BioJava: an open-source framework for bioinformatics.

SUMMARY: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. AVAILABILITY: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

The Ensembl genome database project.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Red cell exchange, erythrocytapheresis, in the treatment of malaria with high parasitaemia in returning travellers.

In severe falciparum malaria with high parasitaemia, removal of parasitized erythrocytes is generally considered to be of value as adjunctive therapy in addition to standard chemotherapy. Such removal is commonly achieved by exchange transfusion but this procedure is time-consuming and may be associated with haemodynamic disturbance. Current-generation automated cell-separator hardware and software allows prompt red cell exchange, erythrocytapheresis, in a single continuous-flow isovolaemic procedure. We describe the application of this procedure to 5 cases of severe falciparum malaria in travellers returning to the UK from the tropics. All patients also received quinine and conventional supportive therapy. In all cases, dramatic reduction in parasitaemia was achieved within 2 h with subsequent complete clinical recovery. Erythrocytapheresis has significant advantages over exchange transfusion in terms of speed, efficiency, haemodynamic stability and retention of plasma components such as clotting factors and may thus represent an improvement in adjunctive therapy for severe malaria.

Automated erythrocytapheresis in the treatment of severe falciparum malaria.

Removal of parasitized erythrocytes is generally considered to be of value as adjunctive therapy in severe falciparum malaria with high parasitaemia. This is commonly achieved by exchange transfusion. We describe three cases of severe falciparum malaria treated by automated erythrocytapheresis (red cell exchange) in addition to quinine and conventional supportive therapy. Erythrocytapheresis consists of removal of the red-cell fraction by apheresis. Plasma, leukocyte and platelet fractions are returned to the patient. In all cases, dramatic reduction in parasitaemia was achieved within 2 h with subsequent complete clinical recovery. Erythrocytapheresis has significant advantages over exchange transfusion in terms of speed, efficiency, haemodynamic stability and retention of plasma components such as clotting factors and may thus represent an improvement in adjunctive therapy for severe malaria.

Parental perceptions regarding healthy behaviours for preventing overweight and obesity in young children: a systematic review of qualitative studies.

Evidence is increasingly pointing towards the importance of early life strategies to prevent childhood overweight and obesity. This systematic review synthesizes qualitative research concerning parental perceptions regarding behaviours for preventing overweight and obesity in young children. During May and June 2008, a range of electronic databases were searched and together with lateral searching techniques 21 studies were identified for review. Data extraction and synthesis using thematic content analysis revealed six organizing and 32 finer level themes. These related to child factors, family dynamics, parenting, knowledge and beliefs, extra-familial influences and resources and environment. Themes were mapped to a socioecological model which illustrated how factors at individual, interpersonal, community, organizational and societal levels interact in complex ways to impact on parental perceptions about healthy behaviours for preventing child overweight. Although parents suggested several ideas to promote healthy child weight-related behaviours, many of their views concerned perceived barriers, some of which may be amenable to practical intervention. Furthermore, intergenerational influences on parental health beliefs and knowledge suggest that health promotion strategies may be more effective if directed at the wider family, rather than parents alone. Significantly, many parents believed strategies to promote healthy weight should start early in a child's life.

A browser for expression data.

SUMMARY: We have written a fully extensible Java application for visually browsing expression data, and clusters of genes or experimental conditions calculated from that data. The application requires a run-time environment for Java2. AVAILABILITY: http://www. sanger.ac.uk/Users/mrp/java/ExpressionBrowser

SPEM: a parser for EMBL style flat file database entries.

SUMMARY: We present a set of Perl modules for the flexible and robust parsing and editing of EMBL/SWISS-PROT databases. AVAILABILITY: The Web page at http://www.sanger.ac. uk/Software/PerlModule/ provides information about downloading the SPEM and PrEMBL modules, and provides links to documentation and example code.

Automated red cell exchange in sickle cell disease.

Red cell exchange is important in the care of acutely ill sickle-cell patients, and may be life-saving. An automated red cell exchange technique has been developed using a Baxter blood cell separator, enabling an isovolaemic exchange to be performed within 2.5 h. A total of 20 procedures have been performed in 15 patients, including one woman in the third trimester of pregnancy, with a mean decrease of 72% in the circulating sickle haemoglobin (HbS) level. This method enables almost all adult patients with sickle cell anaemia to have their HbS reduced to safe levels by only one procedure. The procedure was well tolerated by all patients, including those who were acutely ill. This technique provides an effective procedure for reducing the percentage of circulating HbS rapidly in acutely ill patients with complications of sickle cell anaemia.

Patterns of infection by Salmonella and Yersinia spp. in commensal house mouse (Mus musculus domesticus) populations.

AIMS: This study sought to examine the risk posed by house mice transmitting pathogens to livestock on typical mixed-agriculture farms in the UK. METHODS AND RESULTS: In a 10-month longitudinal study at one farm, 222 faecal samples were taken from mice and 57 swabs from the farm environment; 3.2% and 15.8%, respectively, were positive for Yersinia. Seventy-five intestinal samples were taken from house mice from three other farms and 9.3% were positive for Yersinia. The commonest species was Y. enterocolitica (of a wide range of serotypes); all isolates were non-pathogenic, except one of Y. pseudotuberculosis. Salmonella was not isolated from any sample. CONCLUSION: This study provides additional evidence that house mice are generally not significant vectors of either pathogenic Yersinia strains or Salmonella species. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first longitudinal study of Yersinia in any small mammal population, and shows infection to be a dynamic series of generally non-pathogenic, transient infections.

Report on slide session, British Society for Haematology, 43rd Annual Scientific Meeting, Glasgow, 2003.

Seven patients who had a diagnostic problem were presented at the British Society for Haematology, Annual Scientific Meeting in 2003. The likely diagnosis was discussed on the basis of a synopsis of the history and blood film and trephine biopsy features and forms the basis of this report. Diagnostic problems dealt with included lymphoproliferative and myeloproliferative disorders and haemolytic anaemia.