Search results for "Component analysis"
showing 10 items of 562 documents
Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics
2013
Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers however from the same limitation, i.e. the non trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachadran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates. We illustrate the robustness of this …
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
2010
Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 r…
7keto-stigmasterol and 7keto-cholesterol induce differential proteome changes to intestinal epitelial (Caco-2) cells
2015
Abstract Recent studies have expanded the appreciation of the roles of oxysterols triggering inflammatory, immune cytotoxic and apoptotic processes, but have not been considered for proteome analysis. A comparative proteomic study in intestinal epithelial cell cultures incubated (60 μM/24 h) with 7keto-cholesterol or 7keto-stigmasterol was performed. The influence of both compounds was studied following the nLC-TripleTOF analysis. Findings were compared to results for control cultures. In the principal component analysis (PCA) of proteome patterns, two components were extracted accounting for 99.8% of the variance in the protein expression. PCA analysis clearly discriminated between the per…
Transport of high molecular mass lignin material in the receiving water system of a mechanical pulp mill
1998
High molecular mass material (HMM) of water samples collected from the receiving water system of a mechanical pulp mill was characterized applying cupric oxide oxidation combined with GC and HPLC analysis of the oxidation products. This qualitative method was used to follow the transport of organic HMM discharged by the mill. The interpretation of results was complicated by degradation reactions of HMM in the water system and the assimilation of HMM produced by the mill to natural humic compounds. The analytical data was subjected to the principal component analysis (PCA) to verify the results obtained.
PCA and PLS methods applied to ecotoxicological data: Ecobalance project
1996
Within a case study ‘Ecobalance’, the fate and effects of various chlorinated and non-chlorinated organic compounds and some heavy metals discharged from pulp and paper mills into water, sediment and aquatic animals were studied in a recipient area of southern Lake Saimaa, SE Finland. The main aim of the project was to find an empirical link between chemical emission parameters and ecotoxicological effects expressed in the ecosystem. As part of the \‘Ecobalance’ project, principal component analysis (PCA) and partial least squares (PLS) methods were used to interpret the data of the lake area. The PLS method was used to estimate the lake area affected by mill effluents and to calculate the …
Effects of Plant Density on the Number of Glandular Trichomes and on Yield and Quality of Essential Oils from Oregano.
2016
Plants yields are influenced by agronomic techniques. Plant density is a complex issue and extremely important when maximizing both crop quality, and biomass and essential oil yields. Plants belonging to the Origanum vulgare subspecies hirtum (Link) Ietswaart were grown adopting four types of plant density and were characterized in biometric and chemical terms. The samples were analyzed using the ANOVA (Principal Component Analysis) statistical method regarding biometric aspects, EO yield and peltate hair density. Essential oil (EO) was extracted by hydrodistillation and analyzed using GC-FID and GC-MS. GC-FID and GC-MS analysis led to the identification of 45 compounds from the EO. Plant …
Monitoring of chicken meat freshness by means of a colorimetric sensor array
2012
A new optoelectronic nose to monitor chicken meat ageing has been developed. It is based on 16 pigments prepared by the incorporation of different dyes (pH indicators, Lewis acids, hydrogenbonding derivatives, selective probes and natural dyes) into inorganic materials (UVM-7, silica and alumina). The colour changes of the sensor array were characteristic of chicken ageing in a modi¿ed packaging atmosphere (30% CO2¿70% N2). The chromogenic array data were processed with qualitative (PCA) and quantitative (PLS) tools. The PCA statistical analysis showed a high degree of dispersion, with nine dimensions required to explain 95% of variance. Despite this high dimensionality, a tridimensional re…
Multivariate data analysis of quality parameters in drinking water.
2001
The quality of water destined for human consumption has been treated as a multivariate property. Since most of the quality parameters are obtained by applying analytical methods, the routine analytical laboratory (responsible for the accuracy of analytical data) has been treated as a process system for water quality estimation. Multivariate tools, based on principal component analysis (PCA) and partial least squares (PLS) regression, are used in the present paper to: (i) study the main factors of the latent data structure and (ii) characterize the water samples and the analytical methods in terms of multivariate quality control (MQC). Such tools could warn of both possible health risks rela…
Feature selection strategies for quality screening of diesel samples by infrared spectrometry and linear discriminant analysis.
2012
Abstract A rapid approach has been developed for the characterization of diesel quality, based on attenuated total reflectance – Fourier transform infrared (ATR-FTIR) spectrometry, which could be useful for diagnosing the sample quality condition. As a supervised technique, linear discriminant analysis (LDA) was employed to process the spectrometric data. The role of variable selection methods was also evaluated. Successive projection algorithm (SPA) and genetic algorithm (GA) feature selection techniques were applied prior to the discriminative procedure. It was aimed to compare the effect of feature selection procedures on classification capability of IR spectrometry for the diesel sample…
Detection of batch effects in liquid chromatography-mass spectrometry metabolomic data using guided principal component analysis.
2014
Metabolomics based on liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for studying dynamic responses of biological systems to different physiological or pathological conditions. Differences in the instrumental response within and between batches introduce unwanted and uncontrolled data variation that should be removed to extract useful information. This work exploits a recently developed method for the identification of batch effects in high throughput genomic data based on the calculation of a delta statistic through principal component analysis (PCA) and guided PCA. Its applicability to LC-MS metabolomic data was tested on two real examples. The first example involved t…