BioMed Central Blog
SPARC profiles open access funds at Berkeley and Calgary
In a further indication of the increasing interest in central funding of open access publications fees, the Scholarly Publishing and Academic Resources Coalition has published a profile of open access funds at the University of California at Berkeley and the University of Calgary.
BioMed Central's journal Breast Cancer Research features prominently in the profile:
Dr. Carrie Shemanko, Assistant Professor at the Southern Alberta Cancer Research Institute, Department of Biological Sciences at the University of Calgary was pleased to learn that the library would be providing funds to cover the cost of publication in open-access journals. She led a team that produced an article about how prolactin, a hormone partly responsible for breast development and function, contributes to breast cancer.
The research was funded by the Alberta Cancer Foundation, the Alberta Cancer Board and the Natural Sciences and Engineering Research Council of Canada, and the article highlighted was published in Breast Cancer Research. Shemanko received $1,500 Canadian dollars to publish in the open-access journal, which is very visible in her field and has a high impact factor.
“The article was accessed very rapidly after it became available online, by a large number of users that continues to grow. I have also granted requests from other researchers for the reagents that we used in our work, so that they can further develop related projects,” says Shemanko. “My experience increased my awareness of the need to increase funding for library resources to match the growing need of research and development.”
Posted by Matthew Cockerill at 13:42 Comments (0)
200th title in BioMed Central portfolio marks a growing trend towards open access
With the launch this week of Journal of Angiogenesis Research, the number of journals in BioMed Central’s portfolio reaches 200. This major milestone reflects a growing trend as senior academics and learned societies turn to open access to publish their new journals or to improve the reach and visibility of their existing journals.
The success of any scientific journal, open access or subscription based, depends on it receiving a good number of high-quality papers in its area of interest. But for a subscription-based journal to succeed, it faces the additional hurdle of selling enough subscriptions to pay for its costs. In the current financial environment, libraries are increasingly having to trim their collections and are finding it virtually impossible to purchase new titles. This makes launching new subscription-based journals extremely challenging. Also, learned societies or scientific institutions who publish only a small number of titles are struggling to maintain their subscription numbers in competition with the larger publishers who sell collections of titles under the “big deal”. In contrast, more and more institutions and funding bodies are making funds available for scientists to publish their papers in open access journals (see our recent blog posting on the Open Access Compact).
As a result of this situation, BioMed Central has recently seen an increasing number of institutions and societies choosing to take the open access route, either to launch new journals or increasingly to convert their existing journals to open access. Just this year, additions to our portfolio include Genetics, Selection and Evolution, owned and supported by INRA (the French National Institute for Agricultural Research), and Journal of Biomedical Science, which is supported by the National Science Council of Taiwan. These are established journals with impact factors and good rankings in their subject categories in the Journal Citation Report. Also moving towards a re-launch with BioMed Central is Allergy, Asthma and Clinical Immunology, the official journal of the Canadian Society of Allergy and Clinical Immunology. In addition, several societies have launched new journals with us this year, including Sports Medicine, Arthroscopy, Rehabilitation, Therapy & Technology and Diabetology & Metabolic Syndrome.
Our experience with journals which have transferred to open access shows that they increase their submission levels and impact factors. For instance, the 50 year old Acta Veterinaria Scandanavica has doubled its submissions and nearly trebled its impact factor within three years of moving to BioMed Central. The journal has already risen to an upper mid-table position in the “Veterinary Sciences” category of the Journal Citation Report (57/134 in 2008), from its previous position in the lower reaches of the category.
So if you are considering launching a new journal or looking for a way to increase the visibility and address dwindling subscriptions of your existing journal, drop us a line on independentjournals@biomedcentral.com.
Posted by Deborah Kahn at 13:47 Comments (0)
AGRICOLA starts coverage of selected BioMed Central journals
AGRICOLA, an indexing service from the United States Department of Agriculture National Agricultural Library, has recently accepted the following BioMed Central journals for inclusion:
- Acta Veterinaria Scandinavica
- BMC Ecology
- BMC Plant Biology
- Carbon Balance and Management
- Nutrition Journal
- Nutrition & Metabolism
- Plant Methods
Content from these journals will appear in AGRICOLA from the start of 2010.
In addition, all of these titles are included in PubMed,PubMed Central and Scopus. Full details of all indexing services which cover BioMed Central journals are available from our website.
Posted by Charlotte Hubbard at 09:14 Comments (0)
Journal of Angiogenesis Research publishes first articles
The first articles published in Journal of Angiogenesis Research
today cover a wide range of angiogenesis related topics, reflecting the
journal’s aim of providing a pivotal platform for researchers in 
this area. Dr Meadows and colleagues examine the role of Akt signalling factors in
early embryonic heart development, while Professor Mross and colleagues
assess the cancer drug
vandetanib on tumor vasculature in colorectal and liver cancer patients,
and Professor Ribatti provides an overview on the role of William Harvey in
the circulation of blood.
Angiogenesis, the growth of new blood vessels, is a key process occurring in the progression of diseases such as cancer, diabetic retinopathies, age-related macular degeneration and atherosclerosis. The rapid dissemination and implementation of advances in the field of angiogenesis will impact significantly on the understanding and treatment of these diseases. “For these reasons and due to the continual expansion of this area of biomedical research, we are proud to announce the launch of Journal of Angiogenesis Research.” say Editors-in-Chief, Mark Slevin, Yihai Cao and Jan Kitajewski.
If you are interested in this area of research, please visit the journal homepage and if you would like to receive regular emails detailing the most recently published articles then please sign up for article alerts.
Posted by Anne Braae at 10:55 Comments (0)
Five US universities to provide central funding for open access publication fees
In a major step forward for the open access movement, on September 15th 2009, Berkeley, Cornell, Dartmouth, Harvard and the Massachusetts Institute of Technology announced a joint commitment to provide their researchers with central financial assistance to cover open access publication fees, and encouraged other academic institutions to join them. The aim of the Compact for Open Access Publication Equity (COPE) is to create a level playing field between subscription-based journals (which institutions support centrally via library budgets) and open access journals (which often depend on publication fees).
The Compact commits each university "the timely establishment of durable mechanisms for underwriting reasonable publication charges for articles written by its faculty and published in fee-based open-access journals and for which other institutions would not be expected to provide funds".
BioMed Central has long noted the asymmetry between the central support given by institutions to subscription journals via library budgets, in contrast to the relative lack of such central support for open access publishing models at most academic institutions, even where those institutions have strong policies in favour of increasing access to scholarly research.
Central institutional open access funds are a natural approach to dealing with this problem, but the practical challenges involved in reshaping the flow of funds that support scholarly communication should not be underestimated, especially given the challenging economic circumstances. This makes the achievement of Harvard and its partners in realizing the Open Access Compact all the more impressive.
The two-pronged approach pioneered by Harvard - mandating deposit of faculty publications into the university's Open Access repository while also providing explicit support for fully open publishing models - looks set to be an extremely influential model and has the potential to dramatically accelerate the already rapid growth of open access journals.
Three of the five institutions listed as signatories of the Compact already have open access funds in place:
- Berkeley fund (launched January 2008)
- Cornell fund (launched September 2009)
- Harvard fund (launched September 2009)
Dartmouth and MIT have yet to announce what form their own funding arrangements for open access publishing will take, but are commited, via the Compact, to putting such funding in place in a timely manner.
Posted by Matthew Cockerill at 04:01 Comments (1)
Mapping differences in 1001 genomes – multiple genomes are better than one
Sequencing multiple individuals from a single species allows researchers to ask key biological questions regarding, for example, the diversity and population genetics of that species. The answers to many of these questions rely on the accurate mapping of polymorphisms between individual genomes.
The Human 1000 genomes and the Arabidopsis 1001 genomes projects are taking advantage of the rapid and increasingly affordable next-generation sequencing technologies to do just that. Millions of reads of sequence data can be generated in a relatively short period of time and once this information is pieced together, comparisons of multiple genomes from individuals of a single species are possible.
The advent of these ambitious sequencing projects requires concurrent advances in the software needed to analyse these data. Existing software for aligning short-read sequence data from next generation sequencing technologies have previously relied on aligning new sequences to a single reference genome.
In Genome Biology this month, Detlef Weigel, the Director of the Department of Molecular Biology at the Max Planck Institute for Developmental Biology in Tübingen, and colleagues introduce GenomeMapper, a new, open-source software for the assembly of short-read sequence data to multiple reference genomes at one time; they demonstrate the power of this tool by applying it to new sequence data from the Arabidopsis 1001 genomes project. GenomeMapper greatly increases our ability to compare genomes and the detection of polymorphisms between large numbers of individuals is now possible on a scale that was unimaginable previously.
You can read the full article from Detlef Weigel and colleagues on the Genome Biology website and the GenomeMapper software can be freely downloaded here.
You can also find out more about the Arabidopsis 1001 genomes project from their website http://1001genomes.org/index.html and read an opinion article highlighting the plans for this project, published in the May 2009 issue of Genome Biology.
Posted by Elisabeth Gaskell at 18:10 Comments (0)
Two new awards announced for 4th Annual Research Awards
As part of our 4th Annual Research Awards, we have added some new awards. In 2010, Genome Biology will celebrate its tenth birthday, to mark the occasion we will be presenting the 'Genome Biology Award - Celebrating 10 years of excellence'. The award will recognise any ground-breaking article, methodology or software published in Genome Biology during 2009. The winning article will be judged by a panel including the journal's Editor, Clare Garvey, along with external experts in the field.
In addition, BioMed Central will present another two awards recognising the best image and movie published in Biology Image Library during 2009. The judging panel includes BioMed Central's Biology Director, Dr Michaela Torkar and Associate Editorial Director (Biology), Dr Miranda Robertson.
These awards will be presented alongside our well-established Biology and Medicine Prizes which recognise excellent research published in any of our 199 journals during 2009.
Nominations for any of these awards can be made via the 4th Annual Research Awards website.
The winners will be announced at a ceremony in June 2010.
Posted by Charlotte Webber at 18:11 Comments (0)
Too hot to handle – the effect of temperature on mortality
An article published this week in Environmental Health provides a current review of the epidemiological literature on the effect of temperature on mortality.
Epidemiological studies of temperature and heat-related
mortality have been receiving increased attention recently. Identifying risk
factors and potentially susceptible populations are becoming increasingly
important for public health interventions as temperatures are predicted to rise
worldwide due to climate change.
Previous reviews on temperature and heat-related mortality have focused on methodology and climatology, largely ignoring epidemiological studies on this topic. The review by Dr Rupa Basu provides a timely overview of epidemiology studies examining the effect of temperature on mortality.
Review
High ambient temperature and mortality: a review of epidemiologic studies from
2001 to 2008
Rupa Basu
Environmental Health 2009, 8:40 (16 September 2009)
In her review, Dr Basu includes two sections on the most relevant new topics in the area, the confounding effects of air pollution on heat-related mortality and the identification of subgroups particularly vulnerable to the effects of heat. These aspects of temperature and mortality will be important areas for future research in the field.
Environmental Health publishes articles on all aspects of environmental and occupational medicine and related studies in toxicology and epidemiology. To access the latest articles published in the journal, please click here.
Posted by Anne Braae at 13:24 Comments (0)
New targets for the treatment of methotrexate resistance
Key genes involved in the development of resistance to methotrexate chemotherapy are reported in “Networking of differentially expressed genes in human cancer cells resistant to methotrexate”, a research article recently published in Genome Medicine.
Carlos Ciudad and colleagues used networking analysis of genes mutually deregulated between seven different cancer cell lines to show that DKK1, UGT1A and EEF1A1 play key roles in methotrexate resistance. Excitingly, the application of small interfering RNA (siRNA) specific to these genes re-sensitized the tumor cells to this drug, indicating a potential treatment for chemotherapy resistance.
siRNA is an agent that interferes with gene expression and could in theory silence any specific gene of choice. Its potential as a therapeutic agent was first suggested several years ago, and some siRNA-based drugs have now even reached the clinical trial stage. The potential roles of this technology in disease therapy are wide-ranging, and the identification of prospective genes which could be targetted with siRNAs to prevent or even reverse a cancer’s resistance to chemotherapy will be of great benefit in the future.
Genome Medicine, BioMed Central’s premier medical journal, stands at the forefront of research and clinical practice in the post-genomic era. The journal is led by six Section Editors and is supported by a world renowned Editorial Board.
We welcome cutting-edge genomic and post-genomic research reporting findings that significantly advance our understanding and management of human health and disease.
Keep abreast of recent developments in these exciting times: register for article updates and submit your next outstanding research manuscript to Genome Medicine.
Rebecca Furlong
Assistant Editor, Genome Medicine
Posted by Rebecca Furlong at 18:08 Comments (0)
The Lyn Clearihan Award for the Best Paper has recently been awarded to the authors of the following article in Asia Pacific Family Medicine:
Care for chronic illness in Australian general practice – focus groups of chronic disease self-help groups over 10 years: implications for chronic care systems reforms Carmel M Martin, Chris Peterson, Rowena Robinson and Joachim P Sturmberg
The award, which aims to raise the standard of primary care research, was presented at the recent WONCA Asia Pacific regional conference in June. Research articles published in Asia Pacific Family Medicine were considered for the award with the winner being decided by a panel of experts made up of Prof Bee-Horng Lue, Prof John Campbell Murdoch of and Dr Somjit Prueksaritanond.
Lyn Clearihan recently stepped down as co-Editor-in-Chief of Asia Pacific Family Medicine having been instrumental in the founding of the journal. The award in her name will be presented at future WONCA Asia Pacific regional conferences, with the next being in Cebu, the Philippines in February 2011.
Asia Pacific Family Medicine aims to provide a forum
for the dissemination of high quality regional research and enhance the
standards of family medicine by focusing on best practice. The journal is the official journal of the
Asia Pacific Region of WONCA and is currently inviting submissions for a
thematic series on 'The expanding role of family medicine in medical
education’.
Posted by Charlotte Hubbard at 04:32 Comments (0)
Publication bias – on location at the Peer Review Congress
Evidence of publication bias favouring positive results, both in which studies are reported in journals and in how they are treated by peer reviewers, has emerged at the 6th Peer Review Congress in Vancouver.
Seth Leopold described how in his group's study 2 variations of a fabricated, CONSORT-conforming randomized controlled trial (RCT) were sent to 209 peer reviewers for Journal of Bone and Joint Surgery and Clinical Orthopaedics and Related Research. Peer reviewers were randomized to receive each version of the paper, which were identical apart from the direction of the finding – one reported a positive result whereas the other “no difference”.
Testing for the Presence of Positive-Outcome Bias in Peer Review: A Randomized Controlled Trial
Gwendolyn B. Emerson, Richard A. Brand, James D. Heckman, Winston J. Warme, Fredric M. Wolf, and Seth S. Leopold
They found that the paper reporting a positive result received more positive reviews for methodological rigour, was scrutinized less carefully for errors, and was more likely to receive recommendations to publish.
Moreover, a further analysis of published vs. unpublished Food and Drug Administration (FDA) data on antidepressant trial outcomes, which now includes ‘published’ trials if they appear in review articles, found negative trial results were bundled with positive ones in reviews, rather than being fully published. Of 8 trials reviewed by the FDA in the study period, half of which were deemed positive and half negative, outcomes were reported positively 103 times compared to 8 times negatively.
Multiple Publication of Positive vs Negative Trial Results in Review Articles: Influence on Apparent Weight of the Evidence
Erick Turner
Two other abstracts presented on 11th September investigated the time to publication of manuscripts rejected by major biomedical journals and a common finding was that a quarter of manuscripts in the samples remain apparently unpublished, a number of years of later.
These findings – although not yet published in peer-reviewed journals – seem to add to the evidence of publication bias favouring positive results, and suggest unnecessary gaps in the literature and wasted research efforts continue.
But a number of BioMed Central journals actively encourage publication of these data. The journal, Trials will consider RCT results regardless of outcome or significance of findings, and BMC Research Notes aims to complete the scientific record by publishing scientifically sound research across all fields of biology and medicine.
Last month Trials published 6 new research articles (as well as 8 other articles), including the study by Pibernik-Okanovic et al., which found that psycho-educational treatment for depressed diabetics was no better than the standard care provided to the control group.
The Peer Review Congress - held every 4 years - aims "to improve the quality and credibility of biomedical peer review and publication and to help advance the efficiency, effectiveness, and equitability of the dissemination of biomedical information throughout the world."
Posted by Iain Hrynaszkiewicz at 04:39 Comments (0)
Modeling the spread of influenza infection — two new articles from BMC Medicine
When will the next wave of influenza A (H1N1) or “swine flu” infections occur, how quickly will they spread, and are there dangers of new emerging human strains?
These are some of the questions addressed in two recent papers published by BMC Medicine, both of which use mathematical modeling to make predictions about the spread of this virus if effective management strategies are not employed.
In the first article entitled ‘Seasonal transmission potential and activity peaks of the new influenza A (H1N1): a Monte Carlo likelihood analysis based on human mobility’, Duygu Balcan and colleagues from the United States, France and Italy use simulations to predict the possibility that the next peak of infection in the Northern Hemisphere could occur in late October/early November, before the seasonal vaccines are able to be widely implemented. The authors suggest that additional measures may be required in order to shift this peak and to ensure that vaccination will be maximally effective
In the second article, entitled ‘Modelling the progression of pandemic influenza A (H1N1) in Vietnam and the opportunities for reassortment with other influenza viruses’, Maciej Boni and colleagues from Vietnam and the United Kingdom predict the spread of the virus in Vietnam, a densely populated country, with a high level of human-animal contact, predicting that pandemic H1N1 infection could rise to epidemic proportions in less than 60 days without containment. This article highlights the potential for genetic reassortment with other influenza strains, leading to the possible development of further novel human strains of the virus.
Together, these papers highlight the need for a multi-pronged intervention strategy in order to weaken the severity of a pandemic infection, to minimise the risk of development of new strains, and to delay the predicted peak of infections in order to allow effective vaccination deployment.
Interested in learning more about mathematical modeling for the study of influenza? Read more in the recent review from Editorial Board member Sally Blower’s group.
For more on the latest developments in pandemic influenza A(H1N1) research from BioMed Central, check out our Influenza Gateway.
Robin Cassady-Cain
In-House Editor, BMC Medicine
Posted by Robin Cassady-Cain at 17:45 Comments (0)
Celebrating the life and work of Mary Mandels
Biotechnology
for Biofuels has published a thematic
series in recognition of the life and work of Mary Mandels.
Dr Mandels, who passed away in February 2008, spearheaded the US Army’s national bioconversion studies for four decades, and was an early proponent of efforts to convert biomass to useful products such as sugars and bio-ethanol for eventual use in fuel and chemical production.
With the renewed advent and funding of biomass to biofuels
initiatives, Dr Mandels’ work with cellulase enzymes and the microbes that
produce them remains relevant to current research.
The series features an Editorial and Obituary from friends and colleagues who worked in the field that Dr Mandels was instrumental in pioneering.
Following this is a republication of a seminal article by Mary Mandels and her collaborator Elwyn T. Reese, first published in 1976. The paper describes an assay for measuring cellulose activity - a method widely adopted at the time that is still used in research.
Also included is a previously unpublished commentary article written by Dr Mandels herself, “Reflections on the United States Military”, a poignant commentary, written in 1987, on joint ventures between the military and scientific establishments that has relevance today.
To conclude the ‘first wave’ of publications in the series, Christian Kubicek and colleagues both review recent developments in cellulase biosynthesis and, in outlining strategies for the improvement of cellulase production, look to the future of the field that Dr Mandels helped to establish.
Further articles from authors working in the field will be added to the series over the coming months.
To keep up to date with the latest publications in Biotechnology for Biofuels, sign up for article alerts or follow our RSS feed.
Posted by Ciaran O'Neill at 11:39 Comments (0)
In the mood for genomics of lithium response
Lithium is the most effective prophylactic and therapeutic agent for bipolar disorder, yet we have much still to learn about its mechanisms, report Christina Cruceanau and colleagues in “Lithium: a key to the genetics of bipolar disorder”, a Review article recently published in Genome Medicine.
Bipolar disorder is extremely heterogeneous in terms of susceptibility, symptoms and response to treatment. Genome-wide association studies have revealed many potential susceptibility genes, but their significance is clouded by this extreme phenotypic diversity. It has recently been realized that patients who respond well to the age-old remedy of lithium salts form a useful subgroup for large-scale analysis, sharing a similar disease phenotype with higher heritability of the condition than in the bipolar-affected population as a whole.
Studies of lithium-responders are beginning to unravel some of the complexity surrounding bipolar disorder as well as the mechanisms by which lithium acts. Genome-wide association studies have been followed by candidate gene and microarray analyses, leading to a wide range of disease candidates and drug targets for future study. Knowledge of the molecular pathways affected by lithium may also lead to an understanding of the variable side-effects of this drug. It is clear that new studies of an old therapy hold much promise for the future treatment of bipolar disorder.
Genome Medicine, BioMed Central’s premier medical journal, stands at the forefront of research and clinical practice in the post-genomic era. The journal is led by six Section Editors and is supported by a world renowned Editorial Board.
We welcome cutting-edge genomic and post-genomic research reporting findings that significantly advance our understanding and management of human health and disease.
Keep abreast of recent developments in these exciting times: register for article updates and electronic table of contents, and submit your next outstanding research manuscript to Genome Medicine.
Rebecca Furlong
Assistant Editor, Genome Medicine
Posted by Rebecca Furlong at 11:50 Comments (0)
Two BioMed Central journals added to PsycINFO
PsycINFO, the abstracting database published by the American Psychological Association, has recently extended its coverage of BioMed Central journals to include BMC Neurology and International Journal of Behavioral Nutrition & Physical Activity.
Both journals are also included in a wide range of other indexing services including Thomson Reuters; BMC Neurology with a current impact factor of 2.78 and International Journal of Behavioral Nutrition & Physical Activity due to receive its first impact factor next year.
A full list of all our journals which are indexed by PsycINFO as well as other services is available from our website.Posted by Charlotte Hubbard at 14:49 Comments (0)