Research needed to prevent enrollment error

In a systematic review published this week in Trials, Simpson and colleagues investigate techniques and interventions to reduce inappropriate enrollment of patients into clinical trials. Key eligibility criteria ensure the exclusion of patients likely to be harmed by treatments, and enrollment of patients in violation of these criteria can result in avoidable harm including serious adverse events and death.

A systematic review of techniques and interventions for improving adherence to inclusion and exclusion criteria during enrolment into randomised controlled trials
Fiona Simpson, Elizabeth A Sweetman, Gordon S Doig
Trials 2010, 11:17 (23 February 2010)
[Abstract] [Provisional PDF]

A search of the literature uncovered only one abstract describing an intervention designed to reduce enrollment error - a dummy enrollment run-in phase that was found to be effective in reducing inappropriate enrollment during the actual clinical trial. As a first step to addressing the paucity of literature on this topic, Simpson et al recommend that authors report all protocol violations, including non-adherence to inclusion and exclusion criteria, within the primary results paper. However, given the serious potential implications, it is hard to ignore the authors' call for more research to identify and validate new techniques to reduce enrollment error.

Posted by Victoria Thompson at 16:37    Comments (0)

Predicting progression of Alzheimer's disease

The rate at which Alzheimer's disease progresses varies greatly between patients.  Clinicians are often asked by patients and their families to predict the rate of decline, however there is currently little data available to base such predictions on.  In research published in Alzheimer's Research & Therapy this week, Doody et al. have used a simple, calculated progression rate at initial visit to predict future performance of patients at assessments of cognition and activities of daily living.

Predicting progression of Alzheimer's disease
Rachelle S Doody, Valory Pavlik, Paul Massman, Susan D Rountree, Eveleen Darby, Wenyaw Chan
Alzheimer's Research & Therapy 2010, 2:2 (23 February 2010)
Abstract | Provisional PDF

Their research may have implications for research as well as the clinic.  Incorporating pre-progression rates into clinical trial design should enhance the power of such studies to find real treatment differences.  And their inclusion in trial design may reduce the duration of trials investigating disease-modifying treatments that could potentially benefit patients with this devastating condition.

Posted by Frances Mulvany at 14:48    Comments (0)

Neural Systems & Circuits is now accepting submissions!

 Neural Systems & Circuits, a new open access journal focusing on systems and computational neuroscience, is now accepting submissions.

Neural Systems & Circuits aims to publish exciting research on how individual neurons interact at the network level to perform interesting computations, and welcomes studies combining theory and experiment, reports of technical or analytical innovations and large-scale genetic or connectomic studies.

This new BioMed Central journal is overseen by co-Editors-in-Chief Peter Latham (Gatsby Computational Neuroscience Unit, UCL, UK) and Venkatesh Murthy (Harvard University, USA), who are supported by an expert Editorial Board

For more information on Neural Systems & Circuits, please visit the journal website or contact the Editorial Office. Why not register for updates keeping you abreast of any journal developments?

Submit your research to Neural Systems & Circuits, and take advantage of an efficient online submission process, rapid, high-quality peer-review service, and high visibility. There are no extra charges or limits on the number of color figures or videos you wish to include.

Posted by Emma Pettengale at 10:04    Comments (1)

Meet Professor Jean-Louis Vincent at ISICEM

The International Symposium on Intensive Care Medicine (ISICEM) is an annual event open to all intensivists and clinicians working in the critical care field, and is celebrating its 30-year anniversary this March. To mark this occasion, Critical Care is giving delegates a unique opportunity to meet Editor-in-Chief and ISICEM chairman Prof Jean-Louis Vincent, and ask him any question about the journal, and the critical care field.

To take part in this event, please contact ISICEM@ccforum.com to express your interest and submit your question to Prof Vincent. 

Critical Care Meet the Editor Event:

Thursday 11 March 2010

17:00 - 18:00pm

Room 211

Whether you're asking a question or listening to the answers, please come along and be a part of the debate.  Places will be limited however, so please contact us in advance to avoid disappointment.

Critical Care and BioMed Central will be exhibiting at ISICEM from the 9th -12th March, offering all delegates a free one-year subscription to the journal.  All research published in Critical Care is open access; reviews, commentaries and reports require a subscription.

Surayya Johar - In-house Editor Critical Care

Posted by Frances Mulvany at 08:48    Comments (0)

Pea aphid immune system genomics

Today an annotation of the pea aphid immune system has been published in Genome Biology by Nicole Gerardo and colleagues. This coincides with the publication of the draft pea aphid genome sequence from the International Aphid Genomics Consortium in PLoS Biology.

Due to its unusual process of metamorphosis the pea aphid provides interesting insights into insect development and, as a major vector of plant viruses and cause of crop damage, further understanding of pea aphid biology may lead to the development of control strategies. Pea aphids also display other fascinating biological properties, such as phenotypic plasticity, a lifecycle that alternates between parthenogenic and sexual reproduction, and they have co-evolved with symbiotic bacteria.

In their Genome Biology paper, which is also discussed in a Research Highlight in Genome Biology, Gerardo and colleagues perform an extensive manual annotation of the immune and stress response genes present in the pea aphid genome and they also analyse gene and protein expression in pathogen infected aphids to gain insights into how they respond to challenges to their immune system. They find that pea aphids lack many immune response genes found in other insect species and that their response to pathogen attack is more limited than in other insect species. These features may mirror those seen in other insects or they may be due to the unique biology of pea aphid and their relationship with symbiotic bacteria. Whatever the case turns out to be, the general view of insect immunity may not be as widely applicable as previously thought.

Posted by Emma Ralph at 18:02    Comments (0)

First articles published in Molecular Autism

The launch of Molecular Autism today provides autism researchers with a new forum for basic, translational and clinical study into the molecular basis of autism and related neurodevelopmental conditions.

In their lead editorial, Editors-in-Chief Joseph Buxbaum (Mount Sinai School of Medicine) and Simon Baron-Cohen (University of Cambridge) present Molecular Autism’s mission statement.  The journal’s unique molecular focus is key to identifying the fundamental determinants of autism and achieving one of our primary goals – correcting the bias towards psychological study that has characterized the past 60 years of autism research. Through Molecular Autism, the Editors hope to tackle the multi-level complexity of autism and related syndromes by engendering greater integration across scientific disciplines including genetics, molecular neurobiology, neuropathology and imaging.

Two research articles also published today include an epidemiological study that provides evidence for an association between paternal age and autism risk in an Iranian population sample, and a genome wide linkage analysis of repetitive behavioral phenotypes.

In the next few months, Molecular Autism will continue to publish high quality, original research and provide a platform for topical debates and comprehensive reviews. You can keep up to date with new content published in Molecular Autism by signing up to receive regular article alerts when new research is published.

Posted by Victoria Thompson at 15:51    Comments (1)

Beyond the Genome – a BioMed Central conference

Today BioMed Central announces the launch of ‘Beyond the Genome: The true gene count, human evolution and disease genomics’, an international conference which brings together leading researchers and industry representatives from around the globe.

The conference, organised by BioMed Central, marks Genome Biology’s 10th anniversary and the recent launch of its sister journal Genome Medicine.

At the conference, internationally renowned researchers will deliver cutting edge presentations in key areas of post-genomic research in biology and medicine and future developments, including the Human Microbiome Project and the resequencing of matched tumour and normal genomes from specific types of cancers.

The event is taking place between 11-13 October 2010 in Boston, Massachusetts. The organising committee includes Elaine Mardis from the Washington University School of Medicine and Steven Salzberg of the University of Maryland.

All participants are invited to submit abstracts for oral and poster presentations. A significant number of talks will be selected from registrants.

For up to the minute news, follow us on Twitter (@biomedcentral) or search for #BTG2010

Posted by Charlotte Webber at 17:58    Comments (0)

Journal of Medical Case Reports - 1000 cases in three years

The Journal of Medical Case Reports (JMCR) last week published its 1000th case report. This coincides with the anniversary of the journal's launch three years ago, in February 2007. We would like to thank all our authors, reviewers and Editorial Board members, whose continued support of the journal has been essential in reaching this milestone.

With 1000 cases across all medical disciplines it may be too soon to challenge established evidence-based medicine practices with published "experiences", but the growth of the journal surely challenges traditionally-held views about the place of case reports in the literature. It also  reinforces the need for case reporting as a catalyst for clinical hypothesis and experimental research, and the value of case reports as a source of information and training tools for clinicians.

And in their - JMCR's 1000th - case report, Tofigh and colleagues describe the successful treatment of thoracoabdominal aortic aneurysm using an endovascular stent.

Endovascular treatment of thoracoabdominal aortic aneurysm: a case report
Arash Mohammadi Tofigh, Massoud Ghasemi, Babak Heidari Aghdam, Mersedeh Karvandi, Afsoon Kaboli
Journal of Medical Case Reports 2010, 4:37 (2 February 2010)
[Abstract] [Provisional PDF]

Posted by Victoria Thompson at 14:50    Comments (0)

Multiple microRNAs muscle in on diabetes – research in Genome Medicine

Muscle mRNA expression is invariant with respect to diabetes status, but coordinated changes in numerous microRNAs may control protein abundance and affect skeletal muscle insulin resistance, according to research recently published in Genome Medicine.

Muscle insulin resistance is a condition characterised by normal levels of insulin but a reduction in muscle glucose uptake, which can lead to high blood glucose concentration and is a contributing factor in type 2 diabetes.

In their article “Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in Type 2 Diabetes”, James Timmons and colleagues report a study in which they used gene-chips to examine mRNA and miRNA levels in patients with type 2 diabetes compared to healthy controls.  They found that protein-coding gene expression showed no significant differences, whereas the levels of many miRNAs were altered in disease.  Their analyses suggest that these miRNAs work in concert to affect protein abundance, and their dysregulation may consequently lead to changes in skeletal muscle insulin resistance.

Dysregulation of miRNAs is known to play a part in cancer and vascular disease, but their significance in many other complex diseases is not well understood. This study indicates that miRNAs may have an important role in diabetes, and the authors say that they may be used as diagnostic markers of insulin resistance status in the future.

Rebecca Furlong
Assistant Editor, Genome Medicine

Posted by Rebecca Furlong at 17:06    Comments (0)

Barcoded libraries for 454 sequencing

In a paper recently published in Genome Biology, Robert Nicol and colleagues from the Broad Institute in Massachusetts, report a new method for reducing the time and cost associated with 454 sequencing.

The recent revolution in next-generation sequencing technologies impacted significantly on the genomics field, dramatically reducing the cost of sequencing large genomes, such as those of mammals – the recently published giant panda genome was sequenced entirely using Illumina short-read sequence data.  However, this reduction in cost is less apparent for small or medium-sized genomes, where to run a single lane or channel on a sequencer would result in a vast over-coverage of sequence data, reducing the cost-effectiveness of the process.  In addition, manual preparation of the DNA library prior to sequencing is labour-intensive and time consuming, and also introduces the possibility of researcher error, all of which increases the overall cost.  

The new paper describes the optimization of a series of methods for sample preparation and introduces a new technique for adding short ‘barcode’ sequences to the start of the DNA fragments.  This allows each DNA library to be identified uniquely, meaning more than one library can be mixed together and run on the same sequencer channel, bringing the cost of sequencing several smaller genomes within the reach of labs with smaller budgets.  These new technologies should result in a further increase in the rate at which new genomes are being sequenced.

Posted by Elisabeth Gaskell at 13:46    Comments (0)

The right to adequate pain treatment-new debate in BMC Medicine

In the developed world, we generally tend to take pain treatment and management for granted; if we’re in physical pain, someone will provide treatment to do something about it.  It’s easy to lose sight of the fact that this is not neccessarily true across the globe.  In a new debate published in BMC Medicine, Lohman and colleagues, from Human Rights Watch examine the issues related to access to adequate pain treatment, and why barriers to pain treatment can be tantamount to a violation of human rights.
 
Check out the full article: “Access to pain treatment as a human right”, and while you’re visiting BMC Medicine, why not sign up for article alerts, which will keep you up to date on the latest general medical and clinical research.

Posted by Robin Cassady-Cain at 10:00    Comments (1)

GOseq – a new method for Gene Ontology analysis of RNA-seq data

Until recently, microarrays have been the method of choice for transcriptional profiling.  The advent of next generation sequencing technologies however has seen the rise of direct sequencing of mRNA (RNA-seq) as a new method for such profiling.  In a recent publication in Genome Biology, Alicia Oshlack and colleagues at the Walter and Eliza Hall Institute in Melbourne, Australia have developed a new method for performing Gene Ontology analysis of RNA-seq data, called GOseq.
 
GOseq identifies whether a given transcriptional profile is over-represented with transcripts associated with specific biological processes. Up until now, statistical methods, such as this, used for analysing RNA-seq data have generally been modifications of methods developed for use with microarray data.  Oshlack, however, shows that statistical methods are not interchangeable between the two techniques; in particular, there is a bias inherent in RNA-seq data whereby highly-expressed transcripts are more likely to be called as being differentially expressed compared with short or less highly-expressed genes.  The GOseq algorithm takes this into account, thus correcting the bias and providing a more reliable readout.  As well as providing a useful new tool, this paper highlights the need for new statistical analysis techniques tailored specifically for the new technology of RNA-seq.
 
Given the extent to which RNA-seq is being embraced by the genomics community, for example in defining alternative transcripts, this method is a welcome addition to a growing field.
 

Posted by Andrew Cosgrove at 16:44    Comments (0)

UK government adopts Creative Commons licenses for open data: good news for public-sector researchers publishing in open access journals

The UK government has in recent years made significant amounts of government data openly available for reuse.  They Work for You is an example of a website which creatively reuses data on UK parliamentary activity,  and its parent organization, MySociety, has played an important role in encouraging the UK government towards opening up more data.

The latest development in UK government open data sharing is the launch of data.gov.uk, launched in beta test form last month , which “provides a single access point to over 2,500 central government datasets that have been made available for free re-use”.

Buried in the small print of this announcement is an important change, with significant implications for open access publishing in the UK. This change is the adoption of Creative Commons-compatible licensing for UK government open content.

Up until now, open data  from the UK government was licensed via the Office of Public Sector Information’s ‘Click Use’ license scheme. The Click Use model required any potential users or distrubutors of the data to first request their own ‘Click Use’ license from the UK government website, in order to gain permission to reuse the data.

In contrast musicians, artists and other creators around the world who wish to share content openly while reserving some rights have increasingly standardized on the use of  Creative Commons licenses, which do not require any such license request to be made.

BioMed Central, like many other open access publishers, uses the Creative Commons Attribution License, which requires only that the original version of the work should be correctly attributed when the work or any part of it is reused.

Until now, because work carried out by researchers at UK government agencies is often covered by ‘Crown Copyright’, and because Crown Copyright is legally distinct from the normal Copyright law, the applicability of Creative Commons licenses to such work has been in question. As a result, special license wording has in some cases been necessary for such articles published in BioMed Central journals, in order to indicate that they can be reused only under the ‘Click use’ scheme. This had the potential to cause delays for authors and confusion for readers.

The good news is that the announced intention of OPSI to move away from ‘Click Use’ licensing towards Creative Commons-compatible licensing over the coming months should entirely solve this problem, making life easier for all concerned.

It also provides an important precedent for dealing with similar challenges in other (rather arcane) areas of copyright law. For example, the World Health Organization and other supra-national bodies do not recognize national jurisdictions, which causes similar challenges for Creative Commons licensing to those caused by Crown Copyright,  and requires similar workarounds via special-case license wording. BioMed Central is hopeful that a Creative Commons-compatible licensing scheme specifically designed for such supra-national bodies will soon resolve this and we are working with WHO and Creative Commons towards such a solution.

Posted by Matthew Cockerill at 16:26    Comments (0)