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PubMed1991

A laboratory model to quantitate the resistance of collagen vascular grafts to biodegradation.

Recent reports have shown that despite extensive preclinical testing, vascular grafts of biological origin undergo severe biodegradation and aneurysm formation after two or more years of implantation in man. The purpose of this study was to develop a laboratory model to quantitate and correlate the stability of crosslinked collagen grafts in vitro and in vivo. This resistance to biodegradation was assessed by measuring changes in suture pullout force and sample weight in response to controlled digestion with bacterial collagenase, in 0.5-cm-long cylindrical graft segments (chemically processed bovine carotid artery and human umbilical cord vein) that were implanted in the rat subcutis for 2 to 12 weeks. Scar tissue was removed from the explants by brief enzymatic digestion, a process that was inhibited when graft segments had become infected. Changes in dry weight were more consistent than were changes in wet weight; drying the graft segments had no effect on their degradation in vivo or in vitro. Intact cylindrical rings suffered somewhat less damage than did opened, flattened cylinders. Graft degradation increased markedly with implantation time, and was detected after only 3 weeks. We conclude that the rat subcutis model, when combined with controlled enzymatic digestion, first to remove scar tissue and then to challenge structural integrity, provides an accelerated assay by which to predict the stability of collagen vascular grafts.

Animals↗
PubMed2006

A bivariate quantitative genetic model for a threshold trait and a survival trait.

Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.

Bayes Theorem↗
PubMed2006

Influence of mom and dad: quantitative genetic models for maternal effects and genomic imprinting.

The expression of an imprinted gene is dependent on the sex of the parent it was inherited from, and as a result reciprocal heterozygotes may display different phenotypes. In contrast, maternal genetic terms arise when the phenotype of an offspring is influenced by the phenotype of its mother beyond the direct inheritance of alleles. Both maternal effects and imprinting may contribute to resemblance between offspring of the same mother. We demonstrate that two standard quantitative genetic models for deriving breeding values, population variances and covariances between relatives, are not equivalent when maternal genetic effects and imprinting are acting. Maternal and imprinting effects introduce both sex-dependent and generation-dependent effects that result in differences in the way additive and dominance effects are defined for the two approaches. We use a simple example to demonstrate that both imprinting and maternal genetic effects add extra terms to covariances between relatives and that model misspecification may over- or underestimate true covariances or lead to extremely variable parameter estimation. Thus, an understanding of various forms of parental effects is essential in correctly estimating quantitative genetic variance components.

Analysis of Variance↗
PubMed2000

Quantitative genetic models for the balance between migration and stabilizing selection.

The evolution of a quantitative trait subject to stabilizing selection and immigration, with the immigrants deviating from the local optimum, is considered under a number of different models of the underlying genetic basis of the trait. By comparing exact predictions under the infinitesimal model obtained using numerical methods with predictions of a simplified approximate model based on ignoring linkage disequilibrium, the increase in the expressed genetic variance as a result of linkage disequilibrium generated by migration is shown to be relatively small and negligible, provided that the genetic variance relative to the squared deviation of immigrants from the local optimum is sufficiently large or selection and migration is sufficiently weak. Deviation from normality is shown to be less important by comparing predictions of the infinitesimal model with a model presupposing normality. For a more realistic symmetric model, involving a finite number of loci only, no linkage and equal effects and frequencies across loci, additional changes in the genetic variance arise as a result of changes in underlying allele frequencies. Again, provided that the genetic variance relative to the squared deviation of the immigrants from the local optimum is small, the difference between the predictions of infinitesimal and the symmetric model are small unless the number of loci is very small. However, if the genetic variance relative to the squared deviation of the immigrants from the local optimum is large, or if selection and migration are strong, both linkage disequilibrium and changes in the genetic variance as a result of changes in underlying allele frequencies become important.

Base Sequence↗
PubMed2001

A pharmacokinetic model for quantitative evaluation of spinal cord injury with dynamic contrast-enhanced magnetic resonance imaging.

A multicompartment pharmacokinetic model was proposed to quantitatively describe the distribution of the contrast agent gadopentetate-dimeglumine (Gd) in an experimental spinal cord injury (SCI). Concentration of Gd was measured in different compartments with in vivo dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in the acute phase of injury. The concentration data for each rat was fitted to the model to estimate transfer rates between different compartments. The results indicate: 1) lack of uptake of Gd in normal cord tissue, 2) rapid exchange of Gd between plasma and cerebrospinal fluid in both normal and injured cord tissues, and 3) slower uptake of Gd in injured cord. With this approach, it is possible to quantify the integrity of the blood-spinal cord barrier (BSCB) in vivo, evaluate the pathobiology of injured cord, assess the efficacy of interventions, and monitor the progression of injury with postinjury time.

Animals↗
PubMed2004

Vibrational states of tetrahedral molecular species in electric fields. A theoretical model for quantitative description of the latent symmetry effects in vibrational spectroscopy of matrix isolated tetrahedral species.

A theoretical model that enables a quantitative description of latent symmetry effects in the case of matrix isolated tetrahedral species is developed. Several particular cases are considered, that are of special interest from vibrational spectroscopic viewpoint. It is shown that the observed appearances of the IR spectra of various XY4n- anions isomorphously isolated in solid matrices may be systematically explained in terms of the orientation of the effective local crystalline field vector. The model also principally enables calculation of the magnitude of the effective local homogeneous field vector as well as its direction with respect to the symmetry elements of the dopant species, and it can be successively corrected accounting for the field non-homogeneity. Also, a solid theoretical basis is for the first time presented for the significantly smaller site group splitting of the nu4 modes of dopant XY4n- species in comparison to the splitting of nu3 ones, which is often observed in the IR spectra. However, the presented approach has potentially a much wider applicability, as it in facts considers the vibrational states of tetrahedral molecular species in electric fields, which may be of a different origin, for example, electrodes in electrochemical systems, external fields in Stark-type spectroscopies, etc.

Electricity↗
PubMed1984

A quantitative genetic model of two-policy games between relatives.

Equations are derived for the change per generation of the population mean of the probability that an individual adopts a policy 1 as opposed to a policy 2 in a behavioral interaction between two diploid individuals of the same generation in which two policies are possible. The probability is assumed to be a quantitative genetic trait determined by many additively acting genes of small effects and an independent environmental component. Equations are derived for the case that interactions occur at random between all members of the population and also for the case that interactions occur between relatives of the same average degree of relatedness. It is assumed that each group of relatives and the number of such groups is sufficiently large. For a quantitative genetic trait with the additional assumption of unlinked loci the latter equation can be heuristically derived from the first by substituting the corresponding inclusive fitness effects. When per locus selection coefficients are small and linkage equilibrium holds, the average degree of relatedness can be equated approximately with Wright's coefficient of relationship. Thus, the quantitative genetic model provides a genetic basis for the inclusive fitness approach toward games between relatives. By contrast, in a monogenic system with major gene effects we obtain substantially different results which contradict those obtained by the inclusive fitness approach in game theory. Applications are made to the hawk-dove game, and the simple and iterated forms of the prisoner's dilemma.

Altruism↗
PubMed1986

Characterization of two classes of cardiac glycosine binding sites in rat heart and brain membrane preparations, using quantitative computer modelling.

Cardiac glycoside binding to rat heart and brain membrane preparations was measured by a rapid filtration technique. Data were analysed using quantitative computer analysis. The experimental results were consistent with a model in which cardiac glycoside-specific binding occurs at two independent classes of sites. The high-affinity sites in heart membranes were characterized by dissociation constants (Kd) of 40, 50, and 61 nmol/l for ouabain, digoxin and digitoxin, respectively, and the lower-affinity sites were characterized by Kd of 2.3 mumol/l, 67 nmol/l and 71 nmol/l for ouabain, digoxin and digitoxin, respectively. Comparable results were obtained using brain membranes. Potassium ions inhibit [3H]-ouabain binding in a dose-dependent manner with an IC50 of 500 mumol/l. Quantitative computer modeling indicated that potassium inhibits ouabain binding to approximately the same extent at both classed of binding sites, consistent with the hypothesis that the two classes of binding sites for cardiac glycosides might be associated with the Na+K+-ATPase.

Animals↗
PubMed1990

A model of quantitative traits under frequency-dependent balancing selection.

We describe a computer model that stimulates a combination of stabilizing and frequency-dependent selection acting on a quantitative character determined by several loci. The results correspond to many features of natural variations at both the phenotypic and genotypic levels. The model is robust, and its results are not strongly dependent either on the nature and shape of the function describing the stabilizing selection, or on the precise form of frequency dependence, except near the extrema. It suggests a mechanism for the maintenance of large amounts of variability, and shows a relation between population size and heterozygosity roughly corresponding to that found in nature. In this respect it is unlike the purely neutral model.

Alleles↗
PubMed2004

Quantitative binding models for CYP2C9 based on benzbromarone analogues.

The cytochrome P450 (CYP) isoforms involved in xenobiotic metabolism are enzymes whose substrate selectivity remains difficult to predict due to wide specificity and dynamic protein-substrate interactions. To uncover the determinants of specificity for cytochrome CYP2C9, a novel library of benzbromarone (bzbr) inhibitors was used to reevaluate its pharmacophore. CoMSIA was used with the bzbr ligands to generate both quantitative binding models and three-dimensional contour plots that pinpoint predicted interactions that are important for binding to 2C9. Since this class of compounds is more potent than any other toward 2C9, the small molecule properties deemed most ideal by the software were used to address protein-ligand interactions using new mutagenesis and structural data. Nine new bzbr analogues provide evidence that specific electrostatic and hydrophobic interactions contribute the most to 2C9's specificity. Three of the new analogues are better isosteres of bzbr that contain bulky groups adjacent to the phenol and have increased pK(a) values. These ligands test the hypothesis that anionic substrates bind with higher affinity to 2C9. Since they have higher affinity than the previous nonacidic analogues, the importance of bulky groups on the phenol ring appears to have been underestimated. CoMSIA models predict that these bulky groups are favorable for their hydrophobicity, while a negative charge is favored at the ketone oxygen rather than the phenol oxygen. The overlap of this ketone with electronegative groups of other 2C9 substrates suggests they act as key positive charge acceptors.

Aryl Hydrocarbon Hydroxylases↗
PubMed1994

A minimal model of the single capacitor biphasic defibrillation waveform.

UNLABELLED: A quantitative model of the single capacitor biphasic defibrillation waveform is proposed. The primary hypothesis of this model is that the first phase leaves a residual charge on the membranes of the unsynchronized cells, which can then reinitiate fibrillation. The second phase diminishes this charge, reducing the potential for refibrillation. To suppress this potential refibrillation, a monophasic shock must be strong enough to synchronize a critical mass of nearly 100% of the myocytes. Since the biphasic waveform performs this protection function by removing the residual charge (with its second phase), its first phase may be of a lower strength than a monophasic shock of equivalent performance. A quantitative model was developed to calculate the residual membrane voltage, Vm, assuming a capacitive membrane being alternately charged and discharged by the first and second phases, respectively. It was further assumed that the amplitude of the first phase would be predicted by a minimum value plus a term proportional to Vm2. The model was evaluated on the pooled data of three relevant published studies comparing biphasic waveforms. The model explained 79% of the variance in the first phase amplitude and predicted optimal durations for various defibrillator capacitances and electrode resistances. Assuming a first phase of optimal duration, the optimal second phase duration appears to be about 2.5 msec for all capacitances and resistances now seen clinically. CONCLUSION: The effectiveness of the single capacitor biphasic waveform may be explained by the second phase "burping" of the deleterious residual charge of the first phase that, in turn, reduces the synchronization requirement and the amplitude requirements of the first phase.

Action Potentials↗
PubMed2004

Quantitative genetic models for describing simultaneous and recursive relationships between phenotypes.

Multivariate models are of great importance in theoretical and applied quantitative genetics. We extend quantitative genetic theory to accommodate situations in which there is linear feedback or recursiveness between the phenotypes involved in a multivariate system, assuming an infinitesimal, additive, model of inheritance. It is shown that structural parameters defining a simultaneous or recursive system have a bearing on the interpretation of quantitative genetic parameter estimates (e.g., heritability, offspring-parent regression, genetic correlation) when such features are ignored. Matrix representations are given for treating a plethora of feedback-recursive situations. The likelihood function is derived, assuming multivariate normality, and results from econometric theory for parameter identification are adapted to a quantitative genetic setting. A Bayesian treatment with a Markov chain Monte Carlo implementation is suggested for inference and developed. When the system is fully recursive, all conditional posterior distributions are in closed form, so Gibbs sampling is straightforward. If there is feedback, a Metropolis step may be embedded for sampling the structural parameters, since their conditional distributions are unknown. Extensions of the model to discrete random variables and to nonlinear relationships between phenotypes are discussed.

Bayes Theorem↗
PubMed1989

A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters.

Infinite-dimensional characters are those in which the phenotype of an individual is described by a function, rather than by a finite set of measurements. Examples include growth trajectories, morphological shapes, and norms of reaction. Methods are presented here that allow individual phenotypes, population means, and patterns of variance and covariance to be quantified for infinite-dimensional characters. A quantitative-genetic model is developed, and the recursion equation for the evolution of the population mean phenotype of an infinite-dimensional character is derived. The infinite-dimensional method offers three advantages over conventional finite-dimensional methods when applied to this kind of trait: (1) it describes the trait at all points rather than at a finite number of landmarks, (2) it eliminates errors in predicting the evolutionary response to selection made by conventional methods because they neglect the effects of selection on some parts of the trait, and (3) it estimates parameters of interest more efficiently.

Analysis of Variance↗
PubMedDate not supplied

A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait.

With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The two Weibull baseline parameters were updated jointly using a Metropolis-Hasting step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.

Animals↗
PubMed2004

Toward an aggregated understanding of enzymatic hydrolysis of cellulose: noncomplexed cellulase systems.

Information pertaining to enzymatic hydrolysis of cellulose by noncomplexed cellulase enzyme systems is reviewed with a particular emphasis on development of aggregated understanding incorporating substrate features in addition to concentration and multiple cellulase components. Topics considered include properties of cellulose, adsorption, cellulose hydrolysis, and quantitative models. A classification scheme is proposed for quantitative models for enzymatic hydrolysis of cellulose based on the number of solubilizing activities and substrate state variables included. We suggest that it is timely to revisit and reinvigorate functional modeling of cellulose hydrolysis, and that this would be highly beneficial if not necessary in order to bring to bear the large volume of information available on cellulase components on the primary applications that motivate interest in the subject.

Cellulase↗
PubMed2005

[Study on temperature correctional models of quantitative analysis with near infrared spectroscopy].

Effect of enviroment temperature on near infrared spectroscopic quantitative analysis was studied. The temperature correction model was calibrated with 45 wheat samples at different environment temperaturs and with the temperature as an external variable. The constant temperature model was calibated with 45 wheat samples at the same temperature. The predicted results of two models for the protein contents of wheat samples at different temperatures were compared. The results showed that the mean standard error of prediction (SEP) of the temperature correction model was 0.333, but the SEP of constant temperature (22 degrees C) model increased as the temperature difference enlarged, and the SEP is up to 0.602 when using this model at 4 degrees C. It was suggested that the temperature correctional model improves the analysis precision.

Algorithms↗
PubMed1983

A tissue model for quantitative studies on time course of healing, rate of healing, and cell proliferation after wounding.

The perforated true mesentery of the rat was exploited as a model for the quantitative study of connective tissue wound healing. Healing by closure was examined daily after the virtually-vessel-free mesentery had been perforated with a scalpel. Proliferation was quantitated in fibroblast- and mesothelial-like cells in spreads of mesentery at defined distances from the wound margin, by means of cytophotomeric Feulgen-DNA measurements and by mitotic counting. Proliferation was also estimated by specific DNA-activity in perforated and unperforated mesentery membranes. Mast-cell histamine was quantitated as an indicator of disturbed tissue homeostasis. In young rats, healing by closure started on day 4, and was complete on day 10. The maximum rate of healing occurred on days 5-7. Old animals showed essentially the same rate of healing as young ones but healing was significantly delayed. Sham-operated animals showed a moderate release of histamine and increased proliferation. Wounding caused additional release of histamine and was followed by increased proliferation after 48-96 h. With this novel procedure, the time course, the rate of healing, and the proliferation of cells at defined distances from the wound can be defined quantitatively. The technique may well prove valuable in the study of the interplay between proliferation and healing and in the study of the effect of local and systemic factors on connective tissue wound healing.

Aging↗
PubMed1987

Demonstration and characterization of two classes of cardiac glycoside binding sites to rat heart membrane preparations using quantitative computer modeling.

Cardiac glycoside binding to rat heart membrane preparations was measured by rapid filtration technique. The binding data were analyzed using quantitative computer analysis. The experimental results using [3H]-ouabain as the labeled ligand were consistent with a model in which cardiac glycoside specific binding occurs at two independent classes of sites. The high affinity sites were characterized by a dissociation constants of 40 nM, 50 nM, and 61 nM for ouabain, digoxin and digitoxin, respectively, with a binding capacity of 1.3 pmoles/mg protein. The lower affinity sites for ouabain were characterized by dissociation constants of 2.3 microM, 67 nM and 71 nM for ouabain, digoxin and digitoxin, respectively, with a binding capacity of 3 pmoles/mg protein. Potassium ions inhibit [3H]-ouabain binding in a dose dependent manner with an IC50 of 500 microM. Quantitative computer modelling indicated that potassium inhibits ouabain binding at both binding sites.

Animals↗