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At least 847 records · Page 47Linked to original sources
PubMed2004

Metabolomics and systems biology: making sense of the soup.

Novel techniques for acquiring metabolomics data continue to emerge. Such data require proper storage in suitably configured databases, which then permit one to establish the size of microbial metabolomes (hundreds of major metabolites) and allow the nature, organisation and control of metabolic networks to be investigated. A variety of algorithms for metabolic network reconstruction coupled to suitable modelling algorithms are the ground substances for the development of metabolic network and systems biology. Even qualitative models of metabolic networks, when subject to stoichiometric constraints, can prove highly informative, and are the first step to the quantitative models, which alone can allow the true representation of complex biochemical systems.

Algorithms↗
PubMed2003

Gestalt isomorphism and the primacy of subjective conscious experience: a Gestalt Bubble model.

A serious crisis is identified in theories of neurocomputation, marked by a persistent disparity between the phenomenological or experiential account of visual perception and the neurophysiological level of description of the visual system. In particular, conventional concepts of neural processing offer no explanation for the holistic global aspects of perception identified by Gestalt theory. The problem is paradigmatic and can be traced to contemporary concepts of the functional role of the neural cell, known as the Neuron Doctrine. In the absence of an alternative neurophysiologically plausible model, I propose a perceptual modeling approach, to model the percept as experienced subjectively, rather than modeling the objective neurophysiological state of the visual system that supposedly subserves that experience. A Gestalt Bubble model is presented to demonstrate how the elusive Gestalt principles of emergence, reification, and invariance can be expressed in a quantitative model of the subjective experience of visual consciousness. That model in turn reveals a unique computational strategy underlying visual processing, which is unlike any algorithm devised by man, and certainly unlike the atomistic feed-forward model of neurocomputation offered by the Neuron Doctrine paradigm. The perceptual modeling approach reveals the primary function of perception as that of generating a fully spatial virtual-reality replica of the external world in an internal representation. The common objections to this "picture-in-the-head" concept of perceptual representation are shown to be ill founded.

Consciousness↗
PubMedDate not supplied

Modeling diamagnetic and magnetooptic properties of organic compounds with the TOSS-MODE approach.

The topological substructural molecular design (TOSS-MODE) approach is used to describe the diamagnetic susceptibility of organic compounds. Two data sets composed of 233 aliphatic and 85 aromatic compounds were studied for which good linear correlations were found. The contributions of many different structural fragments and atomic groups were computed by the current approach. The predictive ability of the models developed was tested by using external prediction sets of compounds of different classes than those used in training. A quantitative model based on the current approach was developed to compute the diamagnetic susceptibility exaltation of aromatic compounds, which is exemplified by the study of polycyclic aromatic hydrocarbons. The rotatory power of organic compounds in a magnetic field was also described by the TOSS-MODE approach. Good linear correlations were obtained for this property in aliphatic and aromatic compounds. The predictive abilities of the models found were tested by external prediction sets for which good correlations between calculated and experimental values are found.

Journal Article↗
PubMed2003

Liquid-liquid immiscibility in membranes.

The observation of liquid-liquid immiscibility in cholesterol-phospholipid mixtures in monolayers and bilayers has opened a broad field of research into their physical chemistry. Some mixtures exhibit multiple immiscibilities. This unusual property has led to a thermodynamic model of "condensed complexes." These complexes are the consequence of an exothermic, reversible reaction between cholesterol and phospholipids. In this quantitative model the complexes are sometimes concentrated in a separate liquid phase. The phase separation into a complex-rich phase depends on membrane composition and intensive variables such as temperature. The properties of defined cholesterol-phospholipid mixtures provide a conceptual foundation for the exploration of a number of aspects of the biophysics and biochemistry of animal cell membranes.

Animals↗
PubMed1989

Further tests of an exemplar-similarity approach to relating identification and categorization.

Further tests were provided of an exemplar-similarity model for relating the identification and categorization of separable-dimension stimuli (Nosofsky, 1986). On the basis of confusion errors in an identification paradigm, a multidimensional scaling (MDS) solution was derived for a set of 16 separable-dimension stimuli. This MDS solution was then used in conjunction with the exemplar-similarity model to accurately predict performance in four separate categorization paradigms with the same stimuli. A key to achieving the accurate quantitative fits was the assumption that a selective attention process systematically modifies similarities among exemplars across different category structures. The tests reported go well beyond earlier ones (Nosofsky, 1986) in demonstrating the generalizability and utility of the theoretical approach. Implications of the results for alternative quantitative models of classification performance, including Ashby and Perrin's (1988) general recognition theory, were also considered.

Adult↗
PubMedDate not supplied

[Mechanisms of change in the tonus of depolarized smooth muscle (guinea pig taenia coli) during application of a hyperpolarizing current].

Using double sucrose-gap technique three types of contractile responses of depolarized smooth muscle (guinea-pig taenia-coli) current-induced hyperpolarization were investigated: 1) contractions, 2) relaxations and 3) biphasic responses (relaxation followed by contraction). Every preparation generated generally only one type of responses (of different amplitude) when passing the currents of various strength. These responses were attributed to the changes of calcium fluxes through the cellular membranes under hyperpolarization. The phenomena observed were analysed on the mathematical model. Quantitative analysis showed that description of calcium current changes with equations of Hogkin-Huxley types was not sufficient; the model predicts the existence of non-inactivating channels in the smooth muscle cellular membrane. This very assumption allows to describe correctly all three types of cintractile responses.

Animals↗
PubMed1990

Retinal pigment epithelium wound closure in vitro. Pharmacologic inhibition.

Early-passage bovine retinal pigment epithelium (RPE) cells were grown to confluence in 24-well plates, and a central defect was created mechanically in the monolayer within quadruplicate wells, sequentially over 9 days. Closure of the wounded area occurred by single-cell migration of elongated RPE cells from the edge of the wound and subsequent cell proliferation. Ten days after wounding, the cultures were fixed, stained, and photographed, and the residual wound area was quantified by computerized planimetry. Cell counts of unfixed cultures were determined with a Coulter counter. Wound closure was complete after 10 days. Using this technique, we assessed the response of RPE to various concentrations of 5-fluorouracil (5-Fu), colchicine (COL), and cytochalasin-B (CYT-B). 5-Fu (10 micrograms/ml) and COL (0.1 and 1 microgram/ml) inhibited migration and proliferation of RPE cells. CYT-B (5 micrograms/ml) inhibited migration. This model allows in vitro study of the response of RPE cells after loss of contact inhibition. The technique provides a quantitative model for assessing the dynamic capabilities of RPE cells in response to a localized mechanical defect and for assessing the pharmacologic modulation of these responses.

Animals↗
PubMedDate not supplied

[Analysis of the role of presynaptic adrenoreceptors in adrenergic synaptic transmission].

A mathematical model quantitatively describing the value of secreted mediator per each successive impulse in the series of presynaptic impulses is presented. The model is plotted with the account taken of the role of presynaptic adrenoreceptors regulating noradrenaline secretion. It has been shown that a decrease observed in neurophysiological experiments and further stabilization of postsynaptic responses in the series of presynaptic impulses of given frequency are not connected with a decreased content of noradrenaline in nerve endings, but may be connected with the work of presynaptic alpha and beta adrenoreceptors.

Animals↗
PubMed1995

Saccadic reaction times in gap/overlap paradigms: a model based on integration of intentional and visual information on neural, dynamic fields.

The systematic variations of regular saccadic reaction times induced in gap/overlap paradigms are addressed by a quantitative model. Intentional and visual information are integrated on a retinotopic representation of visual space, on which activity dynamics is related to movement initiation. Using a specific conception of "motor preparation", known effects of general warnings and fixation point on- and offsets are reproduced. Results of new experiments are predicted and the extent to which fixation point offsets are specific to ocular responses is analyzed in the light of the exposed model architecture. Relations of the theoretical framework to neurophysiological findings are discussed.

Fixation, Ocular↗
PubMed2002

Quantitative relationships between molecular structures, environmental temperatures and octanol-air partition coefficients of PCDD/Fs.

A concise quantitative model that incorporates information on both environmental temperature (T) and molecular structures, for logarithm of octanol-air partition coefficient (K(OA)) to base 10 (logK(OA)) of PCDDs, was developed. Partial least squares (PLS) analysis together with 14 quantum chemical descriptors were used to develop the quantitative relationships between structures, environmental temperatures and properties (QRSETP) model. It has been validated that the obtained QRSETP model can be used to predict logK(OA) of other PCDDs. Molecular size, environmental temperature (T), q+ (the most positive net atomic charge on hydrogen or chlorine atoms in PCDD molecules) and E(LUMO) (the energy of the lowest unoccupied molecular orbital) are main factors governing logK(OA) of PCDD/Fs under study. The intermolecular dispersive interactions and thus the size of the molecules play a leading role in governing logK(OA). The more chlorines in PCDD molecules, the greater the logK(OA) values. Increasing E(LUMO) values of the molecules leads to decreasing logK(OA) values, implying possible intermolecular interactions between the molecules under study and octanol molecules. Greater q+ values results in greater intermolecular electrostatic repulsive interactions between PCDD and octanol molecules and smaller logK(OA) values.

Journal Article↗
PubMed1981

Enzyme-incorporated erythrocyte ghosts: a new model system for quantitative enzyme cytochemistry.

The preparation and properties of a new microscopic model system for quantitative enzyme cytochemistry are described. The enzyme to be studied is entrapped in human erythrocyte ghosts by a simple hypotonic procedure. After fixation in suspension the ghosts can be analyzed both biochemically and cytochemically. The system has been tested with alkaline phosphatase. It is demonstrated that an azo method that uses naphthol AS-MX phosphate as substrate and 4-aminodiphenylamine diazonium salt as coupling agent can detect very low levels of enzymic activity. The biochemical activity determinations of alkaline phosphatase loaded erythrocyte ghosts were found to correlate linearly with cytophotometric activity determinations. The possible use of the erythrocyte ghost model system for other cytochemical applications is briefly discussed.

Alkaline Phosphatase↗
PubMed2003

Quantitative relationships between molecular structures, environmental temperatures and octanol-air partition coefficients of polychlorinated biphenyls.

A quantitative model that incorporates information on both environmental temperatures (T) and molecular structures, for logarithm of octanol-air partition coefficient to base 10 (logK(OA)) of polychlorinated biphenyls (PCBs) was developed. Partial least squares (PLS) analysis together with 16 theoretical molecular structural descriptors was used to develop the Quantitative relationships between structures, environmental temperatures and properties (QRSETP) model. The cross-validated Q(cum)(2) value for the optimal QRSETP model is 0.976, indicating a good predictive ability for logK(OA) of PCBs at different environmental temperatures. T, E(LUMO) (the energy of the lowest unoccupied molecular orbital), molecular size or average molecular polarizability (alpha), and the net atomic charges on chlorine, hydrogen and carbon atoms of PCB molecules, are major factors governing logK(OA). The lower the E(LUMO), the greater the intermolecular interactions between octanol and PCB molecules, and thus the greater the logK(OA) values. Because of intermolecular dispersive forces, the more chlorine atoms in PCB molecules, the greater the molecular size or alpha, the greater the logK(OA). The largest negative net atomic charge on a carbon atom (q(C)(-)) and molecular size or average molecular polarizability (alpha) are major factors governing temperature dependence of logK(OA). PCB molecules with low q(C)(-) values and more chlorines (big size or alpha) tend to have strong temperature dependence, due to intermolecular electrostatic interactions and dispersive forces, respectively.

Journal Article↗
PubMed1997

Characterization and modeling of P-type electrosensory afferent responses to amplitude modulations in a wave-type electric fish.

The first stage of information processing in the electrosensory system involves the encoding of local changes in transdermal potential into trains of action potentials in primary electrosensory afferent nerve fibers. To develop a quantitative model of this encoding process for P-type (probability-coding) afferent fibers in the weakly electric fish Apteronotus leptorhynchus, we recorded single unit activity from electrosensory afferent axons in the posterior branch of the anterior lateral line nerve and analyzed responses to electronically generated sinusoidal amplitude modulations of the local transdermal potential. Over a range of AM frequencies from 0.1 to 200 Hz, the modulation transfer function of P-type afferents is high-pass in character, with a gain that increases monotonically up to AM frequencies of 100 Hz where it begins to roll off, and a phase advance with a range of 15-60 degrees. Based on quantitative analysis of the observed gain and phase characteristics, we present a computationally efficient model of P-type afferent response dynamics which accurately characterizes changes in afferent firing rate in response to amplitude modulations of the fish's own electric organ discharge over a wide range of AM frequencies relevant to active electrolocation.

Action Potentials↗
PubMed2000

A Generalized Model for Describing Particle Formation in the Synthesis of Monodisperse Oxide Particles Based on the Hydrolysis and Condensation of Tetraethyl Orthosilicate.

A generalized model considering reaction and diffusion processes as rate determining steps is proposed for the formation of particles from hydrolysis and condensation of tetraethyl orthosilicate (TEOS). Reaction rate constant is assumed to be proportional to contact-surface area of two particles. Diffusion rate constant is given by Fuchs' stability theory with interparticle potential containing van der Waals attraction and electrostatic repulsion. To examine the validity of the model, ammonia-catalyzed reactions of TEOS were carried out in an ethanol-water solution at a water concentration of 11 mol/dm(3), an ammonia concentration of 1.0 mol/dm(3), and TEOS concentrations of 0.2 and 0.4 mol/dm(3) in the presence and in the absence of electrolytes. The experiments included competitive particle growth and seeded and nonseeded reactions. The model quantitatively expressed the results of the competitive growth experiments in which particles with different sizes grew at the same rate. The model gave the expected trend for the effect of ionic strength on particle sizes in the nonseeded reaction and the suppression of secondary particles in the seeded reaction by the addition of an electrolyte KCl. Good estimation was also obtained for transient particle size distributions in the nonseeded reaction and the seeded reaction in which secondary particles were generated. Copyright 2000 Academic Press.

Journal Article↗
PubMed1984

Theory and experiment for the effect of vascular microstructure on surface tissue heat transfer--Part II: Model formulation and solution.

In this paper the conceptual three-layer representation of surface tissue heat transfer proposed in Weinbaum, Jiji and Lemons [1], is developed into a detailed quantitative model. This model takes into consideration the variation of the number density, size and flow velocity of the countercurrent arterio-venous vessels as a function of depth from the skin surface, the directionality of blood perfusion in the transverse vessel layer and the superficial shunting of blood to the cutaneous layer. A closed form analytic solution for the boundary value problem coupling the three layers is obtained. This solution is in terms of numerically evaluated integrals describing the detailed vascular geometry, a capillary bleed-off distribution function and parameters describing the shunting of blood to the cutaneous layer. Representative heat transfer results for typical physiological conditions are presented.

Animals↗
PubMed1999

Insulin-like growth factor (IGF-I) induces myotube hypertrophy associated with an increase in anaerobic glycolysis in a clonal skeletal-muscle cell model.

Insulin-like growth factor-I (IGF-I) is an important autocrine/paracrine mediator of skeletal-muscle growth and development. To develop a definitive cultured cell model of skeletal-muscle hypertrophy, C2C12 cells were stably transfected with IGF-I and clonal lines developed and evaluated. Quantitative morphometric analysis showed that IGF-I-transfected myotubes had a larger area (2381+/-60 micrometer2 versus 1429+/-39 micrometer2; P<0.0001) and a greater maximum width (21.4+/-0.6 micrometer versus 13.9+/-0.3 micrometer; P<0.0001) than control C2C12 myotubes, independent of the number of cell nuclei per myotube. IGF-I-transfected myotubes had higher levels of protein synthesis but no difference in DNA synthesis when compared with control myotubes, indicating the development of hypertrophy rather than hyperplasia. Both lactate dehydrogenase and alanine aminotransferase activities were increased (3- and 5-fold respectively), and total lactate levels were higher (2.3-fold) in IGF-I-transfected compared with control myotubes, indicating an increase in anaerobic glycolysis in the hypertrophied myotubes. However, expression of genes involved in skeletal-muscle growth or hypertrophy in vivo, e.g. myocyte nuclear factor and myostatin, was not altered in the IGF-I myotubes. Finally, myotube hypertrophy could also be induced by treatment of C2C12 cells with recombinant IGF-I or by growing C2C12 cells in conditioned media from IGF-I-transfected cells. This quantitative model should be uniquely useful for elucidating the molecular mechanisms of skeletal-muscle hypertrophy.

Animals↗
PubMed2002

Pre and post 3D modeling of scoliotic patients operated with in situ contouring technique.

A three-dimensional segmental analysis was performed on the stereoradiographic reconstructions of ten right thoracic scoliotic patients. From the quantitative model of the spine and pelvis, the vertebral and intervertebral orientations were computed pre and post operatively. These orientations allow to determine the apical and junctional zones of the high thoracic, thoracic and lumbar curves. The apical zone corresponds to the maximum of vertebral axial rotation. Pre operatively, the tendency was T7 for the thoracic transverse apex with 20 AE of axial rotation. The junctional zone corresponds to the maximum of vertebral lateral rotation and the maximum of intervertebral axial rotation. The tendency was T5 and T12 for the junctional vertebrae of the thoracic curve with, at both levels, 30 AE of vertebral lateral rotation and 10 AE of intervertebral axial rotation. The surgical correction obtained by in situ contouring technique was evaluated through these 3D orientations. The vertebral axial rotation at the high thoracic, thoracic and lumbar apex was corrected with respectively 52%, 60% and 60%.

Adolescent↗
PubMed1981

A test of the null equation for functional antagonism.

1 The quantitative model for functional antagonism and synergism has been tested by studying its ability to fit data obtained from the functional antagonism of (-)-isoprenaline by muscarinic agonists on guinea-pig isolated atria. 2 The general form of the null equation has been shown to fit the experimental curves satisfactorily. 3 Functional interaction between (-)-isoprenaline and muscarinic agonists on atria has been shown to be type I although there does seem to be a discrepancy between values of the functional affinity constants, KA1F and KA2F, estimated in two different ways. 4 The affinity constants, KA, of the muscarinic agonists for their receptors have been estimated by use of the selective irreversible antagonist propylbenzilylcholine mustard. The discrepancy between KAF (i.e. both KA1F and KA2F) and KA is small for pentyltrimethylammonium which is an agonist of low intrinsic efficacy. By contrast the discrepancy between KAF and KA is much greater for methylfurmethide and oxotremorine both of which have much higher intrinsic efficacies. These results are as predicted by the model. 5 It is suggested that the discrepancy between KA1F and KA2F may be due to the limited ability of the equation l/S omega = aI + bI/S alpha to describe quantitatively the relation between sequential stimuli. However, it is concluded that this complication need not interfere with the use of the model to study mechanisms and possible sites of functional interaction.

Animals↗