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Baselines are often chosen by visual inspection of their effect on selected spectra. A more objective procedure for choosing baseline correction algorithms and their parameter values for use in statistical analysis is presented. When the goal of the baseline correction is spectra with a pleasing appearance, visual inspection can be a satisfactory approach. If the spectra are to be used in a statistical analysis, objectivity and reproducibility are essential for good prediction. Variations in baselines from dataset to dataset means we have no guarantee that the best-performing algorithm from one analysis will be the best when applied to a new dataset. This paper focuses on choosing baseline correction algorithms and optimizing their parameter values based on the performance of the quality measure from the given analysis. Results presented in this paper illustrate the potential benefits of the optimization and points out some of the possible pitfalls of baseline correction.

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BackgroundA pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have become popular due to the easy access to whole-genome sequence data for prokaryotes. A pan-genome study reveals species diversity and gene families that may be of special interest, e.g because of their role in bacterial survival or their ability to discriminate strains.ResultsWe present an R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for the heavy computations involved, and the R package provides functions for building a computational pipeline.ConclusionsWe demonstrate parts of the package on a data set for the gram positive bacterium Enterococcus faecalis. The package is free to download and install from The Comprehensive R Archive Network.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0517-0) contains supplementary material, which is available to authorized users.

-The aim of this study was to compare the digestion of milk proteins from different species using an in vitro gastrointestinal model. Raw and heated milks from bovine, caprine, human and equine species were digested by human digestive enzymes. Digestion was performed in two 30-min sequential steps by digestive juices from the stomach (pH 2.5/37°C) and from the duodenum (pH 8.0/37°C). The degradation patterns of the milk proteins were visualized by SDS-PAGE and quantified using the ImageQuant program. Caseins in the equine milk were rapidly digested by the gastric juice in contrast to the caseins from the other species. During the subsequent digestion by the duodenal juice most of the caseins from all species were degraded within 5 min, and within 30 min only traces of caseins were detected. The mean casein micellar size varied between species in the range of 146.0-311.5 nm (equine > caprine > bovine > human). The α-lactalbumin from all species appeared to be very resistant to both gastric and duodenal digestions. A similar trend was shown for β-lactoglobulin from bovine and caprine milks, of which~60% intact protein remained, while only 25% remained intact in equine milk after total digestion. Equine milk contained a high amount of lysozyme, of which 60% remained intact in the present study. In heated milks from all species, only α-lactalbumin degradation increased approximately 12-20% in comparison to the raw milk. This study shows that equine milk with fast digestible proteins could be considered as a replacement for bovine milk in the diet of people with special needs, such as infants and the elderly. equine milk / bovine milk / caprine milk / human milk / digestion / whey protein / casein Résumé -Comparaison de la digestion des caséines et des protéines de lactosérum du lait équin, bovin, caprin et humain par les enzymes gastro-intestinales humaines. Le but de cette étude était de comparer la digestion des protéines laitières provenant de différentes espèces en utilisant un modèle gastro-intestinal in vitro. Des laits crus et traités thermiquement des espèces bovines, caprines, équines et humaines ont été digérés par des enzymes digestives humaines. La digestion a été réalisée au cours de deux étapes séquentielles de 30 min par des sucs digestifs gastriques (pH 2,5/37°C) et duodénaux (pH 8,0/37°C). Les profils de dégradation des protéines laitières ont été visualisés par SDS-PAGE et quantifiés à l'aide du programme ImageQuant. Les caséines du lait équin étaient rapidement digérées par le suc gastrique contrairement aux caséines des autres espèces. Au cours de la digestion suivante par le suc duodénal, la plupart des caséines de toutes les espèces étaient dégradées en 5 min, et après 30 min seules des traces des caséines étaient détectées. La taille moyenne des micelles de caséines variait de 146,0 à 311,5 nm selon les espèces (équin > caprin > bovin > humain). L'α-lactalbumine de toutes les espèces apparaissait être très résistante à la fois à la digestion gastrique et duodénale. Une tendance simila...

a Model-based pre-processing has become wide spread in spectroscopy and is the standard procedure in Fourier-transform infrared spectroscopy. It has also been shown to give valuable contributions in Raman spectroscopy. Extended multiplicative signal correction is flexible enough to handle varying fluorescence background and take into account individual variations in baselines while still keeping enough rigidity through reference spectra and model fitting to avoid degenerate solutions and overfitting, when used correctly. We demonstrate the basic extended multiplicative signal correction method and some extensions, including a novel shift correction, on real Raman data to demonstrate effects on visual appearance, replicate variation and prediction. Comparisons with other standard correction methods are also shown and discussed.

We propose a new data compression method for estimating optimal latent variables in multi-variate classification and regression problems where more than one response variable is available. The latent variables are found according to a common innovative principle combining PLS methodology and canonical correlation analysis (CCA). The suggested method is able to extract predictive information for the latent variables more effectively than ordinary PLS approaches. Only simple modifications of existing PLS and PPLS algorithms are required to adopt the proposed method.

We have compared the efficacy of continuous ultraviolet (UV‐C) (254 nm) and pulsed UV light in reducing the viability of Salmonella Enteritidis, Listeria monocytogenes, Staphylococcus aureus, enterohemorrhagic Escherichia coli, Pseudomonas spp., Brochothrix thermospacta, Carnobacterium divergens, and extended‐spectrum β‐lactamase producing E. coli inoculated on chicken fillet surface. Fluences from 0.05 to 3.0 J/cm2 (10 mW/cm2, from 5 to 300 s) used for UV‐C light resulted in average reductions from 1.1 to 2.8 log cfu/cm2. For pulsed UV light, fluences from 1.25 to 18.0 J/cm2 gave average reductions from 0.9 to 3.0 log cfu/cm2. A small change in the odor characterized as sunburnt and increased concentration of volatile compounds associated with burnt odor posed restrictions on the upper limit of UV treatment, however no sensory changes were observed after cooking the meat. Treatments under modified atmosphere conditions using a UV permeable top film gave similar or slightly lower bacterial reductions.Practical applicationsUltraviolet (UV) light may be used for decontaminating the surface of food products and reduce viability of pathogenic and spoilage bacteria. Exposure of raw chicken fillet surface to various doses of continuous UV‐C or pulsed UV light proposed in the present work represent alternatives for microbiological improvement of this product. Chicken fillets can be treated in intact packages covered with UV permeable top film, thus avoiding recontamination of the meat. UV‐C light treatment is a low cost strategy with low maintenance, whereas pulsed UV light involves more elaborate equipment, but treatment times are short and less space is required. Both methods can be helpful for producers to manage the safety and quality of chicken fillets.