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PubMedDate not supplied

Supervised interpretation of echocardiograms with a psychological model of expert supervision.

We have developed a collaborative scheme that facilitates active human supervision of the binary segmentation of an echocardiogram. The scheme complements the reliability of a human expert with the precision of segmentation algorithms. In the developed system, an expert user compares the computer generated segmentation with the original image in a user friendly graphics environment, and interactively indicates the incorrectly classified regions either by pointing or by circling. The precise boundaries of the indicated regions are computed by studying original image properties at that region, and a human visual attention distribution map obtained from the published psychological and psychophysical research. We use the developed system to extract contours of heart chambers from a sequence of two dimensional echocardiograms. We are currently extending this method to incorporate a richer set of inputs from the human supervisor, to facilitate multi-classification of image regions depending on their functionality. We are integrating into our system the knowledge related constraints that cardiologists use, to improve the capabilities of our existing system. This extension involves developing a psychological model of expert reasoning, functional and relational models of typical views in echocardiograms, and corresponding interface modifications to map the suggested actions to image processing algorithms.

Algorithms↗
PubMed2005

Fish otolith mass asymmetry: morphometry and influence on acoustic functionality.

The role of the fish otolith mass asymmetry in acoustic functionality is studied. The saccular, lagenar and utricular otoliths are weighted in two species of the Black Sea rays, 15 species of the Black Sea teleost fish and guppy fish. The dimensionless otolith mass asymmetry chi is calculated as ratio of the difference between masses of the right and left paired otoliths to average otolith mass. In the most fish studied the otolith mass asymmetry is within the range of -0.2 < chi < +0.2 (< 20%). We do not find specific fish species with extremely large or extremely small otolith asymmetry. The large otoliths do not belong solely to any particular side, left or right. The heavier otoliths of different otolithic organs can be located in different labyrinths. No relationship has been found between the magnitude of the otolith mass asymmetry and the length (mass, age) of the animal. The suggested fluctuation model of the otolith growth can interpret these results. The model supposes that the otolith growth rate varies slightly hither and thither during lifetime of the individual fish. Therefore, the sign of the relative otolith mass asymmetry can change several times in the process of the individual fish growth but within the range outlined above. Mathematical modeling shows that acoustic functionality (sensitivity, temporal processing, sound localization) of the fish can be disturbed by the otolith mass asymmetry. But this is valid only for the fish with largest otolith masses, characteristic of the bottom and littoral fish, and with highest otolith asymmetry. For most fish the values of otolith mass asymmetry is well below critical values. Thus, the most fish get around the troubles related to the otolith mass asymmetry. We suggest that a specific physicochemical mechanism of the paired otolith growth that maintains the otolith mass asymmetry at the lowest possible level should exist. However, the principle and details of this mechanism are still far from being understood.

Animals↗
PubMed2005

The partitioning of heavy metals in incineration of sludges and waste in a bubbling fluidized bed 2. Interpretation of results with a conceptual model.

This work addresses the behavior, fate and/or partitioning of six targeted (Cd, Pb, Cr, Cu, Zn and Ni) heavy metals (HMs) in the incineration of sludges and waste in a bubbling fluidized bed (BFB) of 15 cm i.d. and 5.2m high followed by a filter chamber operated at 750-760 degrees C with a commercial ceramic filter. This paper presents three different things: (1) an in depth review of the published work relating to the problem of partitioning of the HMs in BFBs, (2) some more experimental incineration tests regarding the influence of the temperature of the bed of the BFB and the effect of the chlorine content in the feedstock on the partitioning of the HMs, and (3) the modelling of the partitioning of the HMs in the exit flows: bottom ash, coarse fly ashes, fine fly ash and vapour phase. The partitioning of the HMs is governed by fluid dynamic principles together with the kinetics of the diffusion of the HMs inside the ash particles and the kinetics of the reactions between the HMs and the components of the matrix of the ash. Some thermodynamic predictions do not fit the results from the BFB incinerator well enough because equilibria are not reached in at least three exit ash flows: coarse fly ash, fine fly ash and submicron particles. The residence time of these ash particles in these type of incinerators is very short and most of the HMs have no time to diffuse out of the ash particle. Finally, an examination was made on how in the ceramic hot filter the partition coefficients for the HMs increased, mainly for Cd and Pb, when the Cl-content in the feedstock was increased.

Incineration↗
PubMed2003

Experimental and modeling study of the uranium (VI) sorption on goethite.

Acicular goethite was synthesized in the laboratory and its main physicochemical properties (composition, microstructure, surface area, and surface charge) were analyzed as a previous step to sorption experiments. The stability of the oxide, under the conditions used in sorption studies, was also investigated. The sorption of U(VI) onto goethite was studied under O(2)- and CO(2)-free atmosphere and in a wide range of experimental conditions (pH, ionic strength, radionuclide, and solid concentration), in order to assess the validity of different surface complexation models available for the interpretation of sorption data. Three different models were used to fit the experimental data. The first two models were based on the diffuse double layer concept. The first one (Model 1) considered two different monodentate complexes with the goethite surface and the second (Model 2) a single binuclear bidentate complex. A nonelectrostatic (NE) approach was used as a third model and, in that case, the same species considered in Model 1 were used. The results showed that all the models are able to describe the sorption behavior fairly well as a function of pH, electrolyte concentration, and U(VI) concentration. However, Model 2 fails in the description of the uranium sorption behavior as a function of the sorbent concentration. This demonstrates the importance of checking the validity of any surface complexation model under the widest possible range of experimental conditions.

Journal Article↗
PubMed2003

Pair-edge approximation for heterogeneous lattice population models.

To increase the analytical tractability of lattice stochastic spatial population models, several approximations have been developed. The pair-edge approximation is a moment-closure method that is effective in predicting persistence criteria and invasion speeds on a homogeneous lattice. Here we evaluate the effectiveness of the pair-edge approximation on a spatially heterogeneous lattice in which some sites are unoccupiable, or "dead". This model has several possible interpretations, including a spatial SIS epidemic model, in which some sites are occupied by immobile host-species individuals while others are empty. We find that, as in the homogeneous model, the pair-edge approximation is significantly more accurate than the ordinary pair approximation in determining conditions for persistence. However, habitat heterogeneity decreases invasion speed more than is predicted by the pair-edge approximation, and the discrepancy increases with greater clustering of "dead" sites. The accuracy of the approximation validates the underlying heuristic picture of population spread and therefore provides qualitative insight into the dynamics of lattice models. Conversely, the situations where the approximation is less accurate reveals limitations of pair approximation in the presence of spatial heterogeneity.

Algorithms↗
PubMed2003

A review of currently available in-stream water-quality models and their applicability for simulating dissolved oxygen in lowland rivers.

In this paper, a review is undertaken of the major models currently in use for describing water quality in freshwater river systems. The number of existing models is large because the various studies of water quality in rivers around the world have often resulted in the construction of new 'bespoke' models designed for the particular situation of that study. However, it is worth considering models that are already available, since an existing model, suitable for the purposes of the study, will save a great deal of work and may already have been established within regulatory and legal frameworks. The models chosen here are SIMCAT, TOMCAT, QUAL2E, QUASAR, MIKE-11 and ISIS, and the potential for each model is examined in relation to the issue of simulating dissolved oxygen (DO) in lowland rivers. These models have been developed for particular purposes and this review shows that no one model can provide all of the functionality required. Furthermore, all of the models contain assumptions and limitations that need to be understood if meaningful interpretations of the model simulations are to be made. The work is concluded with the view that it is unfair to set one model against another in terms of broad applicability, but that a model of intermediate complexity, such as QUASAR, is generally well suited to simulate DO in river systems.

Journal Article↗
PubMed2001

X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modelling fits.

Solution scattering is a low resolution diffraction method that provides important structural data on proteins. The ability to model scattering curves by recourse to known crystal structures for proteins under study significantly improves the resolution (and the utility) of the method because of the strict constraints that the crystal structures impose. For these structure determinations, a molecular description of the effect of hydration shells is needed. In calibration studies used for X-ray scattering curve modelling, it has been reproducibly found that a hydration shell is required. In molecular terms, this results from the higher electron density of the hydration shell compared to that of bulk water, which then becomes similar to that of the protein. This is well represented by a level of 0.3 g H(2)O/g glycoprotein and a water molecule volume of 0.0245 nm(3). Procedures for the addition of a hydration shell to a sphere model of a protein are described. For neutron scattering fits, it is not necessary to incorporate a hydration shell, as to a good approximation this is not detectable. In molecular terms, this apparent absence of the neutron hydration shell results from the effect of proton exchange on the scattering densities of bulk water and bound water which causes these to be similar but different from that of the protein.

Models, Chemical↗
PubMed2002

Fluorescence properties of tryptophan residues in the monomeric d-chain of Glossoscolex paulistus hemoglobin: an interpretation based on a comparative molecular model.

The primary structure of the 142 residue Glossoscolex paulistus d-chain hemoglobin has been determined from Edman degradation data of 11 endo-Glu-C peptides and 11 endo-Lys-C peptides, plus the results of Edman degradation of the intact globin. Tryptophan occupies positions 15, 33 and 129. Homology modeling allowed us to assign the positions of these Trp residues relative to the heme and its environment. The reference coordinates of the indole rings (average coordinates of the C(varepsilon2) and C(delta2) atoms) for W15 and W129 were 16.8 and 18.5 A, respectively, from the geometric center of the heme, and W33 was located in close proximity to the heme group at a distance which was approximately half of that for W15 and W129. It was possible to identify three rotamers of W33 on the basis of electrostatic and Van der Waals energy criteria. The calculated distances from the center of the heme were 8.3, 8.4 and 9.1 A for Rot1, Rot2 and Rot3, respectively. Radiationless energy transfer from the excited indole to the heme was calculated on the basis of Förster theory. For W33, the distance was more important than the orientation factor, kappa(2), due to its proximity to the heme. However, based on kappa(2), Rot2 (kappa(2)=0.945) was more favorable for the energy transfer than Rot1 (kappa(2)=0.433) or Rot3 (kappa(2)=0.125). In contrast, despite its greater distance from the heme, the kappa(2) of W129 (2.903) established it as a candidate to be more efficiently quenched by the heme than W15 (kappa(2)=0.191). Although the Förster approach is powerful for the evaluation of the relative efficiency of quenching, it can only explain pico- and sub-nanosecond lifetimes. With the average lifetime, =3 ns, measured for the apomonomer as the reference, the lifetimes calculated for each emitter were: W33-1 (1 ps), W33-2 (2 ps), W33-3 (18 ps), W129 (100 ps), and W15 (600 ps). Experimentally, there are four components for oxymonomers at pH 7: two long ones of 4.6 and 2.1 ns, which contribute approximately 90% of the total fluorescence, one of 300 ps (4%), and the last one of 33 ps (7.4%). It is clear that the equilibrium structure resulting from homology modeling explains the sub-nanosecond fluorescence lifetimes, while the nanosecond range lifetimes require more information about the protein in solution, since there is a significant contribution of lifetimes that resemble the apo molecule.

Amino Acid Sequence↗
PubMed1997

Myasthenic nicotinic receptor mutant interpreted in terms of the allosteric model.

An extended Monod-Wyman-Changeux allosteric-type model is applied to human muscle nicotinic acetylcholine receptors expressed in HEK cells, for both the normal form and the high-affinity human myasthenic mutant, epsilon T264P. The model is based on a concerted transition between the basal (resting) B state and the active (open-channel) A state, with the equilibrium in the absence of ligand determined by the allosteric constant, L0 = [B0]/[A0]. For wild-type receptors the model with L0 = 9 x 10(8) provides a satisfactory representation of published patch-clamp recordings that yields a distribution of open-channel dwell times with a single peak at 0.7 ms. For the epsilon T264P mutant, the model with L0 = 100 accounts for the trimodal distribution reported for open-channel dwell times, with peaks at 0.15, 3.8 and 60 ms that correspond to non-, mono- and bi-liganded receptors, respectively. Possible applications of the allosteric model to other myasthenic mutants are considered.

Allosteric Site↗
PubMedDate not supplied

Variable selection and interpretation in structure-affinity correlation modeling of estrogen receptor binders.

A computational approach for the identification and investigation of correlations between a chemical structure and a selected biological property is described. It is based on a set of 132 compounds of known chemical structures, which were tested for their binding affinities to the estrogen receptor. Different multivariate modeling methods, i.e., partial least-squares regression, counterpropagation neural network, and error-back-propagation neural network, were applied, and the prediction ability of each model was tested in order to compare the results of the obtained models. To reduce the extensive set of calculated structural descriptors, two types of variable selection methods were applied, depending on the modeling approach used. In particular, the final partial least-squares regression model was built using the "variable importance in projection" variable selection method, while genetic algorithms were applied in neural network modeling to select the optimal set of descriptors. A thorough statistical study of the variables selected by genetic algorithms is shown. The results were assessed with the aim to get insight to the mechanisms involved in the binding of estrogenic compounds to the receptor. The variable selection on the basis of genetic algorithm was controlled with the test set of compounds, extracted from the data set available. To compare the predictive ability of all the optimized models, a leave-one-out cross-validation procedure was applied, the best model being the nonlinear neural network model based on error back-propagation algorithm, which resulted in R2= 92.2% and Q2= 70.8%.

Algorithms↗
PubMed2004

Monitoring the simultaneous ostwald ripening and solubilization of emulsions.

The simultaneous Ostwald ripening of an emulsion and the solubilization of its oil droplets by added micellar surfactant solutions are monitored by measurements of time-averaged scattered intensities. A simple computer simulation model for the interpretation of the measurements is presented. Experimental data are analyzed with this model using one single parameter: an effective ratio of oil to surfactant molecules involved in the withdrawal of oil from the Ostwald ripening process by the added micelles. The fitted value of this parameter appears to be more than twice the one that can be predicted from the equilibrium solubilization of oil by the surfactant micelles, indicating that more oil is involved in the nonequilibrium exchange of oil and surfactant between micelles and droplets.

Journal Article↗
PubMed1993

Clarification of the pH-dependent kinetic behaviour of papain by using reactivity probes and analysis of alkylation and catalysed acylation reactions in terms of multihydronic state models: implications for electrostatics calculations and interpretation of the consequences of site-specific mutations such as Asp-158-Asn and Asp-158-Glu.

1. The complex behaviour of papain (EC 3.4.22.2) in acidic media has been investigated by (a) stopped-flow reactivity probe kinetics using 4,4'-dipyrimidyl disulphide (I) and 2,2'-dipyridyl disulphide (II) as thiol-specific time-dependent inhibitors with markedly different susceptibilities to activation by hydronation (protonation) and (b) using the multitasking application program SKETCHER for the rapid evaluation of pH-dependent kinetic data by means of interactive manipulation of calculated curves. 2. The substantially lower basicity of (I) (pKa 0.91) than that of (II) (pKa 2.45) combined with retention of high reactivity permitted the pKa for the formation of the (Cys-25)-S-/(His-159)-Im+H ion-pair state of papain to be determined kinetically as 3.4, a value close to that (3.3) deduced by potentiometric difference titration [Lewis, Johnson and Shafer (1976) Biochemistry 15, 5009-5017] and lower than the value (approx. 4) often reported from pH-dependent kinetic studies. The higher values are now known to arise from inadequate data analysis that does not take account of other overlapping kinetically influential ionizations. 3. Re-evaluation of the extensive sets of pH-kcat/Km data for the hydrolysis of nine substrates by papain reported by Polgár and Halász (1978) (Eur. J. Biochem. 88, 513-521) by making use of SKETCHER, the known pKa value (3.4) from the reaction with compound (I) and two additional kinetically influential pKa values deduced from the reaction with compound (II) now permits the identification of the pH-dependent events in reactions of papain with inhibitors and substrates. 4. A major conclusion is that, whereas in reactions of simple alkylating agents and compound (I) full nucleophilic character of (Cys-25)-S-/(His-159)-Im+H is provided by hydronic dissociation with pKa 3.3-3.4, in catalysis relatively little catalytic competence is produced consequent upon ion-pair formation. Substantial catalytic competence requires further hydronic dissociation with pKa approx. 4, and for cationic substrates further enhancement is produced by hydronic dissociation with pKa approx. 5. 5. The present work, together with the kinetic analysis of reactions of papain in alkaline media reported by Mellor, Thomas, Topham and Brocklehurst [Biochem. J. (1993) 290, 289-296], defines the kinetically influential ionizations of papain as 3.4, 4.0, 5.0, 8.3 and 10.0 of which 3.4 and 8.3 relate to the formation and subsequent dehydronation of the ion-pair state.(ABSTRACT TRUNCATED AT 400 WORDS)

Acylation↗
PubMed2004

A graph-theoretic modeling on GO space for biological interpretation of gene clusters.

MOTIVATION: With the advent of DNA microarray technologies, the parallel quantification of genome-wide transcriptions has been a great opportunity to systematically understand the complicated biological phenomena. Amidst the enthusiastic investigations into the intricate gene expression data, clustering methods have been the useful tools to uncover the meaningful patterns hidden in those data. The mathematical techniques, however, entirely based on the numerical expression data, do not show biologically relevant information on the clustering results. RESULTS: We present a novel methodology for biological interpretation of gene clusters. Our graph theoretic algorithm extracts common biological attributes of the genes within a cluster or a group of interest through the modified structure of gene ontology (GO) called GO tree. After genes are annotated with GO terms, the hierarchical nature of GO terms is used to find the representative biological meanings of the gene clusters. In addition, the biological significance of gene clusters can be assessed quantitatively by defining a distance function on the GO tree. Our approach has a complementary meaning to many statistical clustering techniques; we can see clustering problems from a different viewpoint by use of biological ontology. We applied this algorithm to the well-known data set and successfully obtained the biological features of the gene clusters with the quantitative biological assessment of clustering quality through GO Biological Process.

Algorithms↗
PubMed1999

Corticomuscular coherence: a review.

Corticomuscular coherence measured between electroencephalography (EEG), magnetoencephalography, or local field potentials and electromyography (EMG) should be helpful in understanding the cortical control of movement. EEG-EMG coherence and phase spectra depend on the types of EEG derivation and current source density function of EEG appears to be the most appropriate for computation of EEG-EMG coherence. A new model for the interpretation of the phase spectra ("constant phase shift plus constant time lag model") shows that cortical surface negative potentials are phase-locked to EMG firing. There are functional differences of EEG-EMG coherence among the alpha, beta, and gamma bands suggesting differences in their possible generator mechanisms. Since corticomuscular coherence is a noninvasive measure of corticomotoneuronal function in a specific frequency range, clinical application of this method might be very fruitful in tremor research.

Electroencephalography↗