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

Imaging polarimetry of the fogbow: polarization characteristics of white rainbows measured in the high Arctic

The knowledge on the optics of fogbows is scarce, and their polarization characteristics have never been measured to our knowledge. To fill this gap we measured the polarization features of 16 fogbows during the Beringia 2005 Arctic polar research expedition by imaging polarimetry in the red, green and blue spectral ranges. We present here the first polarization patterns of the fogbow. In the patterns of the degree of linear polarization p, fogbows and their supernumerary bows are best visible in the red spectral range due to the least dilution of fogbow light by light scattered in air. In the patterns of the angle of polarization α fogbows are practically not discernible because their α-pattern is the same as that of the sky: the direction of polarization is perpendicular to the plane of scattering and is parallel to the arc of the bow, independently of the wavelength. Fogbows and their supernumeraries were best seen in the patterns of the polarized radiance. In these patterns the angular distance δ between the peaks of the primary and the first supernumerary and the angular width σ of the primary bow were determined along different radii from the center of the bow. δ ranged between 6.08° and 13.41° , while σ changed from 5.25° to 19.47° . Certain fogbows were relatively homogeneous, meaning small variations of δ and σ along their bows. Other fogbows were heterogeneous, possessing quite variable δ- and σ-values along their bows. This variability could be a consequence of the characteristics of the high Arctic with open waters within the ice shield resulting in the spatiotemporal change of the droplet size within the fog

Spottier Targets Are Less Attractive to Tabanid Flies: On the Tabanid-Repellency of Spotty Fur Patterns

During blood-sucking, female members of the family Tabanidae transmit pathogens of serious diseases and annoy their host animals so strongly that they cannot graze, thus the health of the hosts is drastically reduced. Consequently, a tabanid-resistant coat with appropriate brightness, colour and pattern is advantageous for the host. Spotty coats are widespread among mammals, especially in cattle (Bos primigenius). In field experiments we studied the influence of the size and number of spots on the attractiveness of test surfaces to tabanids that are attracted to linearly polarized light. We measured the reflection-polarization characteristics of living cattle, spotty cattle coats and the used test surfaces. We show here that the smaller and the more numerous the spots, the less attractive the target (host) is to tabanids. We demonstrate that the attractiveness of spotty patterns to tabanids is also reduced if the target exhibits spottiness only in the angle of polarization pattern, while being homogeneous grey with a constant high degree of polarization. Tabanid flies respond strongly to linearly polarized light, and we show that bright and dark parts of cattle coats reflect light with different degrees and angles of polarization that in combination with dark spots on a bright coat surface disrupt the attractiveness to tabanids. This could be one of the possible evolutionary benefits that explains why spotty coat patterns are so widespread in mammals, especially in ungulates, many species of which are tabanid hosts