BioMed Central Blog

Genome Biology publishes a key resource for pea genetics

The field of pea genetics received a boost today with the publication of a resource of pea mutants in Genome Biology.

The pea, Pisum sativum, is one of the most famous tools used in genetics: school children today learn that the 19th century monk Gregor Mendel studied the pea - for example, whether the seeds are wrinkled or not - and showed that this and other traits are inherited in a predictable way.

Peas have kept many of their other genetic clues secret, however, as they are unsuited to the genetic modification techniques that are commonly used to work with plants. Scientists, led by Abdelhafid Bendahmane, at the French National Agricultural research Institute (INRA) used an early flowering pea cultivar, called Caméor, to study mutant plants at different developmental stages (from seedling through to fruit maturation). The team studied DNA samples from 4,704 plants and identified many essential genes. From this they created a database called UTILLdb, which describes each mutant plant at each developmental stage studied, and incorporates digital images of the plants. UTILLdb contains phenotypic as well as sequence information on mutant genes, and can be searched plant traits of interest.

This new tool has implications for both basic science and for crop improvement, and the authors hope that it will fulfill the expectation of crop breeders and scientists who use the pea.

The full article was published today in Genome Biology and has received considerable attention in the media. The London Times features both a news item on the science, and a lead editorial celebrating the preeminent role of the humble pea in the progress of scientific understanding.

Posted by Ruth Rowland at 15:27    Comments (0)

 

EQUATOR - Achieving transparency in the reporting of health research

The EQUATOR Network, an international initiative that aims to improve the reliability of scientific publications by promoting transparent and accurate reporting of health research, is holding its launch meeting in London, UK on Thursday 26th June 2008.

Despite the efforts of researchers, editors and peer reviewers, some published studies are poorly reported. The use of reporting guidelines can lead to the improved accuracy and transparency of publications and several internationally recognized guidelines (e.g. CONSORT, STARD) have been developed through a collaboration of experts, methodologists and journal editors. But they are still not widely used by researchers or supported by many medical journals.

The aim of the meeting, 'Achieving transparency in reporting health research,' is to aid better understanding of problems associated with health research reporting and use of reporting guidelines. It will discuss potential solutions that can lead to the improvement of the health research literature.

The meeting contributors include Professor Doug Altman (University of Oxford), a key member of the CONSORT group and co-Editor-in-Chief of Trials, BioMed Central's journal dedicated to investigating all aspects of the design, performance, and findings of randomized controlled trials relating to healthcare.

BioMed Central and its journals have long-supported initiatives aimed at improving the reporting of biomedical research and the relevant BioMed Central journals can be found on the growing list of CONSORT endorsers.

Posted by Iain Hrynaszkiewicz at 14:33    Comments (0)

 

C. difficile review and commentary published in Critical Care

A new Infection thematic review series, led by Dr Steven Opal (Memorial Hospital of Rhode Island, USA) has just been launched in Critical Care, with the first article published being a timely paper documenting the global spread of Clostridium difficile.

Described as a good reference for clinicians faced with this issue, the authors Carolyn V Gould and L Clifford McDonald, from the Centers for Disease Control, detail the pathogenesis, diagnosis and possible treatment strategies in this most topical of hospital-acquired infections.  The onus is on healthcare professionals to maintain awareness of the changing epidemiology of the disease, as well introducing measures to reduce the risk to patients.  

In a related commentary, Aurora Pop-Vicas and Marguerite Neill (Memorial Hospital of Rhode Island) reiterate the statements made in the review, and conclude that only through following basic standards of hygiene will slow down the spread of transmission, placing the responsibility squarely ‘in our hands’.

Review
Bench-to-bedside review: Clostridium difficile colitis
Carolyn V Gould, L Clifford McDonald
Critical Care 2007, 12:203 (18 January 2008)
[Abstract] [Full text] [PDF]

Commentary
Clostridium difficile: the increasingly difficult pathogen
Aurora Pop-Vicas, Marguerite A Neill
Critical Care 2008, 12:114 (7 February 2008)
[Abstract] [Full text] [PDF]

More authoritative reviews in this exciting new series will be published continuously online in the coming weeks and months. Critical Care’s reviews and commentaries require a subscription for access, but if you do not currently have a subscription to the journal, you can register for a free 30-day trial.

All research articles published in Critical Care are open access.

Surayya Johar
In-house Editor, Critical Care

Posted by Iain Hrynaszkiewicz at 13:25    Comments (3)

 

Harvard Faculty of Arts and Sciences votes to adopt mandatory open access policy

As discussed in the New York Times and the Harvard Crimson, Harvard's Faculty of Arts and Sciences has just considered, and approved, the adoption of a new policy designed to ensure that the results of work published by members of the Faculty remain openly accessible. The policy is the first of its kind in the US, though similar institutional open access mandates are becoming increasingly common around the world.

A new Office for Scholarly Communication will be responsible for implementing the policy, and for addressing the broader issues to ensure that the results of research carried out at Harvard are made universally accessible.

Harvard University's strong move to encourage open access is not an isolated instance. It is hugely encouraging to note the rapid pace of change in the United States on open access issues since the passing of the bill late last year, which made mandatory the National Institutes of Health's Public Access Policy.

For example, the University of Berkeley recently announced the Berkeley Research Impact Initiative, which sets up a central open access fund to assist Berkeley researchers who wish to publish in open access journals. Later this month, Berkeley will also play host to the inaugural US meeting in relation to the SCOAP3 initiative in particle physics. SCOAP3 is a consortium of the world's major particle physics laboratories which has set itself the ambitious yet achievable aim of switching the whole particle physics literature to an open access model, en masse.

What is clear is that the need for open access, and the failure of the traditional model of scientific publishing to make full use of the internet's potential in this respect, are no longer issues of interest only to librarians or to activists These issues are now recognized to be important ones that all serious research institutions need to consider. The recent steps taken by Harvard and Berkeley show that universities are just as willing as research funders to take a stand on this issue. Open access is no longer just a nice idea, but is a concrete objective and over the course of 2008, the key focus will be not on rhetoric, but on the practical issues necessary to make wide-scale open access a reality.

Update: Here is the official announcement from Harvard 

Posted by Matthew Cockerill at 20:36    Comments (3)

 

Osteopathic Medicine and Primary Care celebrates its first birthday and looks to the future

To commemorate its first year of publication, the Editors-in-Chief of Osteopathic Medicine and Primary Care, John Licciardone and Roberto Cardarelli, have published an editorial detailing the progress of the journal  to date, and looking forwards the future.

The article comments on the benefits of open access for the community, current submission to publication times and plans to bring these down to 120 days in 2008, and invites readers to post comments on published articles. The Editors also detail information on journal fund they have established to assist with payment of the article-processing charge.

Osteopathic Medicine and Primary Care publishes articles on all aspects of osteopathic and allopathic treatment, as well as research relevant to the provision of primary care services.

Posted by Charlotte Hubbard at 12:54    Comments (2)

 

Signaling at spinal cord boundaries; a Journal of Biology minireview

The central and peripheral nervous systems of vertebrates are partitioned at specific points within the spinal cord, ensuring that the cell bodies of neurons from each system are not mixed, while still allowing axons to be connected. Previous studies have identified a transient population of cells responsible for this partitioning, termed boundary cap cells. The molecular mechanism of boundary cap formation and function is discussed in a recent minireview for Journal of Biology by Sophie Chauvet and Geneviève Rougon, highlighting two interesting studies published in Neural Development, which illustrate a role for semaphorin-plexin signaling in this process.

The role of semaphorin 6A (Sema6A) was determined by Bron et al. through the study of chick and mouse embryos deficient in either Semaphorin 6A or neuropilin-2. This study illustrates the importance of the interaction between these two molecules in preventing the exit of motor neuron cell bodies from the spinal cord, and identifies Plexin-A2 as a putative interacting partner in this signaling pathway. Using RNA interference, Bron et al. also demonstrate that MICAL3, expressed by motor neurons, is an essential downstream component of this signaling pathway in chick.

In a related study, Mauti et al. showed that depletion of Sema6A expression leads to the ectopic migration of motor neuron cell bodies, a phenotype mimicking the ablation of boundary cap cells. In contrast to the study by Bron et al., the authors identified Plexin-A1 or Plexin-A4, and not Plexin-A2, as candidate interacting molecules in this process. These important findings are discussed in the literature evaluation service, Faculty of 1000 (Biology).

In conjunction, these studies shed new light on the role of extracellular cues in establishing the positional identity of developing neuronal circuits. While the minireview in Journal of Biology highlights the important advance resulting from combining these findings, it also discusses the interesting discrepancies between the two studies.

Posted by Anna Webb at 11:45    Comments (0)

 

Neural Development joins the Neuroscience Peer Review Consortium

We are pleased to announce that Neural Development has joined the Neuroscience Peer Review Consortium (NPRC), enabling the more efficient handling of peer review between several neuroscience journals. 

The NPRC was instigated to reduce the time and effort involved in the peer review of original neuroscience research reports.  Under the new system, neuroscience journals with membership have agreed to accept manuscript reviews from other Consortium journals. By reducing the number of times that a manuscript is reviewed, the Consortium will increase the speed of publication of research results, and lessen the burden on both authors and reviewers alike.

To date, numerous neuroscience journals have joined the consortium, including Neuroscience, and Journal of Neuroscience, with many more, including BioMed Central’s Behavioral and Brain Functions, in the process of joining.  We hope that by joining the consortium, the already rapid peer review of Neural Development can be further streamlined, to the benefit of authors, reviewers, editors, and our readership.

Posted by Anna Webb at 12:43    Comments (0)

 

Open access and the developing world - read the latest

The Food and Agriculture Organisation (FAO) recently participated in The Berlin 5 meeting, Open Access: From Practice to Impact: Consequences of Knowledge Dissemination in Padova, Italy. Stefka Kaloyanova’s presentation acknowledged that research generated in developing countries is currently missing from the international knowledge base. Authors struggle to pay the financial fees associated with publication and have limited access to the internet. Katz suggests a number of initiatives, namely the International Information Systems for Agricultural Sciences and Technology (AGRIS) network which aims to build a common and freely accessible information system for science and technology in agriculture and related subjects. It was also recommended that open access is made mandatory in developing countries so that researchers can publish their research with ease.

The One Laptop Per Child (OLPC) initiative recently introduced its mission at the Indian National Convention for Librarians. The video presentation is now live. The OLPC campaign has been gaining momentum. Mass production of computers began in November 2007 and now Acer, Everex, Gigabyte and Lenovo have also pledged to produce cheaper laptops as part of the campaign.

The Satellite 2008 conference will be taking place in Washington during February.

Michail Bletsas will be joining Thomas Jacobson and Roland Burger for a workshop at the upcoming on 27 February entitled: “Low-cost satellite Internet infrastructure to support education in remote and developing regions.” The website states that exhibits-only registration is all that is needed if you would like to join in the discussion.  

The latest issue (vol. 10, no. 1, 2008) of Medicc Review is devoted to eHealth: Cuba Faces the Digital Divide and contains several useful articles. For example,  Conner Gorry’s feature looks at the issues developing countries are faced with, such as a high incidence of disease, lack of infrastructure, resource scarcity and limited knowledge-sharing, all of which hinder population growth. Nancy Sánchez Tarragó, MSc and J. Carlos Fernández Molina, PhD present a descriptive, cross-sectional study designed to determine the level of knowledge about and the attitudes toward open access journals among Cuban health researchers. The research concluded that there is little knowledge of open access journals and other open access movement terms and initiatives, and little use of open access as a publication means among these researchers.

On the topic of Cuba, Cameron Neylon’s blog, Open Science and the developing world: Good intentions, bad implementation?, discusses his recent trip to Cuba where he talked to scientists about the conditions they work under. Neylon notes:

'One of the strong arguments for Open Science (literature access, data, methods, notebooks) is that it provides access to scientists in less priviledged countries to both peer reviewed research as well as to the details of methodology that can enable them to carry out their science. I was therefore interested to see both what was available to them and whether they viewed our efforts in this area as useful or helpful. I want to emphasise that these people were doing good science in difficult circumstances by playing to their strengths and focussing on achievable goals. This is not second rate science, just science that is limited by access to facilities, reagents, and information.'

Furthermore, there is very limited access to subscriber-only literature and primary data. As such, open access seems to be the solution for these researchers, but Neylon acknowledges this comes with a catch:

'There are many real and potential benefits for scientists in the developing world if we move to more open styles of science communication. This is great, and I think it is a good argument for more openness. However there is a serious problem with the way we present this information and our reliance on modern web tools to do it. Its a very simple problem: bandwidth.'

The In Between The Lines author looks at the issues discussed in the recent North Carolina Scientific Blogging Conference, namely open science in the developing world. In this blog, the author addresses questions about the effects of a $100 laptop, how to improve the penetration of scientific information and how people in these countries find meaningful information on the web.

Posted by Charlotte Webber at 12:05    Comments (0)

 

Improving patient recruitment to clinical trials

Several articles recently published in Trials, BioMed Central's journal dedicated to investigating any aspect of the design, performance, and findings of randomized controlled trials, all explore the issue of improving patient recruitment to clinical trials. The five articles highlight a number of factors that can influence the often-challenging recruitment process.

Education
In their report of patient recruitment to the Women's International Study of long Duration Oestrogen after Menopause (WISDOM) trial, Paine et al., found that conducting group seminars with potential participants,  providing information about hormone therapy and the trial prior to a screening interview was a useful strategy for maximizing recruitment to this large, long-term trial.

Multi-centre collaboration
Rahbari and colleagues report that the establishment of a network of clinical trial centres with affiliated clinical sites improves integration and conduct of multi-centre randomized controlled trials, in a surgical setting.

Automated identification
In their case study, Dugas and colleagues found that routine hospital information system (HIS) data can support recruitment of suitable patients for inclusion in acute myeloid leukemia trials, identified by means of an automated notification workflow.

Targeted recruitment teams
Female students at 22 universities and further education colleges were recruited to a Chlamydia screening trial by female research assistants working in pairs. In their study, Atherton et al., concluded that the key to attaining recruitment targets was the enthusiasm of the research team.

Marketing
Francis and colleagues present a structured assessment framework, derived from the Medical Research Council's Corticosteroid Randomization after Significant Head injury (CRASH) trial, in setting out 12 factors that may affect the success of a clinical trial’s marketing activities, which can in turn have implications for patient recruitment and overall trial performance.

All articles are online and available open access:

Seminars may increase recruitment to randomised controlled trials: lessons learned from WISDOM
Bronwen J Paine, Nigel P Stocks, Alastair H MacLennan

A concept for trial institutions focussing on randomised controlled trials in surgery
Nuh N. Rahbari, Markus K. Diener, Lars Fischer, Moritz N. Wente, Peter Kienle, Markus W. Buchler, Christoph M. Seiler

Workflow to improve patient recruitment for clinical trials within hospital information systems - a case-study
Martin Dugas, Matthias Lange, Wolfgang E Berdel, Carsten Muller-Tidow

Recruitment of young women to a trial of chlamydia screening – as easy as it sounds?
Helen Atherton, Debbie Banks, Ruth Harbit, Linzie Long, Fiona Chadd, Phillip Hay, Sally Kerry, Ian Simms, Pippa Oakeshott

Marketing and clinical trials: a case study
David Francis, Ian Roberts, Diana R Elbourne, Haleema Shakur, Rosemary C Knight, Jo Garcia, Claire Snowdon, Vikki A Entwistle, Alison M McDonald, Adrian M Grant, Marion K Campbell

Trials is overseen by Doug Altman (United Kingdom), Curt Furberg (United States), Jeremy Grimshaw (Canada) and Peter Rothwell (United Kingdom), the Editors-in-Chief, and an expert editorial board. If you would like more information on the journal, please contact the editorial office.

Posted by Iain Hrynaszkiewicz at 16:24    Comments (1)