Tutorial: Multivariate Classification for Vibrational Spectroscopy in Biological Samples

Vibrational spectroscopy techniques, such as Fourier-transform infrared (FTIR) and Raman spectroscopy, have been successful methods for studying the interaction of light with biological materials and facilitating novel cell biology analysis. Spectrochemical analysis is very attractive in disease screening and diagnosis, microbiological studies and forensic and environmental investigations because of its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, there is now an urgent need for multivariate classification protocols allowing one to analyze biologically derived spectrochemical data to obtain accurate and reliable results. Multivariate classification comprises discriminant analysis and class-modeling techniques where multiple spectral variables are analyzed in conjunction to distinguish and assign unknown samples to pre-defined groups. The requirement for such protocols is demonstrated by the fact that applications of deep-learning algorithms of complex datasets are being increasingly recognized as critical for extracting important information and visualizing it in a readily interpretable form. Hereby, we have provided a tutorial for multivariate classification analysis of vibrational spectroscopy data (FTIR, Raman and near-IR) highlighting a series of critical steps, such as preprocessing, data selection, feature extraction, classification and model validation. This is an essential aspect toward the construction of a practical spectrochemical analysis model for biological analysis in real-world applications, where fast, accurate and reliable classification models are fundamental

A Study of Pair Correlation Functions Using Classical DFT

At the heart of physics of fluids are particle distribution functions. If all of these functions of a fluid are known, the state can be fully described. With a universal theory of particle distribution functions, physics of fluids is done. Of particular interest is the radial distribution function (rdf), which is related to the second particle distribution function, because the average excess internal energy, pressure and isothermal compressibility naturally follow from it. Here the function is obtained for `soft' particles by calculating the density profile around a particle fixed in the origin, acting as an external potential. This is called the test-particle method. In order to theoretically describe `soft' particles, the short ranged (repulsive) forces and the long ranged (usually attractive) forces of the interaction potential are separated. The repulsive forces are calculated from a weighted density theory (FMT) and the long ranged forces are added as a `small' perturbation. The FMT has been proven to be accurate, but in order to describe the perturbation well we need to know how particles correlate for larger inter-particle separations in inhomogeneous systems. In particular for inhomogeneous systems it is difficult to say something about this but we can distinguish approximations for high and low densities. The result is a 1D non-linear integral equation with squares, cubes, fractions and logarithms in the weighted form of the unknown for the reference system and a perturbation which is linear in the unknown. The results are satisfactory for high and low densities, but for the intermediate range the results are less satisfactory. For a range of high densities we obtain a measure for the short-ranged correlations by fitting with MD results.Computational Science and EngineeringNumerical AnalysisElectrical Engineering, Mathematics and Computer Scienc

Search for new alternatives in the battle against histomonosis in turkeys

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Reovirus tenosynovitis in a flock of layer breeders

The present paper describes a reovirus infection with clinical course in a flock of layer breeders. Lameness and tenosynovitis of flexor tendons were observed in approximately 15% of the cockerels and 3% of the hens from 17 weeks of age onwards. Affected birds did not die; on the contrary, most of them recovered clinically within a period of 8 weeks. Two other breeds of layer parents that were housed in close contact with the affected flock did not develop clinical signs, although serology indicated that infection with reovirus had taken place. These field observations constitute the first report of clinical reovirus tenosynovitis in layer parents and indicate different susceptibilities of layer parent breeds in developing clinical signs following reovirus infection

Enrichment of Histomonas meleagridis

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