction.  Further, they talk about the different biomarkers that have been investigated for use in earlier diagnosis and prediction of prognosis in myocardial infarction, a condition that leads to significant mortality and morbidity.

Chan and Ng posit that a rich host of biomarkers have been identified for use in myocardial infarction diagnosis and treatment. However, our knowledge of the underlying science remains weak, and many of them are not ready to be used in wider clinical practice; this highlights the need to validate many of these markers in well-designed randomized trials.

Visit the BMC Medicine website to read the full review and explore the authors’ insights into this serious condition.  While you’re there, why not sign up for article alerts for BMC Medicine, and check out the high quality research that we are publishing?

Posted by Robin Cassady-Cain at 14:20    Comments (0)

BioMed Central celebrates excellence in open access publishing

The winners of BioMed Central’s 4th Annual Research Awards were announced at London’s Swiss Re Tower last week. The event was attended by shortlisted authors, eminent researchers, publishers, open access advocates and science journalists from around the world.

The awards, now in their fourth year, acknowledge excellence in research that has been made universally accessible by open access publication. These awards were particularly special this year as BioMed Central also celebrates its 10th anniversary.

In addition to the Biology and Medicine Prizes, this year saw the introduction of a new prize, the BioMed Central Open Data Award, in association with Microsoft Research. This was presented to Yoosook Lee (School of Veterinary Medicine, UC Davis), for her article in Malaria Journal.

Genome Biology also gave a special award recognising the best article published in the journal during 2009, to mark its 10th anniversary. This was awarded to Ben Langmead (Johns Hopkins Bloomberg School of Public Health), for his research ‘Ultrafast and memory-efficient alignment of short DNA sequences to the human genome’.

Matthew Cockerill, Managing Director of BioMed Central, said "We are thrilled with the range and high calibre of this year's award nominees and congratulate the winners, along with those shortlisted, on their outstanding research. We would also like to thank our sponsors, Microsoft Research and Pfizer, for their continued support of the research awards."

Following the ceremony, BioMed Central hosted an auction to raise money for Computer Aid International. Items included a traditional Zambian king’s mask, an iPad and a cricket bat signed by the England team. Over £2,200 was raised in total.

Photos of the event can be found on our Facebook page and full details of winners can be found at the BioMed Central Annual Research Awards website.

Posted by Charlotte Webber at 12:03    Comments (0)

Chiropractic Care for Children - a new thematic series

Many parents take their children to see a chiropractor for various health complaints, including musculoskeletal disorders such as back pain, and non-musculoskeletal disorders such as infant colic and asthma.  However, this is a controversial area of chiropractic management because of concerns regarding the efficacy and safety of chiropractic care for children.

 A thematic series entitled ‘Chiropractic Care for Children’ published in Chiropractic & Osteopathy aims to provide an overview of the current best evidence in key aspects of evaluation and management of chiropractic care for children.

In their Editorial, Chiropractic & Osteopathy’s Editor-in-Chief Bruce Walker, the series’ Guest Editor, Simon French, and one of the journal’s Associate Editors, Stephen Perle, explain that there is currently very little evidence to inform chiropractic treatment of children, for both musculoskeletal and non-musculoskeletal conditions. They outline the type of research needed to inform chiropractic practice, and also comment on what a chiropractic clinician is to do in the light of a lack of evidence to inform practice. They conclude that although some gains have been made, a further coordinated effort by the chiropractic profession is required to generate much more research in this area.

Chiropractic & Osteopathy, the official journal of the Chiropractic & Osteopathic College of Australasia, is ready to receive manuscripts on all aspects of evidence-based information that is clinically relevant to chiropractors, osteopaths and related health care professionals.

Posted by Liz Hoffman at 16:17    Comments (5)

All content on the new-look Genome Biology website free in June

Genome Biology has moved to a new website design, joining its sister journal Genome Medicine on a new platform for BioMed Central journals.

To allow all users to explore and appreciate fully the benefits of the new website, which provides a modern and easy-to-use interface for efficient browsing of journal content, all subscription content in the journal has been made free to access until the end of June.

Genome Biology publishes open access research in all fields of biology informed by genomics and all aspects of genomic research. Alongside the original research, Genome Biology subscription content includes systematic reviews, critical assessments, reports, research news and commentary, covering work published both in the journal and elsewhere.


All Genome Biology content is free to access until June 30th.


This year, Genome Biology is celebrating its 10th anniversary, marking the occasion by publishing a collection of exciting reviews and special content that discuss key developments in the genomics field over the last decade. This specially commissioned content, along with all articles in the Genome Biology archive, will be available to all users during June.

For any questions regarding subscription to Genome Biology following the free period, please contact info@genomebiology.com

Posted by Ciaran O'Neill at 10:58    Comments (0)

Learn something new on World Environment Day

World Environment Day is this Saturday 5th June and to play your part maybe it’s time to find out a little more about our changing world and how to conserve the vital biodiversity of life that it supports. A new cross-journal thematic series presents a chance to brush up on your biodiversity knowledge.

To highlight the importance of biodiversity research and to celebrate 2010 as the United Nations’ International Year of Biodiversity, we recently launched a series on Open Access Biodiversity Research. The articles cover all aspects of biodiversity and environmental research, from the behavioural traits of sympatric fur seals influencing fine-scale species segregation, to the use of genetic tools to track evidence for hunting and smuggling of chimpanzees in Cameroon.

An editorial published today in BMC Ecology by BioMed Central’s Scientific Editor Hans Zauner, explains the need for biodiversity researchers to work together to increase knowledge and understanding of the complex web of life on earth, and how open access to research data is key to progress in working to conserve it. We have recently expanded the scope of BMC Ecology to emphasise the journal’s status as an ideal home for biodiversity research, offering immediate full open access to all articles and the opportunity to publish associated datasets as additional files.

Posted by Genevieve Horne at 17:51    Comments (1)