Classification of probability density functions in the framework of Bayes spaces : methods and applications

The process of supervised classification when the data set consists of probability density functions is studied. Due to the relative information contained in densities, it is necessary to convert the functional data analysis methods into an appropriate framework, here represented by the Bayes spaces. This work develops Bayes space counterparts to a set of commonly used functional methods with a focus on classification. Hereby, a clear guideline is provided on how some classification approaches can be adapted for the case of densities. Comparison of the methods is based on simulation studies and real-world applications, reflecting their respective strengths and weaknesses

Simple enough, but not simpler : reconsidering additive logratio coordinates in compositional analysis

Compositional data, multivariate observations carrying relative information, are popularly expressed in additive logratio coordinates which are easily interpretable as they use one of the components as ratioing part to produce pairwise logratios. These coordinates are however oblique and they lead to issues when applying multivariate methods on them, including widely-used techniques such as principal component analysis and linear regression. In this paper we propose a way to redefine alr coordinates with respect to an orthonormal system and we also extend the idea to the case of compositional tables. The new approach is demonstrated in an application to movement behavior data

Soil organic matter quality of variously managed agricultural soil in the Czech Republic evaluated using DRIFT spectroscopy

This study focuses on the effect of agricultural soil management on soil organic matter (SOM) composition. The addition of manure and crop residues was tested under different pedoclimatic conditions. The quality of SOM was assessed using diffuse reflectance infrared spectroscopy. The following parameters were calculated from the spectra:   sum of aliphatic bands (ΣAL), aromatic bands at wave numbers 1 620 and 1 520 cm-1 (AR1620 and AR1520), potential wettability (PWI), organic matter quality (OMQ), and decomposability (DI) indexes. The addition of manure or crop residues may not cause fundamental changes in the qualitative composition of SOM. Rather, pedoclimatic conditions determine which components are fixed in the soil on a long-term scale. A dominant effect of soil type was found in the distribution of all spectral parameters studied using main effect ANOVA. The main differences between the soil types concern the aromatic, oxygen and nitrogen groups contained in the SOM. Chernozems are soils with higher OMQ and DI, whereas Cambisols are soils with low OMQ and DI and the highest PWI. The stabilisation of SOM in soils can thus be based on the biochemical persistence of organic molecules, their specific affinity for minerals and the formation of aggregates that protect enclosed SOM

Biologically active metabolites produced by the basidiomycete Quambalaria cyanescens.

Four strains of the fungus Quambalaria cyanescens (Basidiomycota: Microstromatales), were used for the determination of secondary metabolites production and their antimicrobial and biological activities. A new naphthoquinone named quambalarine A, (S)-(+)-3-(5-ethyl-tetrahydrofuran-2-yliden)-5,7,8-trihydroxy-2-oxo-1,4-naphthoquinone (1), together with two known naphthoquinones, 3-hexanoyl-2,5,7,8-tetrahydroxy-1,4-naphthoquinone (named here as quambalarine B, 2) and mompain, 2,5,7,8-tetrahydroxy-1,4-naphthoquinone (3) were isolated. Their structures were determined by single-crystal X-ray diffraction crystallography, NMR and MS spectrometry. Quambalarine A (1) had a broad antifungal and antibacterial activity and is able inhibit growth of human pathogenic fungus Aspergillus fumigatus and fungi co-occurring with Q. cyanescens in bark beetle galleries including insect pathogenic species Beauveria bassiana. Quambalarine B (2) was active against several fungi and mompain mainly against bacteria. The biological activity against human-derived cell lines was selective towards mitochondria (2 and 3); after long-term incubation with 2, mitochondria were undetectable using a mitochondrial probe. A similar effect on mitochondria was observed also for environmental competitors of Q. cyanescens from the genus Geosmithia

Left column: Structural formulas, FTMS data, and physical characteristics of naphthoquinones isolated from submerged culture of <i>Quambalaria cyanescens</i>; right column: X-ray structures, the displacement ellipsoids are drawn on 50% probability level.

<p>Left column: Structural formulas, FTMS data, and physical characteristics of naphthoquinones isolated from submerged culture of <i>Quambalaria cyanescens</i>; right column: X-ray structures, the displacement ellipsoids are drawn on 50% probability level.</p

Effect of quambalarine B (2) and mompain (3) on the adenocarcinoma cell line HeLa.

<p>0.25% DMSO was used as a solvent and as a control. Upper panels: visualization of mitochondria using MitoTracker Red CMXRos (red), actin cytoskeleton using Phalloidin (green), lysosomes using monoclonal antibody MEM 259 recognizing the lysosomal protein LAMP2 (white) and nuclei with DAPI (blue). Lower panels: simultaneous visualization of mitochondria, lysosomes and nuclei only.</p