Consensus clustering and functional interpretation of gene-expression data

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas

Dynamics of avian species and functional diversity in secondary tropical forests

Deforestation for agriculture in the tropics, followed by abandonment, has resulted in large areas of secondary forest. Some authors have suggested that this secondary regrowth could help prevent mass extinction in the tropics by providing habitat for forest species. However, there is little generalised understanding of the biodiversity value of secondary forest. To address this knowledge gap, we conducted an analysis of avian responses to secondary forest succession, comparing data from 44 tropical secondary forest sites with nearby primary forest sites and investigating both species and functional diversity based metrics. Total species richness in secondary forests was 12% lower than in primary forests and was not related to secondary forest age. In contrast, forest specialist species richness increased with time since disturbance, reaching 99% of primary forest values after 100 years. In terms of functional diversity, functional dispersion (FDis) and functional divergence (FDiv) were similar in primary and secondary forests. However, functional evenness (FEve) was 5% higher in secondary than in primary forests. The standardized effect size of functional diversity (sesFD) was higher in young secondary forests than primary forests and declined with time since disturbance. Overall, these results suggest that secondary tropical forests can support provision of ecosystem services but that these services may be less stable in young forests. Therefore, secondary tropical forests, particularly older regrowth, have biodiversity value and can support important ecosystem functions. These secondary forests should be protected from further disturbance but preserving primary forest is vital for supporting overall and forest specialist species richness

ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics

Effect of Q-switched laser surface texturing of titanium on osteoblast cell response

Titanium and its alloys are important biomedical materials. It is known that the surface texture of implanted medical devices affects cell response. Control of cell response has the potential to enhance fixation of implants into bone and, in other applications, to prevent undesired cell adhesion. The potential use of a 100W Q-switched YAG laser miller (DMG Lasertec 60 HSC) for texturing titanium is investigated. A series of regular features with dimensions of the order of tens of micrometers are generated in the surface of titanium samples and the cell response to these features is determined. Characterisation of the laser milled features reveals features with a lengthscale of a few microns superposed on the larger scale structures, this is attributed to resolidification of molten droplets generated and propelled over the surface by individual laser pulses. The laser textured samples are exposed to osteoblast cells and it is seen that cells do respond to the features in the laser textured surfaces

Economics of controlled urea fertilizer in cropping systems

Non-Peer ReviewedNitrogen fertilizers are chemical compounds given to plants to promote growth. However, their application can impact the environment through ammonia and greenhouse gas emissions, and through leaching which can lead to deterioration of water quality. To understand the nitrogen dynamics in the soil, a set of experiments were designed by Agriculture and Agri-Food Canada (AAFC) research scientists with funding received from the Environmental Technology Assessment for Agriculture (ETAA) and GAPS programs of AAFC, and Agrium, a fertilizer company. Research trials were conducted to assess the impact of urea with comparison being made between ESN (environmentally sensitive nitrogen) and uncoated urea. Trials were conducted in five provinces and eight research sites. Harrow was the only eastern Canada site. Experiments also included several fertilizer application rates, and at least two tillage systems – conventional and reduced tillage. Zone tillage was also included at Harrow, Ontario. The general conclusion from the foregoing set of data and analyses is that ESN application is a better economic choice for certain crops in some regions, but not in all regions or for all crops. Even a single crop was not found to generate a positive producer surplus in all regions. Reasons for these differences need further investigation

Performance analysis of a dynamic query processing scheme

Traditional query optimizers produce a fixed query evaluation plan based on assumptions about data distribution and processor workloads. However, these assumptions may not hold at query execution time. In this paper, we propose a dynamic query processing scheme and we present the performance results obtained by simulation of a queueing network model of the proposed software architecture