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PubMed1990

Search for faster methods of fitting the regressive models to quantitative traits.

The regressive models describe familial patterns of dependence of quantitative measures by specifying regression relationships among a person's phenotype and genotype and the phenotypes and genotypes of antecedents. When the number of sibs in the pattern of dependence increases, as in the class D regressive model, computation of the likelihood becomes time consuming, since the Elston-Stewart algorithm cannot be used generally. On the other hand, the simpler class A regressive model, which imposes a restriction on the sib-sib correlation, may lead to inference of a spurious major gene, as already observed in some instances. A simulation study is performed to explore the robustness of class A model with respect to false inference of a major gene and to search for faster methods of computing the likelihood under class D model. The class A model is not robust against the presence of a sib-sib correlation exceeding that specified by the model, unless tests on transmission probabilities are performed carefully: false detection of a major gene is reduced from a number of 26-30 to between 0 and 4 data sets out of 30 replicates after testing both the Mendelian transmission and the absence of transmission of a major effect against the general transmission model. Among various approximations of the likelihood formulation of the class D model, approximations 6 and 8 are found to work appropriately in terms of both the estimation of all parameters and hypothesis testing, for each generating model. These approximations lessen the computer time by allowing use of the Elston-Stewart algorithm.

Computer Simulation↗
PubMed1995

Model-free association analysis of a rare disease.

Model-free methods of testing for association of a disease with alleles at a marker locus were used to analyze simulated data for a rare disease locus and 360 marker loci distributed at 2 cM intervals along six chromosomes. After adjustment for multiple tests, there was no evidence of significant heterogeneity of parental allele frequencies between a sample of parents with at least one affected child and a sample of parents with no affected children. Several significant deviations from Hardy-Weinberg equilibrium were detected after Bonferroni correction but these were Type I errors. After adjusting for multiple tests, the model-free test for association detected significant associations of alleles at two loci with the disease. These associations were in fact part of the generating model for the simulated data. However, these methods were unable to detect two other major loci contributing to the disease since these loci were not associated with any of the marker loci.

Alleles↗
PubMed2006

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules.

We have developed a version of our surface generalized Born (SGB) model that employs a Gaussian surface, as opposed to the van der Waals surface used previously. The Gaussian surface is smooth and its properties are analytically differentiable with respect to the positions of atoms. A significant advantage of a solvent model based on this analytically differentiable surface is the availability of analytical gradients of the surface and solvation forces. An efficient and robust algorithm is designed to construct and triangulate the Gaussian surface for large biomolecules with arbitrary shapes, and to compute the various terms required for energy gradients. The Gaussian surface is shown to better mimic the boundary between the solute and solvent by properly addressing solvent accessibility, as is demonstrated by comparisons with standard Poisson-Boltzmann calculations for proteins of different sizes. These results also demonstrate that surface definition is a dominant contribution to differences between GB and PB calculations, especially if the system is large. Application of the new surface to prediction of long loop regions is presented, and significant improvement in the energetics is seen compared with results obtained using the van der Waals surface, even in the absence of optimized empirical correction terms that were used in the latter calculations.

Algorithms↗
PubMed1993

The Cascade Neural Network Model and a Speed-Accuracy Trade-Off of Arm Movement.

We propose a hybrid neural network model of aimed arm movements that consists of a feedforward controller and a postural controller. The cascade neural network of Kawato, Maeda, Uno, and Suzuki (1990) was employed as a computational implementation of the feedforward controller. This network computes feedforward motor commands based on a minimum torque-change criterion. If the weighting parameter of the smoothness criterion is fixed and the number of relaxation iterations is rather small, the cascade model cannot calculate the exact torque, and the hand does not reach the desired target by using the feedforward control alone. Thus, one observes an error between the final position and the desired target location. By using a fixed weighting parameter value and a limited iteration number to simulate target-directed arm movements, we found that the cascade model generated a planning time-accuracy trade-off, and a quasi-power-law type of speed-accuracy trade-off. The model provides a candidate neural mechanism to explain the stochastic variability of the time course of the feedforward motor command. Our approach also accounts for several invariant features of multijoint arm trajectories, such as roughly straight hand paths and bell-shaped speed profiles.

Journal Article↗
PubMed1991

A mathematical model describing the generation of oxygen radicals in mitochondria during ischemia-reperfusion.

A mathematical model for the generation of free radicals by mitochondria in ischemia-reperfusion is proposed. Computations show that normally two stable equilibrium states exist: the intact state, and the state characterized by damage to mitochondrial structures and a high rate of radical formation. Transition from one state to another occurs after hypoxia of a certain degree of severity and duration. The model also describes a number of phenomena observed during development of reperfusion injuries and drug therapy.

Free Radicals↗
PubMed2001

Using light scatter signal to estimate bacterial biovolume by flow cytometry.

BACKGROUND: In the past decade, flow cytometry has become a useful and precise alternative to microscopic bacterial cell counts in aquatic samples. However, little evidence of its usefulness for the evaluation of bacterial biovolumes has emerged in from the literature. METHODS: The light scattering and cell volume of starved bacterial strains and natural bacterial communities from the Black Sea were measured by flow cytometry and epifluorescence microscopy, respectively, in order to establish a relationship between light scattering and cell volume. RESULTS: With the arc-lamp flow cytometer, forward angle light scatter (FALS) was related to cell size in both the starved strains and natural communities, although regression parameters differed. We tested the predictive capacity of the FALS verous cell size relationship in a bacterial community from the North Sea. That analysis showed that a reliable bacterial biovolume prediction of a natural bacterial community can be obtained from FALS using a model generated from natural bacterial community data. CONCLUSIONS: Bacterial biovolume is likely to be related to FALS measurements. It is possible to establish a generally applicable model derived from natural bacterial assemblages for flow cytometric estimation of bacterial biovolumes by light scatter.

Aeromonas hydrophila↗
PubMed2005

Statistical modelling of fatigue-related electromyographic median frequency characteristics of back and hip muscles during a standardized isometric back extension test.

The purpose of the present study was to evaluate which statistical model - linear, logarithmic, quadratic or exponential - best described the fatigue-related electromyographic (EMG) changes of back and hip muscles. Twenty healthy volunteers performed a modified Biering-Sorensen test. The EMG activity of the latissimus dorsi (LD), longissimus thoracis pars thoracis (LTT) and lumborum (LTL), iliocostalis lumborum pars thoracis (ILT) and lumborum (ILL), multifidus (MF), gluteus maximus (GM) and biceps femoris (BF) was measured bilaterally using surface electrodes. Higher R(2) values were found for the quadratic models (p<0.05 for all muscles), and lower R(2) values for the logarithmic models (p<0.05 for LTT, LTL, ILL, MF and GM). The exponential models generated higher R(2) values compared to the linear ones for the LTT, LTL and MF (all p<0.05). Further analyses revealed, however, that these models did not add useful additional information, and therefore would only increase the complexity. The findings of the current study validate the use of simple linear regression techniques when studying fatigue-related EMG median frequency characteristics of back and hip muscles during isometric contractions.

Adult↗
PubMed2000

Potential drugs and nondrugs: prediction and identification of important structural features

Using decision trees, a model to discriminate between potential drugs and nondrugs has been developed. Compounds from the Available Chemical Directory and the World Drug Index databases were used as training set; the molecular structures were represented using extended atom types. The error rate on an independent validation data set is 17.4%. The number of false negatives can be reduced by penalizing the misclassification of drugs so that 92 out of 100 potential drugs are correctly recognized. At the same time, 34 out of 100 nondrugs are classified as potential drugs. The predictions of the model can be used to guide the purchase or selection of compounds for biological screening or the design of combinatorial libraries. The visualization of the generated models in the form of colored trees allowed us to identify a few, surprisingly simple features that explain the most significant differences between drugs and nondrugs in the training set: Just by testing the presence of hydroxyl, tertiary or secondary amino, carboxyl, phenol, or enol groups, already three quarters of all drugs could be correctly recognized. The nondrugs, on the other hand, are characterized by their aromatic nature with a low content of functional groups besides halogens. The general applicability of the model is shown by the predictions made for several Organon databases.

Journal Article↗
PubMedDate not supplied

Ischemia-reperfusion injury in chronic pressure ulcer formation: a skin model in the rat.

Most animal models of chronic pressure ulcers were designed to study only the role of ischemic injury in wound formation, often using single applications of constant pressure. The purpose of this study was to develop and characterize a reproducible model of cyclic ischemia-reperfusion injury in the skin of small un-anesthetized animals using clinically relevant pressures and durations. Ischemia-reperfusion injury was created in a 9 cm2 region of dorsal skin in male rats by periodically compressing skin under a pressure of 50 mm Hg using an implanted metal plate and an overlying magnet. We varied the total number of ischemia-reperfusion cycles, examined the effect of varying the frequency and duration of ischemic insult, and compared ischemia-induced injury to ischemia-reperfusion-induced injury with this model. Tissue injury increased with an increasing number of total ischemia-reperfusion cycles, duration of ischemia, and frequency of ischemia-reperfusion cycles. This model generates reproducible ischemia-reperfusion skin injury as characterized by tissue necrosis, wound thickness, leukocyte infiltration, transcutaneous oxygen tension, and wound blood flow. Using this model, the biological markers of ischemia-reperfusion-induced wound development can be studied and therapeutic interventions can be evaluated in a cost-effective manner.

Animals↗
PubMed2006

A novel peroxisome proliferator-activated receptor responsive element-luciferase reporter mouse reveals gender specificity of peroxisome proliferator-activated receptor activity in liver.

There is a growing interest in peroxisome proliferator-activated receptors (PPARs) as major players in the regulation of lipid and carbohydrate metabolism. Drugs targeting PPARs were in fact shown to have major relevance for the treatment of diseases associated with aging, such as arteriosclerosis and diabetes. However, a variety of toxic effects associated with PPAR ligand administration has been documented, including hepatocarcinogenesis, which may severely limit its therapeutic use. A better comprehension of the multiplicity of PPAR physiological functions is therefore mandatory for the development of novel, safer drugs. We here describe the generation of a novel transgenic mouse for the detection of the generalized activities of PPARs, the PPAR responsive element-Luc reporter mouse. In this model luciferase expression is under the control of a PPAR-inducible promoter in all target organs. By optical imaging and ex vivo analysis, we were able to demonstrate the remarkable gender specificity of the PPAR transcriptional activity in liver. In fact, in the liver of female PPAR responsive element-Luc, the PPAR reporter transgene is more than one order of magnitude less expressed, thus leading to the conclusion that the signaling in females is much less activated than in males. Diet or hormonal manipulations as demonstrated here by treatments with high-fat diet or gonad removal and hormone replacement do not influence this low activation. The extent of the gender difference in PPAR transcriptional activity and the ineffectiveness of hormone treatments or diet to significantly elevate liver PPAR activity in females led us to hypothesize that gender-specific epigenetic events occurring during development may affect PPAR signaling in the liver. This study sets the ground for understanding the differential susceptibility of the two genders to metabolic disorders; furthermore, the model generated provides a novel opportunity for the molecular characterization of PPAR activity in pathophysiological conditions.

Animals↗
PubMedDate not supplied

Fabrication of titanium implant-retained restorations with nontraditional machining techniques.

Traditional laboratory techniques are being supplemented by modern precision technologies to solve complex restorative problems. Electrical discharge machining combined with laser scanning and computer aided design-computer aided manufacturing can create very precise restorations without the lost wax method. A laser scanner is used to create a three-dimensional polyline data model that can then be converted into a stereolithography file format for output to a stereolithography apparatus or other rapid prototyping device. A stereolithography-generated model is used to create an electric discharge machining electrode via copper electroforming. This electrode is used to machine dental restorations from an ingot of titanium, bypassing the conventional lost wax casting process. Retaining screw access holes are machined using conventional drilling procedures, but could be accomplished with electric discharge machining if desired. Other rapid prototyping technologies are briefly discussed.

Computer-Aided Design↗
PubMed1999

Pathophysiology of gene-targeted mouse models for cystic fibrosis.

Pathophysiology of Gene-Targeted Mouse Models for Cystic Fibrosis. Physiol. Rev. 79, Suppl.: S193-S214, 1999. - Mutations in the gene causing the fatal disease cystic fibrosis (CF) result in abnormal transport of several ions across a number of epithelial tissues. In just 3 years after this gene was cloned, the first CF mouse models were generated. The CF mouse models generated to date have provided a wealth of information on the pathophysiology of the disease in a variety of organs. Heterogeneity of disease in the mouse models is due to the variety of gene-targeting strategies used in the generation of the CF mouse models as well as the diversity of the murine genetic background. This paper reviews the pathophysiology in the tissues and organs (gastrointestinal, airway, hepatobiliary, pancreas, reproductive, and salivary tissue) involved in the disease in the various CF mouse models. Marked similarities to and differences from the human disease have been observed in the various murine models. Some of the CF mouse models accurately reflect the ion-transport abnormalities and disease phenotype seen in human CF patients, especially in gastrointestinal tissue. However, alterations in airway ion transport, which lead to the devastating lung disease in CF patients, appear to be largely absent in the CF mouse models. Reasons for these unexpected findings are discussed. This paper also reviews pharmacotherapeutic and gene therapeutic studies in the various mouse models.

Animals↗
PubMed2004

Finding scientific topics.

A first step in identifying the content of a document is determining which topics that document addresses. We describe a generative model for documents, introduced by Blei, Ng, and Jordan [Blei, D. M., Ng, A. Y. & Jordan, M. I. (2003) J. Machine Learn. Res. 3, 993-1022], in which each document is generated by choosing a distribution over topics and then choosing each word in the document from a topic selected according to this distribution. We then present a Markov chain Monte Carlo algorithm for inference in this model. We use this algorithm to analyze abstracts from PNAS by using Bayesian model selection to establish the number of topics. We show that the extracted topics capture meaningful structure in the data, consistent with the class designations provided by the authors of the articles, and outline further applications of this analysis, including identifying "hot topics" by examining temporal dynamics and tagging abstracts to illustrate semantic content.

Databases, Factual↗
PubMed2006

Realistic modeling of entorhinal cortex field potentials and interpretation of epileptic activity in the guinea pig isolated brain preparation.

Mechanisms underlying epileptic activities recorded from entorhinal cortex (EC) were studied through a computational model based on review of cytoarchitectonic and neurobiological data about this structure. The purpose of this study is to describe and use this model to interpret epileptiform discharge patterns recorded in an experimental model of ictogenesis (guinea pig isolated brain perfused with bicuculline). A macroscopic modeling approach representing synaptic interactions between cells subpopulations in the EC was chosen for its adequacy to mimic field potentials reflecting overall dynamics rising from interconnected cells populations. Therefore intrinsic properties of neurons were not included in the modeling design. Model parameters were adjusted from an identification procedure based on quantitative comparison between real and simulated signals. For both EC deep and superficial layers, results show that the model generates very realistic signals regarding temporal dynamics, spectral features, and cross-correlation values. These simulations allowed us to infer information about the evolution of synaptic transmission between principal cell and interneuronal populations and about connectivity between deep and superficial layers during the transition from background to ictal activity. In the model, this transition was obtained for increased excitation in deep versus superficial layers. Transitions between epileptiform activities [interictal spikes, fast onset activity (25 Hz), ictal bursting activity] were explained by changes of parameters mainly related to GABAergic interactions. Notably, the model predicted an important role of GABAa,fast- and GABAb-receptor-mediated inhibition in the generation of ictal fast onset and burst activities, respectively. These findings are discussed with respect to experimental data.

Action Potentials↗
PubMed2001

Transmembrane alpha-helices in the gap junction membrane channel: systematic search of packing models based on the pair potential function.

Recent progress in the field of electron cryo-microscopy and image analysis has shown that there is an overwhelming need to interpret medium resolution (5 to 10 A) three-dimensional maps. Traditional methods of fitting amino acid residues into electron density using molecular modeling programs must be supplemented with further analysis. We have used a potential of mean force (PMF) method, derived from Boltzmann statistics in protein structure, to generate models for the packing of alpha-helices, using pairwise potentials between amino acid residues. The approach was tested using the three-dimensional map of a recombinant cardiac gap junction membrane channel provided by electron cryo-crystallography (Unger et al., 1997; 1999a, 1999b) which had a resolution of 7.5 A in the membrane plane and 21 A in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which was consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. Based on the three-dimensional map and the amino acid sequence for the 4 transmembrane domains determined by hydropathy analysis, we used the modeling utility SymServ (Macke et al., 1998) to build hexameric connexons with 24 transmembrane alpha-helices. Canonical alpha-helices were aligned to the axes of the rods of density and translated along the density so that the center of masses coincided. The PMF function was used to evaluate 162,000 conformations for each of the 24 possible alpha-helical packing models. Since the different packing models yielded different energy distributions, the pair potential function appears to be a promising tool for evaluating the packing of alpha-helices in membrane proteins. The analysis will be refined by energy calculations based on the expectations that the outer boundary of the channel will be formed by hydrophobic residues in contact with the lipids.

Connexins↗
PubMed2003

An image-based finite difference model for simulating restricted diffusion.

Water diffusion in tissues is generally restricted and often anisotropic. Neural tissue is of particular interest, since it is well known that injury alters diffusion in a characteristic manner. Both Monte Carlo simulations and approximate analytical models have previously been reported in attempts to predict water diffusion behavior in the central nervous system. These methods have relied on axonal models, which assume simple geometries (e.g., ellipsoids, cylinders, and square prisms) and ignore the thickness of the myelin sheath. The current work describes a method for generating models using synthetic images. The computations are based on a 3D finite difference (FD) approximation of the diffusion equation. The method was validated with known analytic solutions for diffusion in a cylindrical pore and in a hexagonal array of cylinders. Therefore, it is envisioned that, by exploiting histologic images of neuronal tissues as input model, current method allows investigating the water diffusion behavior inside biological tissues and potentially assessing the status of neural injury and regeneration.

Axons↗
PubMed1997

The influenza A virus M2 channel: a molecular modeling and simulation study.

The M2 protein of influenza virus forms ion channels activated by low pH which are proton permeable and play a key role in the life cycle of the virus. M2 is a 97-residue integral membrane protein containing a single transmembrane (TM) helix. M2 is present as disulfide-linked homotetramers. The TM domain of M2 has been modeled as a bundle of four parallel M2 helices. The helix bundle forms a left-handed supercoil surrounding a central pore. Residue H37 has been implicated in the mechanism of low-pH activation of the channel. Models generated with H37 in a fully deprotonated state exhibit a pore occluded by a ring of H37 side chains oriented toward the lumen of the pore. Models with H37 in a fully protonated state no longer exhibit such occlusion of the pore, as the H37 side chains adopt a more interfacial location. Extended molecular dynamics simulations with water molecules within and at the mouths of the pores support this distinction between the H37-deprotonated and H37-protonated models. These simulations suggest that only in the H37-protonated model is there a continuous column of water extending the entire length of the central pore. A mechanism for activation of M2 by low pH is presented in which the H37-deprotonated model corresponds to the "closed" form of the channel, while the H37-protonated model corresponds to the "open" form. A switch from the closed to the open form of the channel occurs if H37 is protonated midway through a simulation. The open channel is suggested to contain a wire of H-bonded water molecules which enables proton permeability.

Computer Simulation↗
PubMed2003

Advanced modeling environment for developing and testing FES control systems.

Realistic models of neuromusculoskeletal systems can provide a safe and convenient environment for the design and evaluation of controllers for functional electrical stimulation (FES) prior to clinical trials. We have developed a set of integrated musculoskeletal modeling tools to facilitate the model building process. Simulink models of musculoskeletal systems are created using two software packages developed in our laboratory, Musculoskeletal Modeling in Simulink (MMS) and virtual muscle, in addition to one software package available commercially, SIMM (Musculographics Inc., USA). MMS converts anatomically accurate musculoskeletal models generated by SIMM into Simulink(R) blocks. It also removes run-time constraints on kinetic simulations in SIMM, and allows the development of complex musculoskeletal models without writing a line of code. Virtual muscle builds realistic Simulink models of muscles responding to either natural recruitment or FES. Models of sensorimotor control systems can be developed using various Matlab (Mathworks Inc., USA) toolboxes and integrated easily with these musculoskeletal blocks in the graphical environment of Simulink.

Computer Simulation↗