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PubMedDate not supplied

Optimal parametric sensitivity control for the estimation of kinetic parameters in bioreactors.

In this paper the well-known problem of optimal input design is considered. In particular, the focus is on input design for the estimation of kinetic parameters in bioreactors. The problem is formulated as follows: given the model structure (f,g), which is assumed to be affine in the input, and the specific parameter of interest theta;(k) find a feedback law that maximizes the sensitivity of the model output to the parameter under different flow conditions in the bioreactor and, possibly, minimize the input or state costs. Analytical solutions to these problems are presented. As an example a bioreactor with a biomass that grows according to the well-known Monod kinetics is considered.

Bioreactors↗

PubMed2003

CUBIC: identification of regulatory binding sites through data clustering.

Transcription factor binding sites are short fragments in the upstream regions of genes, to which transcription factors bind to regulate the transcription of genes into mRNA. Computational identification of transcription factor binding sites remains an unsolved challenging problem though a great amount of effort has been put into the study of this problem. We have recently developed a novel technique for identification of binding sites from a set of upstream regions of genes, that could possibly be transcriptionally co-regulated and hence might share similar transcription factor binding sites. By utilizing two key features of such binding sites (i.e. their high sequence similarities and their relatively high frequencies compared to other sequence fragments), we have formulated this problem as a cluster identification problem. That is to identify and extract data clusters from a noisy background. While the classical data clustering problem (partitioning a data set into clusters sharing common or similar features) has been extensively studied, there is no general algorithm for solving the problem of identifying data clusters from a noisy background. In this paper, we present a novel algorithm for solving such a problem. We have proved that a cluster identification problem, under our definition, can be rigorously and efficiently solved through searching for substrings with special properties in a linear sequence. We have also developed a method for assessing the statistical significance of each identified cluster, which can be used to rule out accidental data clusters. We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out. We present here a few applications of CUBIC on challenging cases of binding site identification.

Algorithms↗

PubMed2006

Optimal temporal interpolation filter for motion-compensated frame rate up conversion.

Frame rate up conversion (FRUC) methods that employ motion have been proven to provide better image quality compared to nonmotion-based methods. While motion-based methods improve the quality of interpolation, artifacts are introduced in the presence of incorrect motion vectors. In this paper, we study the design problem of optimal temporal interpolation filter for motion-compensated FRUC (MC-FRUC). The optimal filter is obtained by minimizing the prediction error variance between the original frame and the interpolated frame. In FRUC applications, the original frame that is skipped is not available at the decoder, so models for the power spectral density of the original signal and prediction error are used to formulate the problem. The closed-form solution for the filter is obtained by Lagrange multipliers and statistical motion vector error modeling. The effect of motion vector errors on resulting optimal filters and prediction error is analyzed. The performance of the optimal filter is compared to nonadaptive temporal averaging filters by using two different motion vector reliability measures. The results confirm that to improve the quality of temporal interpolation in MC, the interpolation filter should be designed based on the reliability of motion vectors and the statistics of the MC prediction error.

Algorithms↗

PubMed2001

Pharmacokinetic software for the health sciences: choosing the right package for teaching purposes.

Computer assisted learning has an important role in the teaching of pharmacokinetics to health sciences students because it transfers the emphasis from the purely mathematical domain to an 'experiential' domain in which graphical and symbolic representations of actions and their consequences form the major focus for learning. Basic pharmacokinetic concepts can be taught by experimenting with the interplay between dose and dosage interval with drug absorption (e.g. absorption rate, bioavailability), drug distribution (e.g. volume of distribution, protein binding) and drug elimination (e.g. clearance) on drug concentrations using library ('canned') pharmacokinetic models. Such 'what if' approaches are found in calculator-simulators such as PharmaCalc, Practical Pharmacokinetics and PK Solutions. Others such as SAAM II, ModelMaker, and Stella represent the 'systems dynamics' genre, which requires the user to conceptualise a problem and formulate the model on-screen using symbols, icons, and directional arrows. The choice of software should be determined by the aims of the subject/course, the experience and background of the students in pharmacokinetics, and institutional factors including price and networking capabilities of the package(s). Enhanced learning may result if the computer teaching of pharmacokinetics is supported by tutorials, especially where the techniques are applied to solving problems in which the link with healthcare practices is clearly established.

Computer Simulation↗

PubMed2006

Generation of long-range correlations in large systems as an optimization problem.

We propose an efficient method of generating long-range correlations in large systems. The development of this method was motivated by the problem of constructing an optimal model for a large-scale porous medium. There are typically long-range correlations in the properties of such porous media, such as their permeability and porosity, for which there are usually only limited data. The optimal model must not only honor (preserve) the available data and their correlation function, but also accurately predict the future behavior of fluid flow in the media. We formulate the problem of generating the long-range correlations as one of optimization, and utilize simulated annealing to generate a d-dimensional array which contains the correlations and honors the existing data. The optimization process is based on the data's correlation function. The method is, therefore, free of the many numerical difficulties and/or limitations that most previous techniques suffer from. It is completely general and may be used for generating long-range correlations with any type of correlation function, in both isotropic and anisotropic media. Representative examples are presented, and the method's efficiency and accuracy are discussed.

Journal Article↗

PubMed1998

A continuous penalty function method for inverse treatment planning.

Conventional inverse treatment planning attempts to calculate dose distributions that may not be feasible given the specified dose levels to various anatomical structures. A technique for inverse treatment planning has been developed that uses only target dose levels which are easily selectable to be feasible. A nonlinear constrained minimization problem is formulated to reflect the goal of sparing critical organs as much as possible while delivering a certain target dose within specified uniformity. The objective function is the squared dose delivered to critical organs. The constraints require the delivery of certain target dose within specified uniformity and non-negative pencil beam weights. A continuous penalty function method is introduced as a method for solving the large-scale constrained minimization problem. The performance of the continuous penalty function method is optimized by numerical investigation of few numerical integration schemes and a pair of weighting functions which influence the utility of the method. Clinical examples are presented that illustrate several features of the technique. The properties of the continuous penalty function method suggest that it may be a viable alternative to conventional inverse treatment planning.

Biophysical Phenomena↗

PubMed2006

Parallelized Bayesian inversion for three-dimensional dental X-ray imaging.

Diagnostic and operational tasks based on dental radiology often require three-dimensional (3-D) information that is not available in a single X-ray projection image. Comprehensive 3-D information about tissues can be obtained by computerized tomography (CT) imaging. However, in dental imaging a conventional CT scan may not be available or practical because of high radiation dose, low-resolution or the cost of the CT scanner equipment. In this paper, we consider a novel type of 3-D imaging modality for dental radiology. We consider situations in which projection images of the teeth are taken from a few sparsely distributed projection directions using the dentist's regular (digital) X-ray equipment and the 3-D X-ray attenuation function is reconstructed. A complication in these experiments is that the reconstruction of the 3-D structure based on a few projection images becomes an ill-posed inverse problem. Bayesian inversion is a well suited framework for reconstruction from such incomplete data. In Bayesian inversion, the ill-posed reconstruction problem is formulated in a well-posed probabilistic form in which a priori information is used to compensate for the incomplete information of the projection data. In this paper we propose a Bayesian method for 3-D reconstruction in dental radiology. The method is partially based on Kolehmainen et al. 2003. The prior model for dental structures consist of a weighted l1 and total variation (TV)-prior together with the positivity prior. The inverse problem is stated as finding the maximum a posteriori (MAP) estimate. To make the 3-D reconstruction computationally feasible, a parallelized version of an optimization algorithm is implemented for a Beowulf cluster computer. The method is tested with projection data from dental specimens and patient data. Tomosynthetic reconstructions are given as reference for the proposed method.

Algorithms↗

PubMed2005

[Influence of manufacturing procedure on stability of Unguentum contra perniones preparations].

BACKGROUND: Application of various technological procedures for the manufacture of officinal preparation ointment against chilblains (Unguentum contra perniones) produce essential variations in the quality and stability of the final product. Changing the sequence of admixing active substances into the ointment base indicated the presence of incompatibility between the active substances, as well as between the active substances and the ointment base components. The aim was to examine the influence of various technological manufacturing procedures on quality and stability of the preparation. METHODS: Changes in the samples of ointments and aqueous solutions of active substances were analysed microscopically. RESULTS: Microscopic analysis of hydrosoluble active substance solutions demonstrated destruction of ichthammol, induced by an acidic medium due to the dissolution of tannin and resorcinol, which is well known from the literature. It also demonstrated the destruction of tannin and resorcinol in aqueous solution, which had not been described in the literature. Application of the prescribed procedure for the manufacturing of ointment against chilblains, conceals the incompatibility reactions due to a slow dissolution of the tannin suspended in the officinal ointment base Unguentum cera lanae. Admixture of an ready-made aqueous solution of tannin caused an instant contact between ichthammol and the acidic medium, which caused the destruction or the complete absence of the formation of emulsion droplets. The problem of incompatibility reactions between lanolin alcohols in the ointment base and ichthammol and resorcinol, as well as the reaction between Peruvian balsam and sulfur from the ichthammol sulfate ion was observed. Numerous incompatibility reactions of ointment against chilblains, components indicated that it was necessary to introduce alterations in both the qualitative and quantitative composition of the preparation. CONCLUSION: Excipient preparation procedure, as well as the technological procedure for incorporation of active ingredients can cause the incompatibilities and therefore the formulation stability problems.

Chemistry, Pharmaceutical↗

PubMed2000

Development of a lyophilization formulation that preserves the biological activity of the platelet-inducing cytokine interleukin-11 at low concentrations.

Recombinant human interleukin-11 (rhIL-11) is a licensed biological therapeutic product in at least one country and is used to combat thrombocytopenia during chemotherapeutic regimens, as well as undergoing clinical trials for a range of other disorders. Following attempts to lyophilize IL-11 at low concentrations, it was clear that a significant loss of recoverable biological activity occurred. Investigation of a variety of factors, including the type of container in which the rhIL-11 was lyophilized, revealed that surface adsorption to glass was a major factor resulting in loss of activity of rhIL-11 in solution (> 40% reduction after 3 h at room temperature), in addition to losses of activity post-lyophilization. To overcome this problem, different formulations containing combinations of human serum albumin (HSA), trehalose and Tween-20 have been investigated. Two formulations were successful in entirely preserving the biological activity of rhIL-11 through lyophilization and subsequent reconstitution (potency estimates of formulated relative to original material being > or =0.97). Accelerated degradation studies, performed at intervals over a six-month period, demonstrated the stability of freeze-dried rhIL-11 using these formulations (predicted annual reduction in potency after storage at -20 degrees C < or =1.4%). In conclusion, we have developed a working combination of excipients (0.5% HSA, 0.1% trehalose and 0.02% Tween-20 in potassium phosphate buffer (pH 7.4)) to formulate a stable rhIL-11 freeze-dried product in glass containers, with no loss in potency. These findings should facilitate development of low dose rhIL-11 products and be an indicator of caution to those using this and other material with similar physical properties, without taking appropriate precautions to avoid losses through adsorption.

Adsorption↗

PubMedDate not supplied

Scheduling the resident 80-hour work week: an operations research algorithm.

OBJECTIVE: The resident 80-hour work week requires that programs now schedule duty hours. Typically, scheduling is performed in an empirical "trial-and-error" fashion. However, this is a classic "scheduling" problem from the field of operations research (OR). It is similar to scheduling issues that airlines must face with pilots and planes routing through various airports at various times. The authors hypothesized that an OR approach using iterative computer algorithms could provide a rational scheduling solution. METHODS: Institution-specific constraints of the residency problem were formulated. A total of 56 residents are rotating through 4 hospitals. Additional constraints were dictated by the Residency Review Committee (RRC) rules or the specific surgical service. For example, at Hospital 1, during the weekday hours between 6 am and 6 pm, there will be a PGY4 or PGY5 and a PGY2 or PGY3 on-duty to cover Service "A." A series of equations and logic statements was generated to satisfy all constraints and requirements. These were restated in the Optimization Programming Language used by the ILOG software suite for solving mixed integer programming problems. RESULTS: An integer programming solution was generated to this resource-constrained assignment problem. A total of 30,900 variables and 12,443 constraints were required. A total of man-hours of programming were used; computer run-time was 25.9 hours. A weekly schedule was generated for each resident that satisfied the RRC regulations while fulfilling all stated surgical service requirements. Each required between 64 and 80 weekly resident duty hours. CONCLUSIONS: The authors conclude that OR is a viable approach to schedule resident work hours. This technique is sufficiently robust to accommodate changes in resident numbers, service requirements, and service and hospital rotations.

Adult↗

PubMed1980

Diagnostic aids.

In clinical oncology, the decisional problems encountered are rarely problems of diagnosis, and this article may appear out of place in the present framework. Its aim, however, is twofold: i) to present the potential contribution of data processing techniques to the whole diagnostic process; ii) to define a few methodological aspects which, while useful in assisting diagnosis, can be transposed to other decisional aspects (determination of prognosis, aids to therapy, optimalization of investigation strategies) more frequently met in clinical oncology, as will be shown in the numerous articles presented here. This methodology is first and foremost an apprenticeship in reasoning, in self-interrogation, and in the formulation of problems.

Decision Making↗

PubMed2002

The use of mixed-integer programming for inverse treatment planning with pre-defined field segments.

Complex intensity patterns generated by traditional beamlet-based inverse treatment plans are often very difficult to deliver. In the approach presented in this work the intensity maps are controlled by pre-defining field segments to be used for dose optimization. A set of simple rules was used to define a pool of allowable delivery segments and the mixed-integer programming (MIP) method was used to optimize segment weights. The optimization problem was formulated by combining real variables describing segment, weights with a set of binary variables, used to enumerate voxels in targets and critical structures. The MIP method was compared to the previously used Cimmino projection algorithm. The field segmentation approach was compared to an inverse planning system with a traditional beamlet-based beam intensity optimization. In four complex cases of oropharyngeal cancer the segmental inverse planning produced treatment plans, which competed with traditional beamlet-based IMRT plans. The mixed-integer programming provided mechanism for imposition of dose-volume constraints and allowed for identification of the optimal solution for feasible problems. Additional advantages of the segmental technique presented here are: simplified dosimetry, quality assurance and treatment delivery.

Algorithms↗

PubMed1984

Issues in the growth of cities of the USSR in light of the decisions of the 26th party congress.

The author discusses "varying strategies of urbanization and city growth for the Soviet macroregions--European USSR, Siberia, and Central Asia." Several important research areas are outlined, including global aspects of urbanization, forecasts of urban growth in the USSR, formulation of a theory and methods for categorizing urban formation, urbanization and environmental concerns, mathematical modeling of urban systems, and research on specific urban systems.

Demography↗

PubMed2002

A deterministic annealing algorithm for approximating a solution of the max-bisection problem.

The max-bisection problem is an NP-hard combinatorial optimization problem. In this paper an equivalent linearly constrained continuous optimization problem is formulated and a deterministic annealing algorithm is proposed for approximating its solution. The algorithm is derived from the introduction of a square-root barrier function, where the barrier parameter behaves as temperature in an annealing procedure and decreases from a sufficiently large positive number to 0. The algorithm searches for a better solution in a feasible descent direction, which has a desired property that lower and upper bounds on variables are always satisfied automatically if the step length is a number between 0 and 1. We prove that the algorithm converges to at least an integral local minimum point of the continuous problem if a local minimum point of the barrier problem is generated for a sequence of descending values of the barrier parameter with zero limit. Numerical results show that the algorithm is much faster than one of the best existing approximation algorithms while they produce more or less the same quality solution.

Algorithms↗

PubMed2000

Approximating a solution of the s-t max-cut problem with a deterministic annealing algorithm.

The s-t max-cut problem is an NP-hard combinatorial optimization problem. In this paper an equivalent linearly constrained continuous optimization problem is formulated and an algorithm is proposed for approximating its solution. The algorithm is derived from an application of a logarithmic barrier function, where the barrier parameter behaves as temperature in an annealing procedure and decreases to zero from a sufficiently large positive number satisfying that the barrier function is convex. The algorithm searches for a better solution in a feasible descent direction, which has a desired property that lower and upper bounds are always satisfied automatically if the step length is a number between zero and one. We prove that the algorithm converges to at least a local minimum point if a local minimum point of the barrier problem is generated for a sequence of descending values of the barrier parameter with zero limit. Numerical results show that the algorithm seems effective and efficient.

Algorithms↗

PubMed2006

From single-objective to multiple-objective multiple-rainfall events automatic calibration of urban storm water runoff models using genetic algorithms.

The calibration of storm water runoff models is a complex task. Early attempts focused on the choice of a performance criterion function that could capture all the facets of the problem into a single-objective framework. Subsequently, the awareness that a good calibration must necessarily take into account conflicting objectives led to the adoption of more sophisticated multi-objective approaches. Only recently, the focus has shifted towards effective ways of exploiting the mounting information provided by the availability of many sets of concurrent rainfall and flow measurements. This paper revisits through a case study the transition just elucidated: the calibration of a SWMM model applied to a catchment in Singapore is tackled through a single-objective, a multi-objective and a multi-objective multiple-event (MOME) paradigm respectively. A new approach to support the latter is presented herein. It consists in formulating the problem of model calibration as a multi-objective problem with m x r objective functions, where m and r are the number of performance criteria and rainfall events respectively, that must be optimized simultaneously. Results suggest that the new MOME framework performs significantly better than the others tested on the case study presented.

Algorithms↗

PubMed1997

The inverse problem of depth dose curve estimation.

The inverse problem of the depth dose curve is formulated and a proposition for its solution is presented. The solution is based on the approximation of the observation equation with a numerical quadrature operator and the regularization of this inverse problem with a smoothness side constraint. The problem formulation is applicable for both the electron and the photon depth dose curve estimation. Moreover, the method is equivalent for, for example, all energies, field sizes and source-to-phantom distances. Simulations show that the estimation error is smaller with the proposed method than with direct linear interpolation. The main result of the paper, however, is the formulation of the problem that allows feasible extensions and modifications for different measurement situations.

Biophysical Phenomena↗

PubMed2002

Studies on clonogenic hemopoietic cells of vertebrate in space: problems and perspectives.

Hemopoietic tissues were studied in vertebrates launched aboard the Soviet (Russian) biosatellites ("Cosmos-1129, 1514, 1667, 1887 and 2044"; "Bion-10 and 11") between 1980 and 1996. In the bone marrow of rats exposed to spaceflight conditions, a statistically significant decrease in cell number was revealed in the progenitor cell compartment accounting for the compensatory response of granulocyte-macrophage (CFU-gm) and erythrocyte lineages (BFU-e and CFU-e) and in the compartment of multipotent hemopoietic stem cells (CFU-s), which is responsible for the permanent renewal of hemopoietic tissue. The number of stromal fibroblastic progenitors (CFC-f) in the bone marrow of these rats was also reduced. Apparently, changes in the hemopoietic stroma damage the hemopoietic microenvironment and, hence, may be responsible for changes observed in the hemopoietic tissue proper. Attempts were made to develop methods for analyzing morphologically indiscernible clonogenic hemopoietic cells of newts, and studies on the effects of spaceflight factors on these cells were performed. The results showed that the numbers of clonogenic cells in newts of the flight group newts were significantly lower than in control newts. The data obtained are used as the basis for formulating the problems to be studied, drawing up a program for further research on the effects of spaceflight factors on stem and other clonogenic hemopoietic cells, and developing new experimental models for analyzing stem cells, the state of the hemopoietic stroma, etc.

Animals↗