Search results for "Biological system"
showing 10 items of 319 documents
"Design and application of a data-independent precursor and product ion repository."
2012
The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative spac…
General Statistical Framework for Quantitative Proteomics by Stable Isotope Labeling
2014
Pedro J. Navarro et al.
A Study of the Coevolution of Digital Organisms with an Evolutionary Cellular Automaton
2021
This article belongs to the Section Evolutionary Biology.
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…
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…
Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing…
1998
We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by "homology distance constraints," while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good …
Active spike responses of analog electrical neuron: Theory and experiments
2010
Using an analog electrical FitzHugh-Nagumo neuron including complex threshold excitation (CTE) properties, we analyze its spiking responses under pulse stimulation corresponding to oscillating threshold manifold. The system is subjected to outside pulse stimulus and can generate nonlinear integrate-and-flre and resonant responses which are typical for excitable neuronal cells ("all-or-none"). The answer of the neuron strongly depends on the number and the characteristics of incoming impulses (amplitude, width, strength and frequency). For certain parameters range, there is a possibility to trigger a spiking sequence with a finite number of spikes in response of a single short stimulus pulse…
Use of molecular topology for the prediction of physico-chemical, pharmacokinetic and toxicological properties of a group of antihistaminic drugs
2002
We used molecular connectivity to search mathematical models for predicting physico-chemical (e.g. the partition coefficient, P), pharmacokinetic (e.g. the time of maximum plasma level, and toxicological properties (lethal dose, LD) for a group of antihistaminic drugs. The results obtained clearly reveal the high efficiency of molecular topology for the prediction of these properties. Randomization and cross-validation by use of leave-one-out tests were also performed in order to assess the stability and the prediction ability of the connectivity functions selected.
New set of 2D/3D thermodynamic indices for proteins. A formalism based on "Molten Globule" theory
2010
Abstract We define eight new macromolecular indices, and several related descriptors for proteins. The coarse grained methodology used for its deduction ensures its fast execution and becomes a powerful potential tool to explore large databases of protein structures. The indices are intended for stability studies, predicting Φ -values, predicting folding rate constants, protein QSAR/QSPR as well as protein alignment studies. Also, these indices could be used as scoring function in protein-protein docking or 3D protein structure prediction algorithms and any others applications which need a numerical code for proteins and/or residues from 2D or 3D format.
Predicting antitrichomonal activity: A computational screening using atom-based bilinear indices and experimental proofs
2006
Existing Trichomonas vaginalis therapies are out of reach for most trichomoniasis people in developing countries and, where available, they are limited by their toxicity (mainly in pregnant women) and their cost. New antitrichomonal agents are needed to combat emerging metronidazole-resistant trichomoniasis and reduce the side effects associated with currently available drugs. Toward this end, atom-based bilinear indices, a new TOMOCOMD-CARDD molecular descriptor, and linear discriminant analysis (LDA) were used to discover novel, potent, and non-toxic lead trichomonacidal chemicals. Two discriminant functions were obtained with the use of non-stochastic and stochastic atom-type bilinear in…