GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

Deinking flotation of recycled linerboard for food packaging applications

Brown packaging linerboard, made entirely from recovered pulp, was subjected to deinking flotation for evaluating the possible improvements in its chemical, optical and mechanical properties. The increase in the rate of recovered paper utilisation, along with the tendency towards lower basis weights, in the packaging paper production, has created a growing need for the utilisation of secondary fibers of improved quality. To attain better quality fibers, flotation deinking of brown grades is being considered, along with the addition of primary fibers to recovered paper furnish. Numerous conducted studies, in which the flotation technology was used in the treatment of brown grades, support this idea. Most of them show that the quality of fibers is improved after flotation deinking, resulting in higher mechanical properties of the deinked handsheets and in lower amounts of chemical contaminants. As to food and human health safety, packaging paper has to meet specific requirements, to be classified as suitable for its direct contact with foods. Recycled paper and board may contain many potential contaminants, which, especially in the case of direct food contact, may migrate from packaging materials into foodstuffs. In this work, the linerboard sample selected for deinking was made from recycled fibers not submitted previously to chemical deinking flotation. Therefore, the original sample contained many noncellulosic components, as well as the residues of printing inks. The studied linerboardsample was a type of packaging paper used for contact with food products that are usually peeled before use, e.g. fruits and vegetables. The decrease in the amount of chemical contaminants, after conducting deinking flotation, was evaluated, along with the changes in the mechanical and optical properties of the deinked handsheets. Food contact analysis was done on both the original paper samples and the filter pads and handsheets made before and after deinking flotation. Food contact analysis consisted of migration tests of brightening agents, colorants, PCPs, formaldehydes and metals. Microbiological tests were also performed to determine the possible transfer of antimicrobial constituents