Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

<p>Abstract</p> <p>Background</p> <p>The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components.</p> <p>Results</p> <p>We compared over 3,000 PB2 protein sequences of human-transmissible and avian isolates, to produce a catalogue of sites involved in adaptation to human-to-human transmission. This analysis identified 17 characteristic sites, five of which have been present in human-transmissible strains since the 1918 Spanish flu pandemic. Sixteen of these sites are located in functional domains, suggesting they may play functional roles in host-range specificity. The catalogue of characteristic sites was used to derive sequence signatures from historical isolates. These signatures, arranged in chronological order, reveal an evolutionary timeline for the adaptation of the PB2 protein to human hosts.</p> <p>Conclusion</p> <p>By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful tool for comparative characterization of sequence sets. In addition to confirming previously reported findings, several novel characteristic sites within PB2 are reported. Sequence signatures generated using the characteristic sites catalogue characterize concisely the adaptation characteristics of individual isolates. Evolutionary timelines derived from signatures of early human influenza isolates suggest that characteristic variants emerged rapidly, and remained remarkably stable through subsequent pandemics. In addition, the signatures of human-infecting H5N1 isolates suggest that this avian subtype has low pandemic potential at present, although it presents more human adaptation components than most avian subtypes.</p

Animal health aspects of adaptation to climate change: beating the heat and parasites in a warming Europe

Weather patterns in northern European regions have changed noticeably over the past several decades, featuring warmer, wetter weather with more extreme events. The climate is projected to continue on this trajectory for the foreseeable future, even under the most modest warming scenarios. Such changes will have a significant impact on livestock farming, both directly through effects on the animals themselves, and indirectly through changing exposure to pests and pathogens. Adaptation options aimed at taking advantage of new opportunities and/or minimising the risks of negative impacts will, in themselves, have implications for animal health and welfare. In this review, we consider the potential consequences of future intensification of animal production, challenges associated with indoor and outdoor rearing of animals and aspects of animal transportation as key examples. We investigate the direct and indirect effects of climate change on the epidemiology of important livestock pathogens, with a particular focus on parasitic infections, and the likely animal health consequences associated with selected adaptation options. Finally, we attempt to identify key gaps in our knowledge and suggest future research priorities.</p

The fire safety of TV set enclosure materials, a survey of European statistics

The composition of enclosure materials used in many TV sets sold on the European market has changed significantly since the early 1990s. To determine the potential impact of this change on TV fire safety, a review of European and US TV set fire statistics has been carried out. TV set fires can have internal electrical causes due to faults not apparent at the time of manufacture, simple wear and tear, or a variety of external causes. Recent detailed statistics suggest that about one third of all TV fires are due to external ignition. Available data show that the significant drop in the rate of TV set fires experienced in Europe during the 1980s is not continuing today. In fact, the rate appears to be increasing in some countries, such as the UK and Sweden. The number of TV set fires in Europe is estimated as 100 fires per million TV sets per year due to internal ignition sources, at least an order of magnitude higher than in the USA where the fire safety classifications for TV set enclosure materials has been historically high. TV set fires have a dramatic impact on life and property. To avoid an increase in TV set fires, fire safety requirements should be increased, and public awareness of the importance of fire safety in TVs heightened. Copyright (C) 2000 John Wiley & Sons, Ltd

Mycobacterium tuberculosis genome-wide screen exposes multiple CD8(+) T cell epitopes

Mounting evidence suggests human leucocyte antigen (HLA) class I-restricted CD8(+) T cells play a role in protective immunity against tuberculosis yet relatively few epitopes specific for the causative organism, Mycobacterium tuberculosis, are reported. Here a total genome-wide screen of M. tuberculosis was used to identify putative HLA-B*3501 T cell epitopes. Of 479 predicted epitopes, 13 with the highest score were synthesized and used to restimulate lymphocytes from naturally exposed HLA-B*3501 healthy individuals in cultured and ex vivo enzyme-linked immunospot (ELISPOT) assays for interferon (IFN)-γ. All 13 peptides elicited a response that varied considerably between individuals. For three peptides CD8(+) T cell lines were expanded and four of the 13 were recognized permissively through the HLA-B7 supertype family. Although further testing is required we show the genome-wide screen to be feasible for the identification of unknown mycobacterial antigens involved in immunity against natural infection. While the mechanisms of protective immunity against M. tuberculosis infection remain unclear, conventional class I-restricted CD8(+) T cell responses appear to be widespread throughout the genome