PDB_REDO: automated re-refinement of X-ray structure models in the PDB

The majority of previously deposited X-ray structures can be improved by applying current refinement methods

The EMBRACE web service collection

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definition

Adoption of Electronic Personal Health Records in Canada: Perceptions of Stakeholders

Background: Healthcare stakeholders have a great interest in the adoption and use of electronic personal health records (ePHRs) because of the potential benefits associated with them. Little is known, however, about the level of adoption of ePHRs in Canada and there is limited evidence concerning their benefits and implications for the healthcare system. This study aimed to describe the current situation of ePHRs in Canada and explore stakeholder perceptions regarding barriers and facilitators to their adoption. Methods: Using a qualitative descriptive study design, we conducted semi-structured phone interviews between October 2013 and February 2014 with 35 individuals from seven Canadian provinces. The participants represented six stakeholder groups (patients, ePHR administrators, healthcare professionals, organizations interested in health technology development, government agencies, and researchers). A detailed summary of each interview was created and thematic analysis was conducted. Results: We observed that there was no consensual definition of ePHR in Canada. Factors that could influence ePHR adoption were related to knowledge (confusion with other electronic medical records [EMRs] and lack of awareness), system design (usability and relevance), user capacities and attitudes (patient health literacy, education and interest, support for professionals), environmental factors (government commitment, targeted populations) and legal and ethical issues (information control and custody, confidentiality, privacy and security). Conclusion: ePHRs are slowly entering the Canadian healthcare landscape but provinces do not seem wellprepared for the implementation of this type of record. Guidance is needed on critical issues regarding ePHRs, such as ePHR definition, data ownership, access to information and interoperability with other electronic health records (EHRs). Better guidance on these issues would provide a greater awareness of ePHRs and inform stakeholders including clinicians, decision-makers, patients and the public. In turn, it may facilitate their adoption in the country

A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis

Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5′RACE-derivative method coined ‘5′tagRACE’, to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5′tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5′tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin–antitoxin modules

Operational Research: Methods and Applications

Throughout its history, Operational Research has evolved to include a variety of methods, models and algorithms that have been applied to a diverse and wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first aims to summarise the up-to-date knowledge and provide an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion. It should be used as a point of reference or first-port-of-call for a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order