Molecular classification for biliary atresia

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A molecular signature for biliary atresia classifies samples into inflammation or fibrosis stages at diagnosis and will be valuable for personalized clinical management of this disease, according to research recently published in Genome Medicine.

Biliary atresia is a blockage or absence of the bile duct usually diagnosed soon after birth.  The cause of this condition is not well understood, but the management of the resulting liver fibrosis is well-studied due to its importance for prognosis.  In their study ‘Staging of biliary atresia at diagnosis by molecular profiling of the liver‘, Jorge Bezerra and colleagues asked whether liver gene expression levels at diagnosis could be used to predict disease severity, the response to surgical reconstruction of the bile duct …

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BioMed Central launches Japan Gateway

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BioMed Central has recently launched a Japan Gateway, bringing together resources and information from researchers across Japan as well as highlighting high-impact research from the region.

The Japan Gateway also hosts a new brochure (available in both Japanese and English), which demonstrates the benefits of publishing in open access journals. Profiles of highly respected scientists who have chosen to publish with us, including Masahiro Fujii and Yoshihide Hayashizaki, are also featured. The gateway also provides details of our journals with affiliations to Japanese societies:

BioPsychoSocial Medicine, the official journal of the Japanese Society of Psychosomatic Medicine
Sports Medicine, Arthroscopy, Rehabilitation, Therapy & Technology, the official journal of the Japanese Orthopaedic Society for of Knee, Arthroscopy …

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The real difference between me and you: a map of structural variation in the human genome

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As we have been told many times since the publication of the human genome, the age of personal genomics is upon us. However, the vast difference between one human genome and the next, in the form of single nucleotide polymorphisms (SNPs) or other structural variations, is only just becoming apparent with the sequencing of more personal genomes.

In this month’s issue of Genome Biology, Steven Scherer and colleagues present a new map of the structural variation in the human genome.

This map presents more detail on structural variations, such as copy number variations (CNVs), insertions and deletions (indels), inversions and SNPs than ever before. The authors detected over 12,000 structural variants, impacting nearly 5,000 genes, that were not detected …

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Sequence periodicity discovered in human genome

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In an article just published in Genome Biology, Charles Hebert and Hugues Roest Crollius of the Ecole Normale Supérieure in Paris have shown the existence of a novel periodicity of nucleotide frequencies in the human genome that may have implications for the positioning of nucleosomes and gene regulation.

In their study, Hebert and Roest Crollius have aligned human genes relative to their transcription start sites and observe a pattern of YY dinucleotides (where Y is either C or T) spaced 10 base pairs apart in phase with the transcription start site. Importantly, analysis of nucleosome-positioning data shows that the nucleosomes are associated with the dinucleotides. The pattern is enriched in genes with binding sites for the EP300 nucleosome-modelling …

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Diagnosing Alzheimer’s disease – how good is neuropathology?

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Advances in clinical diagnostics, such as neuroimaging, as well as the development of new biomarkers, have raised questions as to whether neuropathological assessment is both accurate and specific enough to diagnose Alzheimer’s disease (AD).  Two articles published last week in Alzheimer’s Research & Therapy address this issue and make up a pro/con debate discussing whether neuropathology can confirm the exact diagnosis of AD.

Arguing the case for, Margaret Esiri stresses that neuropathology is still the gold standard by which to reach a reliable diagnosis of AD and suggests that because diseases change and evolve over time, only this tool is in a position to provide a concrete distinction between pathological processes.  Esiri acknowledges that novel clinical diagnostics will …

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Trials publishes first extended protocol

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Yesterday, Trials published a substantially extended version of Zinkstok and colleagues’ protocol for a randomized controlled trial of a new combination therapy for ischemic stoke, which was originally published in Cerebrovascular Diseases. In this extended protocol, the authors expand upon key methodological elements of their study, giving full details of enrollment procedures, outcome measures and planned statistical analyses as well as providing example data collection forms as additional files.

A
randomised controlled trial of antiplatelet therapy in combination with
Rt-PA thrombolysis in ischemic stroke: rationale and design of the
ARTIS-Trial

S M Zinkstok, M Vermeulen, J Stam, R J de Haan, Y B Roos, Artis Study group
Trials 2010, 11:51 (12 May 2010)

Transparency and completeness …

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Canine vector-borne diseases – a new thematic series

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Parasites & Vectors has published a thematic
series
grouping together a number of
articles recently presented at a symposium on canine vector-borne diseases
(CVBDs) in New York in April 2010.

 The aim of the
5th Symposium
on Canine Vector-Borne Diseases, sponsored by Bayer Animal Health GmbH, was to
facilitate the advancement of understanding in the diversity and prevalence of
canine vector-borne diseases, and their significance for veterinary and public
health.

 The articles address
a number of such diseases, looking at the biological interactions between
ectoparasite, pathogen and host, as well as their distribution across the
globe. Contributions to the thematic series, edited by Chris Arme, include
original research articles, alongside several reviews and short reports.

 If you …

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On its 10th anniversary Ensembl publishes a thematic series with the BMC-series

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The last 15 years has seen an explosion in genomic
research and sequenced genomes. With the build up to sequencing larger chordate
genomes it became very clear that manually annotating the billion base pairs of
sequence produced was not practical and automated annotation systems were
required. Several large organisations have helped address this issue, but the
Ensembl project, a joint venture between
the European Bioinformatics Institute and the Wellcome Trust Sanger Institute,
has in particular provided high-quality integrated annotation on vertebrate
genomes within a consistent and open source infrastructure. This year marks the
10th anniversary of the Ensembl project’s launch, and BioMed
Central is today publishing …

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Bona fide ancient DNA sequence from Neandertal bone

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An article published in Genome Biology assesses the pitfalls of sequencing ancient DNA and presents a new approach for improved identification of ancient DNA sequences.

The DNA sequence of extinct species are of enormous value in determining evolutionary relationships to living species. However, ancient DNA from fossil is notoriously difficult to sequence due to the presence of bacterial contamination and DNA damage. Kay Prüfer and colleagues at the Max-Planck Institute for Evolutionary Anthropology investigated the biases inherent in short read sequencing of ancient DNA samples with an analysis of Neandertal (Homo neanderthalensis) DNA, generated as part of the Neandertal genome project, from 38,000-year-old fossil bone. The full draft Neandertal genome sequence is published today in Science

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Introducing the Open Data Award

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In recognition of the fact that science publishing now goes beyond the traditional journal article, we have teamed up with Microsoft Research and Panton Principles to introduce the Open Data Award as part of our 4th Annual Research Awards. Data sharing, its preservation and re-use, is an increasingly important part of the research and publication process. But there are many challenges associated with openly sharing scientific data, particularly when sharing goes against cultural or community norms. 

The Open Data Award celebrates researchers who have published in any of our 207 journals during 2009 and have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data.

We are honoured that Peter Murray-Rust, Cameron Neylon, Rufus …

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