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Results for “parameter identification”

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PubMed2004

Effects of naturally occurring osmolytes on protein stability and solubility: issues important in protein crystallization.

Protein solubility and stability are issues of consideration in attempts to crystallize proteins. These two properties of proteins are also at issue in the cells of organisms that have adapted to water stress conditions that could ordinarily denature or inactivate some proteins. Most organisms that have adapted to environmental stresses have done so by production and accumulation of certain small organic molecules, known as osmolytes, that arose by natural selection and have the ability to stabilize intracellular proteins against the environmental stress. Here, concepts developed to understand the special properties of the naturally occurring osmolytes in effecting protein stability and solubility, and the principles that have come from studies of these compounds have been presented. Along with excluded volume and preferential interaction parameters, identification of the osmophobic effect and the attenuation of this effect by favorable interactions of solute with side-chains appear to contribute to the full set of effects protecting osmolytes have on protein stability and solubility. With these concepts in mind and the fact that urea interacts favorably with the peptide backbone we note that: (1) osmolyte-induced effects on protein stability ranging from denaturation to forcing proteins to fold can be achieved experimentally and the underlying principles understood at near molecular-level detail, and (2) osmolyte-mediated solubility effects ranging from protein precipitation to protein solubilization are predictable based on these principles. These effects are contrasted and compared with effects of 2-methyl-2,4-pentanediol and polyethylene glycol on proteins, and how the principles found for the naturally occurring osmolytes can be applied to these two commonly used protein crystallizing agents.

Amino Acids↗

PubMed2002

Mechanical model of the inspiratory pump.

The inspiratory pump (inspiratory muscles and the rib cage) translates inspiratory commands in alveolar ventilation by applying expanding forces to the lungs. Its functioning is of paramount importance to the physiology of breathing and of many pathological situations. Major difficulties in studying its function in relationship with its structure arise from the extremely complex geometrical disposition of its active and passive elements. We herein describe a two-compartment model of the inspiratory pump, with model parameters identification derived from actual measurements obtained by magnetic resonance imaging in normal humans. The equations governing the model are presented. Numerical simulations validate the model by showing a behaviour similar to physiological observations. This opens the possibility of predicting the behaviour of the respiratory system during diseases involving changes in its mechanical or geometrical characteristics.

Biomechanical Phenomena↗

PubMed1983

Automated gas chromatographic analysis of pesticide residues in food samples by means of fused-silica capillary columns and data processing.

A conventional gas chromatograph with one system for split and splitless injection and one on-column injection system for fused-silica capillary columns and the two selective nitrogen-phosphorus and electron-capture detectors is applied to pesticide residue analysis in food samples. The gas chromatograph is equipped with a two-channel data processor that can be programmed with BASIC. Additionally an autosampler is used with the splitless injector. This automated injection system is connected to a 25-m methylsilicone fused-silica column which is coupled via an effluent splitter parallel to both detectors and used for screening in routine analysis. Calibration is performed on this column by means of three calibration test mixtures which include three internal standards. All compounds are calibrated on both detectors in parallel and the response calculated as an additional identification parameter. After the analysis of a of food samples together with the calibration mixture a report is plotted, containing all pesticide residues which may be present in the samples and their tentative quantities. The final confirmation is achieved on the second column, coated with methylphenyl-silicone phase, connected to the on-column injector.

Autoanalysis↗

PubMed1991

Mathematical model of antiviral immune response. I. Data analysis, generalized picture construction and parameters evaluation for hepatitis B.

The present approach to the mathematical modelling of infectious diseases is based upon the idea that specific immune mechanisms play a leading role in development, course, and outcome of infectious disease. The model describing the reaction of the immune system to infectious agent invasion is constructed on the bases of Burnet's clonal selection theory and the co-recognition principle. The mathematical model of antiviral immune response is formulated by a system of ten non-linear delay-differential equations. The delayed argument terms in the right-hand part are used for the description of lymphocyte division, multiplication and differentiation processes into effector cells. The analysis of clinical and experimental data allows one to construct the generalized picture of the acute form of viral hepatitis B. The concept of the generalized picture includes a quantitative description of dynamics of the principal immunological, virological and clinical characteristics of the disease. Data of immunological experiments in vitro and experiments on animals are used to obtain estimates of permissible values of model parameters. This analysis forms the bases for the solution of the parameter identification problem for the mathematical model of antiviral immune response which will be the topic of the following paper (Marchuk et al., 1991, J. theor. Biol. 15).

Hepatitis B↗

PubMed2001

Simulation of acid-base condition and copper speciation in the fish gill microenvironment.

pH, alkalinity, and mucus content in the fish gill microenvironment of carp (Cyprinus carpio) were measured by exposing fish to copper at various water pH levels using an apparatus which separates inspired and expired water. The relationship between pH levels inside and outside of the gill microenvironment, between pH and alkalinity, and between mucus secretion, pH, and copper exposure concentration were modeled. Copper speciation in the surrounding water and in the fish gill microenvironment was simulated using MINTEQA2 chemical equilibrium calculation software. The results of the modeling for pH, alkalinity, and mucus calculation were then adopted as inputs for purposes of parameter identification in the speciation modeling. The differences observed in the copper species distribution between that of the fish gill microenvironment and the surrounding water were based on the speciation modeling. The change in copper bioavailability for fish uptake was also examined. The results indicate the presence of an experimental pH balance point at 6.9, where the pH in the fish gill microenvironment is identical to that of the surrounding water. The observed deviation range in pH levels between that found at the gills and that of the surrounding water varied from -0.4 to 0.8 units. A sinusoidal model was developed for calculation of gill pH based on the pH of the surrounding water. Models calculating alkalinity either in the gill microenvironment or in the surrounding water and for estimating mucus secretion were also developed. The results of the chemical equilibrium calculations demonstrate that, within a pH range of 6-9, the dominant species of copper in bulk solution shifted from free ions to that of the hydroxo complex. With respect to the fish gill microenvironment, the dominant species found under acidic conditions were the mucus copper complex and free ions. Because of the influence of mucus complexation and pH change, bioavailable copper species in the fish gill microenvironment were significantly lower than that in the bulk solution, especially under acidic conditions.

Acid-Base Equilibrium↗

PubMed2001

Design of an active vibration dummy of sitting man.

OBJECTIVE: The determination of vibration transmission through vehicle seats today is still performed with small groups of test subjects. This method suffers from several severe disadvantages, in particular poor repeatability and objectivity due to varying test conditions and limited group sizes. Replacing test persons with a vibration dummy helps to solve this problem. DESIGN: The active vibration dummy simulates the dynamic behaviour of sitting man expressed in terms of the driving point impedance for arbitrary body masses and excitation signals. METHODS: The dummy is realized as a mechatronic system basing on a single degree of freedom setup. A real-time control loop of mass accelerations (and thus acting forces) fits the active dummy to the desired driving point impedance data set. Model and controller parameters are determined by a parameter-identification technique giving meaningful results for arbitrary impedance data sets. RESULTS: The prototype shows excellent agreement with the target data under laboratory conditions. Body mass and excitation level can be varied over the full range of car seat test requirements. RELEVANCE: The determination of vibration transmission through vehicle seats should be possible without human experiments. An active vibration dummy with adjustable vibration behaviour expressed by the vertical driving point impedance covering the entire scope of car seat tests (masses/excitation intensities) is presented. With the dummy, improved seat test procedures could be established, leading to design improvements and therefore to prevention of whole-body vibration injuries.

Acceleration↗

PubMed2003

[Toxicity and anti-tumour efficacy of oxaliplatin on Glasgow osteosarcoma induced in mice: a mathematical model].

To study time-scheduled regimens in the treatment of tumours by cytotoxic drugs delivered by IV injection, we propose a mathematical model of the action of a chemotherapy on the population of tumoral cells on the one hand, on a population of fast renewing healthy cells on the other hand. We chose for model parameter identification the treatment by oxaliplatin of Glasgow Osteosarcoma in mice.

Animals↗

PubMed1997

Pharmacokinetic-based minibolus delivery as an alternative to continuous infusion for drugs that exhibit a biophase lag.

The presence of a biophase compartment in a pharmacokinetic model indicates that the response to an administered dose of drug is damped such that the time to peak effect occurs after the peak concentration in the bloodstream. This phenomenon, which is common to most intravenous anesthetic agents, can be exploited by a drug delivery method that administers minibolus doses of drug rather than a continuous infusion. Through analysis of the frequency response behavior of the biophase compartment, a bolus magnitude and dose frequency or interval (1/frequency) can be chosen such that the oscillation in drug effect is minimized even though the plasma concentration may be changing significantly with each supplemental dose. A pharmacokinetic and pharmacodynamic based method for calculating the bolus dose size and dosing interval is presented. The trade-off between dose interval and change in drug effect is exemplified through computer simulation of this strategy applied to delivery of the neuromuscular blocking agent pancuronium. The method provides a repetitive perturbation to the pharmacokinetic and pharmacodynamic system that can aid in model parameter identification during closed loop applications.

Body Fluid Compartments↗

PubMed1993

Identity of tumorigenic human urothelial cell lines and 'spontaneously' transformed sublines.

Restriction fragment length polymorphism (RFLP) analysis, comparative marker chromosome analysis, and polymorphic enzyme analysis was carried out on a total of eight human urothelial cell lines and sublines selected according to our knowledge of their HLA-A,B phenotype. RFLP analysis and cytogenetic analysis showed that the cell lines Hu1703He, Hu1922, and T24 are genuine cell lines of different origin. The identity of Hu1703He could not be confirmed by its isozyme phenotype which was identical to the T24 phenotype. RFLP analysis and isozyme analysis revealed that three cell lines, Hu456, Hu549, and Hu961a, and two transformed sublines, HCV-29Tmv and Hu609Tmv, are sublines of T24. A common origin of Hu456, Hu549, Hu961a, HCV-29Tmv, and Hu609Tmv was confirmed by marker chromosome analysis. However, the T24 origin of these cytogenetically related cell lines was not supported by chromosome analysis of T24. RFLP analysis and HLA phenotyping of two tumorigenic and invasive sublines isolated from a culture of non-tumorigenic Hu609 cells showed that non-tumorigenic Hu609 cells can transform 'spontaneously' in vitro into tumorigenic Hu609T cells. The results emphasise the need for careful monitoring and screening of cell lines for their identity using more than one identification parameter.

Cell Line↗

PubMed2006

Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway.

Parameter estimation is a major challenge for mathematical modelling of biological systems. Given the uncertainties associated with model parameters, it is important to understand how sensitive the model output is to variations in parameter values. A local sensitivity analysis determines the model sensitivity to parameter variations over a localised region around the nominal parameter values, whereas a global sensitivity analysis (GSA) investigates the sensitivity over the entire parameter space. Using a T-cell receptor-activated Erk-MAPK signalling pathway model as an example, the authors present a comparative study of a variety of different sensitivity analysis techniques. These techniques include: local sensitivity analysis, existing GSA methods of partial rank correlation coefficient, Sobol's, extended Fourier amplitude sensitivity test, as well as a weighted average of local sensitivities and a new GSA method to extract global parameter sensitivities from a parameter identification routine. Results of this study revealed critical reactions in the signalling pathway and their impact on the signalling dynamics and provided insights into embedded regulatory mechanisms such as feedback loops in the pathway. From this study, a recommendation emerges for a general sensitivity analysis strategy to efficiently and reliably infer quantitative, dynamic as well as topological properties from systems biology models.

Algorithms↗

PubMed2001

Correct Identification of Passiflora incarnata Linn., a Promising Herbal Anxiolytic and Sedative.

Passiflora incarnata Linn. and Passiflora edulis Sims are the two important plants of the family Passifloraceae that have often been reported as synonymous because of their identical morphological and microscopic characteristics. P. incarnata is a popular sedative and anxiolytic, whereas, P. edulis is rarely reported to possess significant central nervous system depressant activity. P. edulis, as the name of the species reflects, is mainly grown for edible purposes. During a survey of literature on the genus Passiflora, it was noticed that in many references the two plants are mentioned synonymously. The designation by Sir William J. Hooker in 1843, followed by the citation of P. edulis as the synonym of P. incarnata in Index Kewensis of 1895, not only substantiated the controversial identity but also caused confusion to researchers. The prevailing confusion might have led to improper selection of the bioactive plant, thereby accounting for inconclusive and contradictory pharmacological reports on either of the two plants. In this work, we establish key identification parameters to differentiate P. incarnata from P. edulis. Various leaf constants such as vein-islet number, vein-termination number, stomatal number, and stomatal index are different for the two species. Physicochemical parameters such as ash values and extractive values and the thin layer chromatography profile of the petroleum ether extract of P. incarnata and P. edulis are also distinct and different. Various clinical uses of P. incarnata for anxiety and allied diseases are discussed.

Journal Article↗

PubMed2003

Modular modeling of cellular systems with ProMoT/Diva.

MOTIVATION: Need for software to setup and analyze complex mathematical models for cellular systems in a modular way, that also integrates the experimental environment of the cells. RESULTS: A computer framework is described which allows the building of modularly structured models using an abstract, modular and general modeling methodology. With this methodology, reusable modeling entities are introduced which lead to the development of a modeling library within the modeling tool ProMot. The simulation environment Diva is used for numerical analysis and parameter identification of the models. The simulation environment provides a number of tools and algorithms to simulate and analyze complex biochemical networks. The described tools are the first steps towards an integrated computer-based modeling, simulation and visualization environment Availability: Available on request to the authors. The software itself is free for scientific purposes but requires commercial libraries. SUPPLEMENTARY INFORMATION: http://www.mpi-magdeburg.mpg.de/projects/promot

Algorithms↗

PubMed2001

Analysis of amphetamine and congeners in illicit samples by liquid chromatography and capillary electrophoresis.

Screening methods based on liquid chromatography (HPLC) and capillary electrophoresis (CE) have been developed for the identification and determination of amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine, and 3,4-methylenedioxyethylamphetamine in illicit tablets. Diethylpropione, (-)-ephedrine, and 3-amino-1-phenylbutane were also included in the study as amphetamino-related compounds. The HPLC-diode-array detection method involved on-line photochemical derivatization to enhance the selectivity of detection allowing amphetamines to be distinguished from related compounds such as diethylpropione (amfepramone). When the CE approach was adopted, two identification parameters (UV spectra and migration index) were used and the enantioresolution of the racemic amphetamines was achieved using hydroxypropyl-beta-cyclodextrin as chiral selector.

Amphetamine↗

PubMedDate not supplied

Psychological differences between children with and without chronic encopresis.

OBJECTIVE: To validate a theoretical model of encopresis in terms of psychological factors that differentiates children with and without chronic encopresis and to identify scales that demonstrate these differences. METHODS: Eighty-six children with encopresis were compared to 62 nonsymptomatic children on five psychometric instruments. Differences in the mean scores and the percentages of children falling beyond preselected clinical thresholds were compared across the patient-control groups. RESULTS: Children with encopresis were found to have more anxiety/depression symptoms, family environments with less expressiveness and poorer organization, more attention difficulties, greater social problems, more disruptive behavior, and poorer school performance (ps =.01 < or =.001 on 15/20 subscales). There were no differences in self-esteem. On those subscales where proportionately more encopretic children exceeded clinical thresholds, approximately 20% more of the encopretic children exceeded thresholds than control children. CONCLUSIONS: As a group, children with encopresis differ from children without encopresis on a variety of psychological parameters. However, only a minority of children with encopresis demonstrated clinically significant elevations in these parameters. Identification and treatment of such clinical issues may enhance treatment efficacy.

Adolescent↗

PubMed2003

RNABase: an annotated database of RNA structures.

RNABase is a unified database of all three-dimensional structures containing RNA deposited in either the Protein Data Bank (PDB) or Nucleic Acid Data Base (NDB). For each structure, RNABase contains a brief summary as well as annotation of conformational parameters, identification of possible model errors, Ramachandran-style conformational maps and classification of ribonucleotides into conformers. These same analyses can also be performed on structures submitted by users. To facilitate access, structures are automatically placed into a variety of functional and structural categories, including: ribozymes, pseudoknots, etc. RNABase can be freely accessed on the web at http://www.rnabase.org. We are committed to maintaining this database indefinitely.

Databases, Nucleic Acid↗

PubMed2001

Oscillometric blood pressure measurement: progress and problems.

Oscillometric blood pressure measurement has become very popular, but although a number of devices have now passed both the Association for the Advancement of Medical Instrumentation and British Hypertension Society criteria, complacency with the state of the technique is as yet premature. In individual subjects, a substantial number of readings may deviate more than a clinically relevant 5 mmHg in devices that have earned a British Hypertension Society grade A rating. The marketing of pressure-wave-simulating devices is a welcome development as monitors can now be tested for reproducibility; an intra-device standard deviation of less than 2 mmHg has been proposed as the limit. Authors suggest that these simulators are currently better suited to intra- than between-device testing since they are not yet fully confident that the simulated waveforms are indistinguishable from the man-made pressure waves. Simulators should, however, be incorporated into our standard validation protocols in order eventually to obviate the human, fallible, factor in the validation protocols. The currently employed maximal amplitude algorithm has many drawbacks as the parameter identification points for systolic and diastolic pressure depend on many factors, for example pulse pressure, heart rate and arterial stiffness. These errors have now been demonstrated in clinical studies. Modern pattern recognition algorithms are being constructed but have not yet produced convincing results. As repeatedly stated, the development of a more robust and more widely applicable algorithm than the maximal amplitude approach should be allocated a high priority.

Algorithms↗

PubMed1998

Systematic method for determining intravenous drug treatment strategies aiding the humoral immune response.

This paper delineates a systematic method for determining "optimal" intravenous drug delivery strategies for patients having illnesses that primarily evoke a humoral immune response and are treatable by antibiotics. The method derives from a nonlinear, distributed predator-prey model that captures the dominant antigen and antibody interaction. This model is developed from relevant physiology, past predator-prey-type modeling work, available data, and pertinent parameter identification. Embedding this predator-prey model into a larger class of uncertain systems, by a finite dimensional approximation and a transformation to a linear fractional representation, enables the application of robust control based on linear matrix inequality optimization techniques. The optimization problem is solved by minimizing an upper bound on a measure of the total drug delivered subject to patient recovery (stability to healthy equilibrium state). Specifically, the paper addresses the treatment of Haemophilus influenzae through modeling, controller development, and simulations of infected adult patients subjected to typical and proposed intravenous antibiotic treatments. Through simulations the proposed intravenous drug strategy shortens patient recovery time, lowers peak drug concentrations and decreases the total drug administered when compared to standard antibiotic strategies.

AIDS-Related Opportunistic Infections↗

PubMed1999

An approach to a muscle model with a stimulus frequency-force relationship for FES applications.

A simplified model of electrically stimulated muscle for use in applications of functional electrical stimulation (FES) is discussed in this paper. The muscle model was required to have both stimulus frequency and stimulus intensity (amplitude/width) inputs. The stimulus frequency versus force relationship of rabbit muscle was modeled first with a small number of model parameters that could be identified by simple experiments in a short time. The model identified was found to be applicable to human muscles. The frequency-force relationships of electrically stimulated fast and slow type muscles were also predicted by the model. The frequency-force model and a simplified model of muscle activation dynamics were used to construct a muscle model that described the summation of muscle contraction. The use of this model decreased the time burden on patients during parameter identification at the clinical site. The clinical applicability of these new model descriptions was suggested through computer simulations.

Animals↗