Comparison of Several Methods of Chromatographic Baseline Removal with a New Approach Based on Quantile Regression

The article is intended to introduce and discuss a new quantile regression method for baseline detrending of chromatographic signals. It is compared with current methods based on polynomial fitting, spline fitting, LOESS, and Whittaker smoother, each with thresholding and reweighting approach. For curve flexibility selection in existing algorithms, a new method based on skewness of the residuals is successfully applied. The computational efficiency of all approaches is also discussed. The newly introduced methods could be preferred to visible better performance and short computational time. The other algorithms behave in comparable way, and polynomial regression can be here preferred due to short computational time

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations

The Spectral Game: leveraging Open Data and crowdsourcing for education

<p>Abstract</p> <p>We report on the implementation of the Spectral Game, a web-based game where players try to match molecules to various forms of interactive spectra including 1D/2D NMR, Mass Spectrometry and Infrared spectra. Each correct selection earns the player one point and play continues until the player supplies an incorrect answer. The game is usually played using a web browser interface, although a version has been developed in the virtual 3D environment of Second Life. Spectra uploaded as Open Data to ChemSpider in JCAMP-DX format are used for the problem sets together with structures extracted from the website. The spectra are displayed using JSpecView, an Open Source spectrum viewing applet which affords zooming and integration. The application of the game to the teaching of proton NMR spectroscopy in an undergraduate organic chemistry class and a 2D Spectrum Viewer are also presented.</p