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Background\ud \ud BC2001, the largest randomised trial of bladder-sparing treatment for muscle-invasive bladder cancer, demonstrated improvement of local control and bladder cancer–specific survival from the addition of concomitant 5-fluorouracil and mitomycin C to radiotherapy.\ud \ud \ud \ud Objective\ud \ud To determine the impact of treatment on the health-related quality of life (HRQoL) of BC2001 participants.\ud \ud \ud \ud Design, setting, and participants\ud \ud 458 UK patients with T2-T4a N0 M0 transitional cell carcinoma of the bladder.\ud \ud \ud \ud Intervention\ud \ud Patients were randomised to the chemotherapy comparison (radiotherapy, 178, or chemoradiotherapy, 182); and/or to the radiotherapy comparison (standard, 108, or reduced high-dose volume radiotherapy, 111).\ud \ud \ud \ud Outcome measurements and statistical analysis\ud \ud Patients completed Functional Assessment of Cancer Therapy—Bladder (FACT-BL) questionnaires at baseline, end of treatment (EoT), and 6, 12, 24, 36, 48, and 60 months after radiotherapy. The primary endpoint was change from baseline in the bladder cancer subscale (BLCS) at 12 months.\ud \ud \ud \ud Results and limitations\ud \ud Data were available for 331 (92%) and 204 (93%) participants at baseline and for 192 (54%) and 114 (52%) at 12 months for the chemotherapy and radiotherapy comparisons, respectively. HRQoL declined at EoT (BLCS –5.06 [99% confidence interval: –6.12 to –4.00, p < 0.001]; overall FACT-B TOTAL score –8.22 [–10.76 to –5.68, p < 0.01]), recovering to baseline at 6 months and remaining similar to baseline subsequently. There was no significant difference between randomised groups at any time point.\ud \ud \ud \ud Conclusions\ud \ud Immediately following (chemo)radiotherapy, a significant proportion of patients report declines in HRQoL, which improve to baseline after 6 months. Two-thirds of patients report stable or improved HRQoL on long-term follow-up. There is no evidence of impairment in HRQoL resulting from the addition of chemotherapy.\ud \ud \ud \ud Patient summary\ud \ud Quality of life of bladder cancer patients treated with radiotherapy ± chemotherapy deteriorates during treatment, but improves to at least pretreatment levels within 6 months. Addition of chemotherapy to radiotherapy does not affect patient-reported quality of life.

Invasive group A s treptococcal infection has a 15% case fatality rate and a risk of secondary transmission. This retrospective study us ed two national data sources from England ; enhanced surveillance ( 2009) and a case management system ( 2011 - 13) to identify clusters of sever e group A streptococcal disease . 2 4 household pairs were identified. The median onset interval between cases was 2 days (range 0 - 28) with simultaneous onset in 8 pairs . The attack rate during the 30 days after first exposure to a primary case was 4 52 0 per 100000 person - years at risk (95% CI 2 900 - 673 0 ) a 19 40 ( 12 40 - 28 80 ) fold elevation over the background incidence . The theoretical number needed to treat ( NNT ) to prevent one secondary case using antibiotic prophylaxis was 2 71 ( 194 - 454 ) overall, 50 for mother - neonate pairs ( 2 7 - 3 93 ) and 8 2 for couples aged 75 years and over ( 46 - 417 ). Whilst a dramatic increased risk of infection was noted in all household contacts, increased ris k was greatest for mother - neonate pairs and couples aged 75 and over , suggesting targeted prophylaxis c ould be considered. Offering prophylaxis is challenging due to the short time interval between cases emphasising the importance of immediate notification and assessment of contacts .

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence-related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from

SummaryHigh throughput genomic studies can identify large numbers of potential candidate genes, which must be interpreted and filtered by investigators to select the best ones for further analysis. Prioritization is generally based on evidence that supports the role of a gene product in the biological process being investigated. The two most important bodies of information providing such evidence are bioinformatics databases and the scientific literature. In this paper we present an extension to the Ondex data integration framework that uses text mining techniques over Medline abstracts as a method for accessing both these bodies of evidence in a consistent way. In an example use case, we apply our method to create a knowledge base of Arabidopsis proteins implicated in plant stress response and use various scoring metrics to identify key protein-stress associations. In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone. Ondex is an open-source software project and can be downloaded, together with the text mining features described here, from www.ondex.org.

SummaryThe automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.

The APPLAUSE ESPRIT Project is building major applications using the ElipSys parallel constraint logic programming system developed at ECRC. Two major aims of the project are to advance the state of the art in four commercially significant application areas and to promote the use of ElipSys-like languages among applications developers. This brief paper gives an outline of ElipSys and an overview of the applications being developed within the APPLAUSE Project. © Springer-Verlag Berlin Heidelberg 1993.