Proteomic analysis of circulating immune complexes in juvenile idiopathic arthritis reveals disease-associated proteins

Juvenile idiopathic arthritis reflects a group of clinically heterogeneous arthritides hallmarked by elevated concentrations of circulating immune complexes. In this study, the circulating immune complex proteome was examined to elucidate disease-associated proteins that are overexpressed in patients with an aggressive, and at times destructive, disease phenotype. To solve this proteome, circulating immune complexes were isolated from the sera of patients with chronic, erosive or early-onset, aggressive disease and from patients in medical remission or healthy controls subsequent to protein separation by 2-DE. Thirty-seven protein spots were overexpressed in the circulating immune complexes of the aggressive disease groups as compared to controls, 28 of which have been confidently identified to date. Proteolytic fragments of glyceraldehyde-3-phosphate dehydrogenase, serotransferrin, and a-1-antitrypsin have been identified among others. In total, these 28 putative disease-associated proteins most definitely contribute to immune complex formation and likely have a significant role in disease etiology and pathogenesis. Moreover, these proteins represent markers of aggressive disease, which could aid in diagnosis and management strategies, and potential therapeutic targets to prevent or control disease outcome. This is the first in-depth analysis of the circulating immune complex proteome in juvenile idiopathic arthritis.

Transcriptome analysis of a parasitic clade V nematode:comparative analysis of potential molecular anthelmintic targets in Cylicostephanus goldi

Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generated, which were assembled into 26,910 contigs. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, 27% of the transcriptome was annotated. Further in-depth analysis was carried out by comparing the C. goldi dataset with the next generation transcriptomes and genomes of other clade V nematodes, with the Oesophagostomum dentatum transcriptome and the Haemonchus contortus genome showing the highest levels of sequence identity with the cyathostomin dataset (45%). The C. goldi transcriptome was mined for genes associated with anthelmintic mode of action and/or resistance. Sequences encoding proteins previously associated with the three major anthelmintic classes used in horses were identified, with the exception of the P-glycoprotein group. Targeted resequencing of the glutamate gated chloride channel α4 subunit (glc-3), one of the primary targets of the macrocyclic lactone anthelmintics, was performed for several cyathostomin species. We believe this study reports the first transcriptome dataset for an equine helminth parasite, providing the opportunity for in-depth analysis of these important parasites at the molecular level. Sequences encoding enzymes involved in key processes and genes associated with levamisole/pyrantel and macrocyclic lactone resistance, in particular the glutamate gated chloride channels, were identified. This novel data will inform cyathostomin biology and anthelmintic resistance studies in future.

Recent advances in the analysis of behavioural organization and interpretation as indicators of animal welfare

While the incorporation of mathematical and engineering methods has greatly advanced in other areas of the life sciences, they have been under-utilized in the field of animal welfare. Exceptions are beginning to emerge and share a common motivation to quantify 'hidden' aspects in the structure of the behaviour of an individual, or group of animals. Such analyses have the potential to quantify behavioural markers of pain and stress and quantify abnormal behaviour objectively. This review seeks to explore the scope of such analytical methods as behavioural indicators of welfare. We outline four classes of analyses that can be used to quantify aspects of behavioural organization. The underlying principles, possible applications and limitations are described for: fractal analysis, temporal methods, social network analysis, and agent-based modelling and simulation. We hope to encourage further application of analyses of behavioural organization by highlighting potential applications in the assessment of animal welfare, and increasing awareness of the scope for the development of new mathematical methods in this area.

The discursive turn in policy analysis and the validation of policy stories

This paper is concerned with the language of policy documents in the field of health care, and how ‘readings’ of such documents might be validated in the context of a narrative analysis. The substantive focus is on a comparative study of UK health policy documents (N=20) as produced by the various assemblies, governments and executives of England, Scotland, Wales and Northern Ireland during the period 2000-2009. Following an identification of some key characteristics of narrative structure the authors indicate how text-mining strategies allied with features of semantic and network analysis can be used to unravel the basic elements of policy stories and to facilitate the presentation of data in such a way that readers can verify the strengths (and weaknesses) of any given analysis – with regard to claims concerning, say, the presence, absence, or relative importance of key ideas and concepts. Readers can also ‘see’ how the different components of any one story might fit together, and to get a sense of what has been excluded from the narrative as well as what has been included, and thereby assess the reliability and validity of interpretations that have been placed upon the data.

Accuracy of Death Certificates in COPD: Analysis from the TORCH Trial

The Towards a Revolution in COPD Health (TORCH) trial was an international clinical trial of chronic obstructive pulmonary disease (COPD) patients where cause of death was assigned by an independent committee. Comparison of death certificate data and adjudicated cause of death allows a unique opportunity to determine death certificate accuracy and frequency of COPD listing on death certificates of COPD patients. In this analysis, the authors determine the concordance between adjudicated cause of death and primary and secondary cause of death from death certificates. In 317 (80%) of informative deaths, the primary or secondary cause of death from certificates agreed with adjudicated cause of death. Only 229 (58%) of death certificates in these COPD patients listed COPD on the certificate. COPD was not listed on the death certificate in 21% of deaths adjudicated to be caused by COPD exacerbation. Compared with pulmonary causes, the listing of COPD on certificates occurred with less frequency than cardiovascular, cancer and other categories of death. The combined primary and secondary listing on death certificates has good concordance with actual cause of death. COPD is under-reported on death certificates, and this under-reporting is more frequent when the primary cause of death is not pulmonary.