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PubMed2005

Complementary identification of multiple flux distributions and multiple metabolic pathways.

Cell robustness and complexity have been recognized as unique features of biological systems. Such robustness and complexity of metabolic-reaction systems can be explored by discovering, or identifying, the multiple flux distributions (MFD) and redundant pathways that lead to a given external state; however, this is exceedingly cumbersome to accomplish. It is, therefore, highly desirable to establish an effective computational method for their identification, which, in turn, gives rise to a novel insight into the cellular function. An effective approach is proposed for complementarily identifying MFD in metabolic flux analysis and multiple metabolic pathways (MMP) in structural pathway analysis. This approach judiciously integrates flux balance analysis (FBA) based on linear programming and the graph-theoretic method for determining reaction pathways. A single metabolic pathway, with the concomitant flux distribution and the overall reaction manifesting itself as the desired phenotype under some environmental conditions, is determined by FBA from the initial candidate sequence of metabolic reactions. Subsequently, the graph-theoretic method recovers all feasible MMP and the corresponding MFD. The approach's efficacy is demonstrated by applying it to the in silico Escherichia coli model under various culture conditions. The resultant MMP and MFD attaining a unique external state reveal the surprising adaptability and robustness of the intricate cellular network as a key to cell survival against environmental or genetic changes. These results indicate that the proposed approach would be useful in facilitating drug discovery.

Algorithms↗
PubMed1984

Transport properties of polymer solutions. A comparative approach.

A variety of transport properties have been measured for solutions of the water soluble polymer poly(ethylene oxide)(PEO) with molecular weights ranging from 200 to 14,000, and volume fractions ranging from 0-80%. The transport properties are thermal conductivity, electrical conductivity at audio frequencies (in solutions containing dilute electrolyte), and water self-diffusion. These data, together with dielectric relaxation data previously reported, are amenable to analysis by the same mixture theory. The ionic conductivity and water self-diffusion coefficient, but not the thermal conductivity, are substantially smaller than predicted by the Maxwell and Hanai mixture relations, calculated using the known transport properties of pure liquid water. A 25% (by volume) solution of PEO exhibits an average dielectric relaxation frequency of the suspending water of one half that of pure water, with clear evidence of a distribution of relaxation times present. The limits of the cumulative distribution of dielectric relaxation times that are consistent with the data are obtained using a linear programming technique. The application of simple mixture theory, under appropriate limiting conditions, yields hydration values for the more dilute polymer solutions that are somewhat larger than values obtained from thermodynamic measurements.

Biological Transport↗
PubMed1996

"Adaptive" behavior of ligand-gated ion channels: constraints by thermodynamics.

The calcium-induced calcium release channel of the cardiac sarcoplasmic reticulum has been reported to inactivate in a novel manner (termed "adaptation"), which permits reactivation by exposure to successively higher concentrations of calcium. I examined the limitations placed by thermodynamics on the possible kinetic mechanisms for such behavior. The mechanism suggested by Gyorke and Fill, in which the affinity of a calcium-binding site decreases during adaptation, is not thermodynamically feasible for a passive system, but requires an external input of free energy. Possible sources of such energy are 1) metabolic energy, which is excluded by the fact that adaptation was observed in isolated channels in the absence of ATP, or 2) coupling of ion permeation to gating, for which there is currently no evidence. I derived a general limit on the thermodynamic feasibility of a sequence of channel activations and adaptations, irrespective of channel kinetics, from the requirement that the free energy must decrease during the spontaneous evolution of the system from the state existing immediately after a step increase in [Ca2+] to the state of maximum open probability that follows. The opening of the channel must involve an increase in free energy, which must be compensated by the free energy released by the incremental binding of calcium. This requirement leads to a complicated system of inequalities, which was simplified and manipulated algebraically into the form of a linear programming problem. Numerical solution of this problem showed that the sequence of adaptations of the SR channel observed by Gyorke and Fill requires the presence of at least 10 calcium-binding sites on the channel if it is to occur in the absence of exogenous sources of free energy. This indicates either that a large number of calcium-binding sites participate in the regulation of the SR calcium release channel, or that the existing data are significantly flawed with respect to the low open probability in the resting state, the importance of "calcium spike" artifacts from flash photolysis, or both.

Adaptation, Physiological↗
PubMed2004

Solution of low-dimensional constrained model predictive control problems.

Large benefits are possible by utilizing the solution of the constrained optimization problem involved in model predictive control. For a special case of these problems, the solution can be obtained relatively easily from its relationship with the unconstrained optimum. In this paper, a visualization of the relationship between the constrained and unconstrained optimum is presented. Based upon this relationship, a method for finding the constrained optimum is proposed that is suitable for low-dimensional control systems. A comparison with a linear programming formulation on 2 x 2 and 3 x 3 problems shows that the computational effort can be 10-35 times lower. For such processes, the proposed approach may allow one to avail the benefits of optimization by using the small process control systems already present in many plants.

Journal Article↗
PubMed2005

Computation of stabilizing PI and PID controllers for processes with time delay.

In this paper, a new method for the computation of all stabilizing PI controllers for processes with time delay is given. The proposed method is based on plotting the stability boundary locus in the (kp, ki) plane and then computing the stabilizing values of the parameters of a PI controller for a given time delay system. The technique presented does not need to use Pade approximation and does not require sweeping over the parameters and also does not use linear programming to solve a set of inequalities. Thus it offers several important advantages over existing results obtained in this direction. Beyond stabilization, the method is used to compute stabilizing PI controllers which achieve user specified gain and phase margins. The proposed method is also used to design PID controllers for control systems with time delay. The limiting values of a PID controller which stabilize a given system with time delay are obtained in the (kp, ki) plane, (kp, kd) plane, and (ki, kd) plane. Examples are given to show the benefits of the method presented.

Journal Article↗
PubMed2001

Muscle recruitment by the min/max criterion -- a comparative numerical study.

This paper introduces the min/max criterion for simulation of muscle recruitment in multiple muscle systems. The criterion is introduced and justified by comparison to two known criterion types: the polynomial criterion and the soft saturation criterion. The comparison is performed on a planar three-muscle elbow model performing a dumbbell curl. A generalized form of the soft saturation criterion is introduced, and it is shown that the min/max criterion can be interpreted as the limit of the classical criteria when the exponents in their mathematical expressions approach infinity. We finally show how the min/max criterion can be cast into a form that allows for efficient and robust numerical solution by linear programming. It is concluded that the min/max criterion possesses a number of attractive physiological as well as algorithmic advantages.

Algorithms↗
PubMed2001

A method to predict muscle control in the kinematically and mechanically indeterminate human masticatory system.

A method is proposed to generate muscle activation patterns for goal-directed movements of the human masticatory system. This system is special because apart from a larger amount of muscles than degrees of freedom its joints do not restrict its movements a priori. Therefore, each muscle is able to influence all six degrees of freedom which makes the system kinematically and mechanically indeterminate. Furthermore, its working space is principally determined by the dynamical properties of its muscles and not by passive constraints. The presented method determines the contribution of each degree of freedom to a movement of a reference point on the mandible. It avails of straightforward mathematical techniques like Linear Programming. It does not require a separate trajectory planning step. It was applied in a six degrees of freedom dynamical mathematical model of the human masticatory system. This model which was based upon rigid-body dynamics incorporating skull morphology and muscle architecture including dynamical properties. Movements were exclusively defined by a goal position of the mandibular reference point. The method proved to be robust in generating muscle activation patterns for both feasible and infeasible movement tasks. Generally, they were accomplished faster than habitually observed. If the task was infeasible the movement stopped at the outer boundary of the working space at the side of the unreachable goal. The method, therefore, enables to explore the working space of the mandible and the factors that are relevant for its boundaries.

Biomechanical Phenomena↗
PubMed1999

A multi-phase optimal control technique for the simulation of a human vertical jump.

A multi-phase optimal control technique is presented that can be used to solve dynamic optimization problems involving musculoskeletal systems. The biomechanical model consists of a set of differential equations describing the dynamics of the multi-body system and the generation of the dynamic forces of the human muscles. Within the optimization technique, subintervals can be defined in which the differential equations are continuous. At the boundaries the dimension of the state- and control vector as well as the dimension of the right-hand side may change. The problem is solved by a multiple shooting approach which converts the problem into a non-linear program. The method is applied to simulate a human jump movement.

Computer Simulation↗
PubMed2000

Effect of optimization criterion on spinal force estimates during asymmetric lifting.

Optimization-based muscle force prediction models of the lumbar region are used in research and ergonomic practice, usually as a subroutine of a job analysis software package. Various optimization criteria have been put forward for use in rationally selecting a set of muscle forces to satisfy moment equilibrium, including the sum of cubed muscle contraction intensities and a double linear programming procedure for minimizing the spinal compression force and maximum muscle contraction intensity. A laboratory study was conducted to determine whether these two model formulations produce significantly different estimates of spinal forces for a dynamic asymmetric lift. Although statistically significant differences were found between the predictions of the two models, the difference in peak spinal compression force was only 1.1%.

Adult↗
PubMed1997

Economic reduction of acidifying deposition in Finland by decreasing emissions in Finland, Estonia and Russia.

Here we consider cost-effective solutions of emission control measures in Finland and the nearby areas of Estonia, St. Petersburg region, Karelia and Kola, in order to limit the acidifying deposition in Finland. In the study, the emission control costs of SO2, NOx and NH3 are assessed for the areas studied and an optimisation model developed for calculation of cost-optimal deposition control policies. The input data of the model consist of the cost functions describing the emission control costs to achieve lower emission levels for the gases and areas considered and of dispersion coefficients which describe the deposition due to an emission source in the deposition receptor grid squares. In addition, the model includes a description to calculate the acidifying load. The optimisation is based on linear programming. When the acidifying load of Southern Finland is reduced by minimising the total control costs, approx, three quarters of the total control costs are due to measures in the nearby areas, Estonia, St. Peterburg region, Karelia and Kola, and approx. one quarter due to measures in Finland. The distribution of costs in the cost-optimised cases depends relatively little on the level to which the acidifying load due the source areas considered are required to be reduced. If the load reduction target is moderate, the emission control measures should mainly be allocated to sulphur emissions and to some extent to ammonia emissions and, if the load reduction target is stricter, also to the emissions of nitrogen oxides.

Acid Rain↗
PubMed2002

A graph-theoretic method to identify candidate mechanisms for deriving the rate law of a catalytic reaction.

Stoichiometrically, exact candidate pathways or mechanisms for deriving the rate law of a catalytic or complex reaction can be determined through the synthesis of networks of plausible elementary reactions constituting such pathways. A rigorous algorithmic method is proposed for executing this synthesis, which is exceedingly convoluted due to its combinatorial complexity. Such a method for synthesizing networks of reaction pathways follows the general framework of a highly exacting combinatorial method established by us for process-network synthesis. It is based on the unique graph-representation in terms of P-graphs, a set of axioms, and a group of combinatorial algorithms. In the method, the inclusion or exclusion of a step of each elementary reaction in the mechanism of concern hinges on the general combinatorial properties of feasible reaction networks. The decisions are facilitated by solving linear programming problems comprising a set of mass-balance constraints to determine the existence or absence of any feasible solution. The search is accelerated further by exploiting the inferences of preceding decisions, thereby eliminating redundancy. As a result, all feasible independent reaction networks, i.e. pathways, are generated only once; the pathways violating any first principle of either stoichiometry or thermodynamics are eliminated. The method is also capable of generating those combinations of independent pathways directly, which are not microscopically reversible. The efficiency and efficacy of the method are demonstrated with the identification of the feasible mechanisms of ammonia synthesis involving as many as 14 known elementary reactions.

Journal Article↗
PubMed1999

Developing a clinical competency examination in radiology: part II--test results.

BACKGROUND: This is the second of two articles introducing a clinical competency examination in radiology. The first article described the structure, administration, and postexamination student comments for two versions of the radiology competency examination. This article reports the results obtained from these two administrations of the examinations. OBJECTIVE: To measure and identify potential outcome predictors of student aptitude in clinical film interpretation. DESIGN: Experimental. METHODS: An examination was developed to simulate the radiologic interpretive skills needed in clinical chiropractic practice. Two versions of the examination were given to a class of 210 ninth trimester students in a 10-trimester chiropractic program. Linear regression and bivariate correlations were performed on possible predictors of student success and test scores on the version 2 examination. RESULTS: On version 1 of the examination, students were able to identify an average of 59.6% of the normal cases as normal and 51.6% of abnormal cases as abnormal. On version 2, 55.6% of the normal cases were recognized as normal and 58.2% of abnormal cases as abnormal. On both versions, students were less successful at correctly categorizing, managing, or naming pathologic conditions they found. Of the predictors evaluated, only the students' grades in the third radiology course (tumors, arthritides, and extremity trauma) and the scores on the diagnostic imaging section of National Boards part II were significant predictors. DISCUSSION: Our results should cause some concern for educators who use content-based radiology curricula. Students demonstrated poor abilities to recognize, categorize, manage, and identify common radiographic pathologic conditions. Educators cannot rely on National Board scores and course grades to determine student clinical competency. More radiology clinical competency exercises that emphasize film interpretation need to be incorporated into content-based curricula.

Aptitude↗
PubMed1997

Noise deconvolution based on the L1-metric and decomposition of discrete distributions of postsynaptic responses.

A statistical approach to analysis of amplitude fluctuations of postsynaptic responses is described. This includes (1) using a L1-metric in the space of distribution functions for minimisation with application of linear programming methods to decompose amplitude distributions into a convolution of Gaussian and discrete distributions; (2) deconvolution of the resulting discrete distribution with determination of the release probabilities and the quantal amplitude for cases with a small number (< 5) of discrete components. The methods were tested against simulated data over a range of sample sizes and signal-to-noise ratios which mimicked those observed in physiological experiments. In computer simulation experiments, comparisons were made with other methods of 'unconstrained' (generalized) and constrained reconstruction of discrete components from convolutions. The simulation results provided additional criteria for improving the solutions to overcome 'over-fitting phenomena' and to constrain the number of components with small probabilities. Application of the programme to recordings from hippocampal neurones demonstrated its usefulness for the analysis of amplitude distributions of postsynaptic responses.

Animals↗
PubMed2001

Three dimensional reconstruction of coronary arteries from two views.

Geometric representation and measurements of localized lumen stenosis of coronary arteries are important considerations in the diagnosis of cardiovascular diseases. This discrete narrowing of the arteries typically impairs blood flow in regions of the heart, and can be present along the entire length of the artery. Three-dimensional (3-D) reconstruction of coronary arterial tree allows clinician to visualize vascular geometry. Three-dimensional representation of tree topology facilitates calculation of hemodynamic measurements to study myocardial infarction and stenosis. The 3-D arterial tree, computed from two views, can provide more information about the tree geometry than individual views. In this paper, a 3-step algorithm for 3-D reconstruction of arterial tree using two standard views is presented. The first step is a multi-resolution segmentation of the coronary vessels followed by medial-axis detection along the entire arterial tree for both views. In the second step, arterial trees from the two views are registered using medial-axis representation at the coarsest resolution level to obtain an initial 3-D reconstruction. This initial reconstruction at the coarsest level is then modified using 3-D geometrical a priori information. In the third step, the modified reconstruction is projected on the next higher-resolution segmented medial-axis representation and an updated reconstruction is obtained at the higher resolution. The process is iterated until the final 3-D reconstruction is obtained at the finest resolution level. Linear programming based constrained optimization method is used for registering two views at the coarse resolution. This is followed by a Tree-Search method for registering detailed branches at higher resolutions. The automated 3-D reconstruction method was evaluated on computer-simulated as well as human angiogram data. Results show that the automated 3-D reconstruction method provided good registration of computer-simulated data. On human angiogram data, the computed 3-D reconstruction matched well with manual registration.

Algorithms↗
PubMed2003

Technical and cost efficiency of oral health care provision in Finnish health centres.

In this study we measured the productive efficiency of public dental health provision across Finland. The analysis was based on data envelopment analysis (DEA) using linear programming. In addition, we investigated various factors explaining the technical and cost efficiency of public dental care using a parametric Tobit model. These analyses revealed substantial variation in productive efficiency between health centres in different municipalities. The level of cost inefficiency was generally between 20% and 30%. Good dental health of the population, high rates of unemployment and high per capita expenditure on primary care in the municipality were associated with technical and cost inefficiency. According to the results, cost efficiency would not be improved by shifting input allocation towards more auxiliary manpower in health centres. Individual efficiency scores were clearly sensitive to the choice of output specification. Changing the unit of output measurement from visit- to patient-based measures affected markedly the ranking of dental health centres. However, the set of exogenous correlates associated to inefficiency was strikingly similar for both types of output specification. More resources are needed if the coverage of public dental care is extended to all age groups. The health centre specific efficiency scores obtained in this study can be used locally to evaluate, design and implement structural changes in the production processes.

Adolescent↗
PubMed1982

Study of leucine-enkephalin in rat brain by a new high-performance liquid chromatographic method.

A specific method is presented for the assay of leucine-enkephalin (Leu-Enk) and its metabolites by reversed-phase high-performance liquid chromatography on a muBondapak C18 column with a mobile phase of methanol-water and 0.005 M tetrabutylammonium phosphate. The four substances are resolved by a linear program from 8 to 70% methanol in 25 min. Detection is achieved by monitoring the absorbance at 280 nm. Time of analysis can be reduced by means of a new high-speed liquid chromatography package. This method allows the study of the effect of Phe-Ala on the cerebral metabolism of Leu-Enk. For this purpose, membrane preparations from rat striatum were incubated in the presence of [3H]Leu-Enk with different concentrations of Phe-Ala from 10(-7) to 10(-3) M during 1 h at 37 degrees C. Collected eluates were counted by liquid scintillation. The results suggest the presence of three membrane enzymes which generate the three metabolites, Tyr, Tyr-Gly-Gly and Tyr-Gly, in order of abundance. Maximum inhibition of [3H]Leu-Enk degradation is obtained at a concentration of 10(-3) M Phe-Ala.

Animals↗
PubMed2002

Learning generative models of natural images.

This work proposes an unsupervised learning process for analysis of natural images. The derivation is based on a generative model, a stochastic coin-flip process directly operating on many disjoint multivariate Gaussian distributions. Following the maximal likelihood principle and using the Potts encoding, the goodness-of-fit of the generative model to tremendous patches randomly sampled from natural images is quantitatively expressed by an objective function subject to a set of constraints. By further combination of the objective function and the minimal wiring criterion, we achieve a mixed integer and linear programming. A hybrid of the mean field annealing and the gradient descent method is applied to the mathematical framework and produces three sets of interactive dynamics for the learning process. Numerical simulations show that the learning process is effective for extraction of orientation, localization and bandpass features and the generative model can make an ensemble of a sparse code for natural images.

Learning↗
PubMedDate not supplied

Application of the kernel method to the inverse geosounding problem.

Determining the layered structure of the earth demands the solution of a variety of inverse problems; in the case of electromagnetic soundings at low induction numbers, the problem is linear, for the measurements may be represented as a linear functional of the electrical conductivity distribution. In this paper, an application of the support vector (SV) regression technique to the inversion of electromagnetic data is presented. We take advantage of the regularizing properties of the SV learning algorithm and use it as a modeling technique with synthetic and field data. The SV method presents better recovery of synthetic models than Tikhonov's regularization. As the SV formulation is solved in the space of the data, which has a small dimension in this application, a smaller problem than that considered with Tikhonov's regularization is produced. For field data, the SV formulation develops models similar to those obtained via linear programming techniques, but with the added characteristic of robustness.

Earth, Planet↗