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At least 811 records · Page 45Linked to original sources

PubMed2002

Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction.

Experimental observations suggest that electronic characteristics play a role in the rates of substrate oxidation for cytochrome P450 enzymes. For example, the tendency for oxidation of a certain functional group generally follows the relative stability of the radicals that are formed (e.g., N-dealkylation > O-dealkylation > 2 degrees carbon oxidation > 1 degree carbon oxidation). In addition, results show that useful correlations between the rates of product formation can be developed using electronic models. In this article, we attempt to determine whether a combined computational model for aromatic and aliphatic hydroxylation can be developed. Toward this goal, we used a combination of experimental data and semiempirical molecular orbital calculations to predicted activation energies for aromatic and aliphatic hydroxylation. The resulting model extends the predictive capacity of our previous aliphatic hydroxylation model to include the second most important group of oxidations, aromatic hydroxylation. The combined model can account for about 83% of the variance in the data for the 20 compounds in the training set and has an error of about 0.7 kcal/mol.

Computer Simulation↗

PubMed1997

Anatomically accurate, finite model eye for optical modeling.

There is a need for a schematic eye that models vision accurately under various conditions such as refractive surgical procedures, contact lens and spectacle wear, and near vision. Here we propose a new model eye close to anatomical, biometric, and optical realities. This is a finite model with four aspheric refracting surfaces and a gradient-index lens. It has an equivalent power of 60.35 D and an axial length of 23.95 mm. The new model eye provides spherical aberration values within the limits of empirical results and predicts chromatic aberration for wavelengths between 380 and 750 nm. It provides a model for calculating optical transfer functions and predicting optical performance of the eye.

Biometry↗

PubMed2003

A dynamic model of metabolizable energy utilization in growing and mature cattle. III. Model evaluation.

Component models of heat production identified in a proposed system of partitioning ME intake and a dynamic systems model that predicts gain in empty BW in cattle resulting from a known intake of ME were evaluated. Evaluations were done in four main areas: 1) net efficiency of ME utilization for gain, 2) relationship between recovered energy and ME intake, 3) predicting gain in empty BW from recovered energy, and 4) predicting gain in empty BW from ME intake. An analysis of published data showed that the net partial efficiencies of ME utilization for protein and fat gain were approximately 0.2 and 0.75, respectively, and that the net efficiency of ME utilization for gain could be estimated using these net partial efficiencies and the fraction of recovered energy that is contained in protein. Analyses of published sheep and cattle experimental data showed a significant linear relationship between recovered energy and ME intake, with no evidence for a nonlinear relationship. Growth and body composition of Hereford x Angus steers simulated from weaning to slaughter showed that over the finishing period, 20.8% of ME intake was recovered in gain. These results were similar to observed data and comparable to feedlot data of 26.5% for a shorter finishing period with a higher-quality diet. The component model to predict gain in empty BW from recovered energy was evaluated with growth and body composition data of five steer genotypes on two levels of nutrition. Linear regression of observed on predicted values for empty BW resulted in an intercept and slope that were not different (P < 0.05) from 0 and 1, respectively. Evaluations of the dynamic systems model to predict gain in empty BW using ME intake as the input showed close agreement between predicted and observed final empty BW for steers that were finished on high-energy diets, and the model accurately predicted growth patterns for Angus, Charolais, and Simmental reproducing females from 10 mo to 7 yr of age.

Animal Feed↗

PubMed2001

Bayesian analysis of liability of clinical mastitis in Norwegian cattle with a threshold model: effects of data sampling method and model specification.

First-lactation records of Norwegian Cattle were used to infer heritability of liability to clinical mastitis with a threshold sire model. Mastitis was defined as a binary response (presence or absence) in a defined period of first lactation (opportunity period). Length of opportunity period (from 30 d before calving up to 120 or 300 d of lactation) had less effect on heritability estimates than data sampling methods (include or exclude records of cows culled before the end of the opportunity period) whereas sire ranking was more affected by the former. Including all cows, whether culled before the end of the opportunity period or not, gave a sharper and more symmetric posterior distribution of heritability of liability to clinical mastitis. When we analyzed data for all cows, model specification had a small effect on heritability estimates, while sire ranking was affected markedly. Posterior means of heritability range from 0.058 to 0.074. A model regressing on the length of the opportunity period for culled cows without mastitis, was shown favorable for the two opportunity periods using Bayes factors and the deviance information criterion for model comparison. This model, in which liability of mastitis depends on time to culling, may allow utilizing information from all first lactations in genetic evaluation, irrespectively of duration and culling outcome.

Animals↗

PubMed2002

Prediction of early and delayed postoperative deaths after coronary artery bypass surgery alone in Italy. Multivariate predictions based on Cox and logistic models and a chart based on the accelerated failure time model.

BACKGROUND: The aim of the multicenter OP-RISK (OPerative RISK) study was to investigate the early (28 days) and delayed (365 days) death rates following coronary artery bypass grafting (CABG) among patients representing a nationwide distribution [Centers in Northern (2), Central (1) and Southern (1) Italy] and further to define the multivariate risk factors for the early and delayed mortality after CABG. METHODS: Data were collected from 1126 patients undergoing CABG alone. Data were analyzed using Cox and logistic regression models, to accurately assess the major factors influencing survival over time after CABG. Having defined the significant factors, we constructed a chart of the absolute early risk of mortality using the accelerated failure time model. RESULTS: Using the Cox proportional hazards model and logistic regression we have demonstrated that age, preoperative ejection fraction and heart rate, and the duration of aortic cross-clamping are multivariate risk factors in the short and long term. The role of one arterial conduit was also assessed. CONCLUSIONS: The OP-RISK study produced relevant information for risk assessment and control in CABG and the results may form the basis for the objective quality assurance and accreditation of cardiac surgical institutions in Italy. Incidentally, Cox model appeared more adequate than logistic model for the assessment of the major factors influencing survival over time after CABG. The risk factors so assessed were used to construct a chart for practical predictive purposes.

Adult↗

PubMed1990

Modelling of binding sites of the nicotinic acetylcholine receptor and their relation to models of the whole receptor.

Models for the acetylcholine (ACh)-binding site of the nicotinic acetylcholine receptor (nAChR) are proposed. These models have been developed by using the concept of the ligand-gated ion-channel (LGIC) superfamily of receptors that have evolved from a common ancestor. An initial component of the binding site was identified as a highly conserved 15-residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits, based on aligned sequence data of LGICs. This subregion, termed the Cys-loop, was modelled as an amphiphilic beta-hairpin and we propose that it forms a major determinant of the binding cleft for agonists. This initial, partial binding-site model has been extended to include residues biochemically identified as spatially adjacent to the binding cleft. A recently developed technique for rapidly scanning the known protein structural database for 'non-homologous similarity' using just sequence information identified the known structure of the enzyme pyrophosphatase (PPase) as a candidate scaffold for the N-terminal domain of the nAChR. This similarity was investigated further using sequence alignments. A framework model of the full N-terminal domain in which the position of the Cys-loop and other binding-site determinants, as well as the main immunogenic region (MIR), have been mapped on to the PPase structure.

Amino Acid Sequence↗

PubMed1989

[Modelling of the regulatory system of tryptophan biosynthesis using generalized threshold models].

A mathematical model of the tryptophan biosynthesis regulatory system (TBRS) in Escherichia coli has been constructed and studied by the method of generalized threshold models. The system includes the tryptophan operon, the operon producing aporepressor and multienzyme chain of tryptophan synthesis. The kinetic curves for molecular components of the system (mRNA, proteins, tryptophan) are obtained by means of computer calculations using mathematical model of the TBRS. The dynamics of normal and mutant regulatory systems of tryptophan biosynthesis and the system with cloned blocks have been analysed. Functioning of the following mechanisms regulating tryptophan biosynthesis is studied: feed-back inhibition of enzyme activity, repression and attenuation of the tryptophan operon transcription. It is shown that the method of generalized threshold models reflects the dynamics of a molecular genetic regulatory system more completely than the method of threshold models.

Escherichia coli↗

PubMed1987

[Model and model-independent methods of describing pharmacokinetics: the advantages, drawbacks and interrelationship].

A system for classification of the main quantitative approaches used in describing drug pharmacokinetics is proposed. The basis of the system is occupied by the systemic approach ignoring a detailed picture of the processes observed in the organism with participation of drugs and providing only integral description of such processes by parameters not depending on the concrete structure of the model. The second level is represented by stochastic models which also ignore the process detailed mechanism but provide concrete definition of the drug retention time frequency and distribution. The upper level is occupied by structural models (compartment and physiological) fixating a priori the concrete picture of the drug mass transfer in the organism which is more or less close to the real one. Interrelation of the three levels is analyzed. Definitions of the main model independent pharmacokinetic parameters such as total clearance, apparent volume distribution and mean retention time of the drug molecules in the organism are presented. A relationship between the drug concentration profile in blood and the drug retention time density distribution was developed. This relationship is the ground of the stochastic pharmacokinetic models.

Animals↗

PubMed1981

[Biomechanical simulation model of the developmental morphology of the human skull. Further observations on the model construction].

The implementation of a software simulation of a biomechanical model of the human skull, requires a high complexity construction made by a different ellipsoids and planes. At present our model is made by a facial, post-facial, occipital and palatal ellipsoids, a basal plane with a hole, walls of the nasal cavity and conic walls of the orbital cavities. Dimension of the model resemble closely an adult human skull. The physical constants given for the constituting material those of compact bone. The cavity of the model is closed except for the hole of the basal plane and for the posterior openings of the orbital cavities. The number of elements of the model is 416.

Humans↗

PubMedDate not supplied

Mortality model based on delays in progression of chronic diseases: alternative to cause elimination model.

For the analysis of the impact of major chronic diseases on a population, a life table model is proposed in which the age at death due to specific cause (chronic disease) is postponed. Even though many of the major causes of death related to intrinsic aging processes are impossible to eliminate, these causes might be significantly delayed or retarded. To illustrate the use of this model, the effects of a delay of 5, 10, and 15 years in deaths due to three chronic degenerative diseases (cancer, ischemic heart disease, and stroke) are calculated for specific race-sex components of the U.S. population in 1969. These calculations show that even moderate delays in the progression of major chronic diseases will yield a sizable portion of the total gain in longevity that would be available if the diseases were totally eliminated. Thus, they demonstrate that a life table model based on cause delay provides a more biomedically plausible representation of the health impact of a chronic disease on a population than does the cause elimination life table model. Additionally, the cause-delay model provides a mechanism for incorporating the likely effects of medical innovation on survival.

Actuarial Analysis↗

PubMed1994

Advantages and inconveniences of the Cox model compared with the logistic model: application to a study of risk factors of nursing cow infertility.

The survival Cox model and the logistic model were compared on a data set obtained from an ecopathological survey relative to the risk factors of nursing cow infertility. The risk factors resulting from the 2 models were the same. The Cox model has the advantage of preserving the variable in its original quantitative form, and of using a maximum of information. However, very restrictive conditions of application of this model make its use rather limited.

Animals↗

PubMed1998

The linear-quadratic model and most other common radiobiological models result in similar predictions of time-dose relationships.

One of the fundamental tools in radiation biology is a formalism describing time-dose relationships. For example, there is a need for reliable predictions of radiotherapeutic isoeffect doses when the temporal exposure pattern is changed. The most commonly used tool is now the linear-quadratic (LQ) formalism, which describes fractionation and dose-protraction effects through a particular functional form, the generalized Lea-Catcheside time factor, G. We investigate the relationship of the LQ formalism to those describing other commonly discussed radiobiological models in terms of their predicted time-dose relationships. We show that a broad range of radiobiological models are described by formalisms in which a perturbation calculation produces the standard LQ relationship for dose fractionation/protraction, including the same generalized time factor, G. This approximate equivalence holds not only for the formalisms describing binary misrepair models, which are conceptually similar to LQ, but also for formalisms describing models embodying a very different explanation for time-dose effects, namely saturation of repair capacity. In terms of applications to radiotherapy, we show that a typical saturable repair formalism predicts practically the same dependences for protraction effects as does the LQ formalism, at clinically relevant doses per fraction. For low-dose-rate exposure, the same equivalence between predictions holds for early-responding end points such as tumor control, but less so for late-responding end points. Overall, use of the LQ formalism to predict dose-time relationships is a notably robust procedure, depending less than previously thought on knowledge of detailed biophysical mechanisms, since various conceptually different biophysical models lead, in a reasonable approximation, to the LQ relationship including the standard form of the generalized time factor, G.

Brachytherapy↗

PubMed1997

Comparison of population pharmacokinetic modeling methods using simulated data: results from the Population Modeling Workgroup.

Statistical modeling methods have had increasing use in drug disposition studies, both to estimate pharmacokinetic parameters and to develop regression models that relate these parameter estimates to patient characteristics. These methods are particularly flexible as they allow non-linearity and sparse within-patient information. In the past few years, multiple analysis methods have become available, but there is a lack of systematic comparisons of their estimates on the same data sets. Two simulated data sets were therefore developed by the Population Modeling Workgroup of the Biopharmaceutical Section of the American Statistical Association. We analysed these data sets using seven population modeling programs, some of which contain multiple analysis methods. Although each data set represents a single replicate from a given model and data collection design, the results suggest that the behaviour of some methods differs from that of the others.

Anti-Arrhythmia Agents↗

PubMed2001

Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure.

The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher.

Computer Simulation↗

PubMed2006

Optimization of the cell seeding density and modeling of cell growth and metabolism using the modified Gompertz model for microencapsulated animal cell culture.

Cell microencapsulation is one of the promising strategies for the in vitro production of proteins or in vivo delivery of therapeutic products. In order to design and fabricate the optimized microencapsulated cell system, the Gompertz model was applied and modified to describe the growth and metabolism of microencapsulated cell, including substrate consumption and product formation. The Gompertz model successfully described the cell growth kinetics and the modified Gompertz models fitted the substrate consumption and product formation well. It was demonstrated that the optimal initial cell seeding density was about 4-5 x 10(6) cells/mL of microcapsule, in terms of the maximum specific growth rate, the glucose consumption potential and the product formation potential calculated by the Gompertz and modified Gompertz models. Modeling of cell growth and metabolism in microcapsules provides a guideline for optimizing the culture of microencapsulated cells.

Alginates↗

PubMed1984

Cusp and butterfly catastrophe modeling of two opponent process models: drug addiction and work performance.

This article concerns a cross-level formal identity between systems at the level of the organism and the level of an organization. It discusses catastrophe modeling for a class of theories, opponent process models, particularly two that have been proposed for drug addiction and the job satisfaction-performance relationship. The resulting models are then expanded to butterfly catastrophes; results converge with models proposed from other vantage points. While job satisfaction and drug addiction appear to have little to do with each other, the mathematical modeling common to them offers a systemic link between an individual and a foreign chemical substance, and an individual within a job in an organization.

Humans↗

PubMed2004

Solids modeled by ab initio crystal field methods, part 22: the Fock matrix transformed supermolecule model and the structure determination of D-erythronic acid-3,4-carbonate.

To eliminate the cutoff effects in the supermolecule model (SM), the Fock matrix transformed supermolecule model (FTSM) is developed. In this model a cyclization of the cluster is performed by means of transformations of elements of the Fock matrix, thereby restoring the translational symmetry. Besides this fundamental enhancement, significant CPU time savings are realized because, in this new procedure, not all Fock matrix elements need to be calculated. The method is applied in a study of the structure of D-erythronic acid-3,4-carbonate in the crystal phase, where the new model is compared to the supermolecule model as well as the XRD experiment. The results are found to be in good agreement with experimental data.

Algorithms↗

PubMed2004

The Consensus Conference and Combined-Integrated model of doctoral training in professional psychology--overview of part 1: nature and scope of the Combined-Integrated model.

This special series of articles on the Consensus Conference and Combined-Integrated (C-I) model of doctoral training in professional psychology consists of 13 articles in two successive volumes of the Journal of Clinical Psychology. Six articles are presented in Part 1 (Vol. 60, Issue 9), which collectively describe the "nature and scope" of the C-I model (e.g., historic and definitional issues; the potential advantages of this model; implications for the profession). In Part 2 of this special series (Vol. 60, Issue 10), articles 7 through 12 address the broader implications and potential applications of the C-I model within a range of professional and societal contexts (e.g., for interprofessional collaboration; the health care field; development of a global curriculum; the unified psychology movement; issues of assessment and professional identity; and higher education); article 13 provides a summary of the series as well as a discussion of future directions. As an overview, this paper provides the abstract for each of the articles in Part 1, and describes the various topics of the articles in Part 2. Taken together, the articles in this special series are designed to provide a coherent account of how and why the C-I model is timely and relevant, and therefore warrants serious consideration by the larger education and training community in professional psychology.

Consensus Statements as Topic↗