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At least 73 records · Page 4Linked to original sources
PubMed1988

Identifiability of left ventricular end-systolic pressure-volume relationships.

A widely accepted model of the left ventricle (LV) consisting of a time-varying elastance and a nonlinear internal resistance was investigated to make inferences about the identifiability of its parameters by means of simulated experiments. We aimed to retrieve maximum elastance (Emax) and dead volume (Vd) by the usual slope method or end-systolic pressure-volume relations (ESPVR) and by model-based parameter identification. The ESPVR deviated increasingly from the assigned values with increasing internal resistance depending on the type of loading intervention. Model-based parameter identification proved to be hampered by considerable error propagation if applied to single contractions with noise on the data. Better results were obtained by reducing the number of parameters to be estimated or by combining contractions with different loading conditions. The LV model was also matched with experimental data in three open-chest anesthetized dogs when both methods of estimation were used. The trend of ESPVR was in accordance with the model predictions, with larger Emax and larger Vd observed with arterial rather than with venous loading. Inclusion of an internal resistance in the classical elastance model can explain the dependence of the ESPVR on the type of loading intervention. However, application of model-based parameter identification indicates that the model fails to represent the entire systolic pressure-volume time course of the in situ LV.

Animals↗
PubMed2004

Stochastic modelling of landfill leachate and biogas production incorporating waste heterogeneity. Model formulation and uncertainty analysis.

A mathematical model simulating the hydrological and biochemical processes occurring in landfilled waste is presented and demonstrated. The model combines biochemical and hydrological models into an integrated representation of the landfill environment. Waste decomposition is modelled using traditional biochemical waste decomposition pathways combined with a simplified methodology for representing the rate of decomposition. Water flow through the waste is represented using a statistical velocity model capable of representing the effects of waste heterogeneity on leachate flow through the waste. Given the limitations in data capture from landfill sites, significant emphasis is placed on improving parameter identification and reducing parameter requirements. A sensitivity analysis is performed, highlighting the model's response to changes in input variables. A model test run is also presented, demonstrating the model capabilities. A parameter perturbation model sensitivity analysis was also performed. This has been able to show that although the model is sensitive to certain key parameters, its overall intuitive response provides a good basis for making reasonable predictions of the future state of the landfill system. Finally, due to the high uncertainty associated with landfill data, a tool for handling input data uncertainty is incorporated in the model's structure. It is concluded that the model can be used as a reasonable tool for modelling landfill processes and that further work should be undertaken to assess the model's performance.

Biodegradation, Environmental↗
PubMed2005

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

Database Management Systems↗
PubMed1995

Identification of cDNA sequences by specific oligonucleotide sets. Computer tool and application.

A computer tool has been developed for revealing sets of oligonucleotides invariant for isofunctional families of DNA (RNA) and for using these in functional identification of nucleotide sequences. The tool allows one to: build up vocabularies of invariant oligonucleotides for the families of isofunctional nucleotide sequences; assess significance of the vocabularies; identify nucleotide sequences with the vocabularies of invariant oligonucleotides; determine the most effective identification parameters to minimize first and second type errors; assess the efficiency of identification of individual isofunctional families with the oligonucleotide vocabularies; determine the evolutionary characteristics of the families of isofunctional sequences on which vocabulary volume depends. Based on the system mentioned, we have analyzed a total of 322 protein-encoding gene families and have built up sets of invariant oligonucleotides, or again, oligonucleotide vocabularies that are characteristic of gene families and subfamilies. Identification of nucleotide sequences belonging to these families with the sets of invariant oligonucleotides revealed has been shown. Under the most effective identification parameters, the first type error (false negative) on control (independent) data was 10-15%, the second type error (false positive) was just 1-2 redundant sequences per sequence being examined. As has been shown, the volume of a vocabulary of invariant oligonucleotides depends on the percentage of variable positions in the multiple alignment within a family.

Base Sequence↗
PubMed2003

Validity of hematologic parameters in identification of early and late onset neonatal infection.

This study was designed to evaluate the utility of hematological parameters and C-reactive protein (CRP) to formulate a sepsis screen to detect sepsis in early and late onset infection. Hundred and fifty neonates clinically suspected of bacterial infection, based on risk factors and/or clinical features were selected for the study. Blood was collected by venipuncture at the time of admission in all neonates. A total leukocyte count (TLC), differential leukocyte count (DLC), its derivatives [Total neutrophil count (TNC or T), ratio of immature to total neutrophil count (I/T), ratio of immature to mature neutrophil count (I/M)] and CRP were obtained. TLC = 10x10(9)/L, TNC = 8x10(9)/L, I/T = 0.16, I/M = 0.25 and CRP = 0.6 mg/dl were found to be good parameters in detection of sepsis. During the first three days of life leukopenia, neutropenia, elevated I/T ratio, elevated I/M ratio and CRP were good diagnostic aids while after 3 days of life CRP was the best single test. This emphasizes use of multiple indicators for detection of sepsis. Using these parameters a sepsis screen was formulated which detected >90% of proven early and late onset sepsis suggesting that other neonates with positive sepsis screen but blood culture negativity may have been truly infected.

Age of Onset↗
PubMed2006

[Markov Chain Monte Carlo scheme for parameter uncertainty analysis in water quality model].

Parameter identification plays an important role in environmental model application. Markov Chain Monte Carlo method was introduced to estimate parameter uncertainty, since usual Bayes discrete methods were not applicable to produce posterior distribution of complicated environmental model due to the limit of computation. In order to study the performance and efficiency of MCMC, two case studies were used. Results indicate that, either sampling performance or sampling efficiency, MCMC method both has its special advantages in producing posterior distribution. Moreover, results of Gelman convergence diagnostics indicate that sampling sequence can converge to a stationary distribution. A key finding was that the MCMC scheme presented herein provided a powerful means of parameter identification and uncertainty analysis.

Models, Theoretical↗
PubMed2005

Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data.

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.

Chromatography, Liquid↗
PubMed1989

Ion-channel gating mechanisms: model identification and parameter estimation from single channel recordings.

Patch-clamp data may be analysed in terms of Markov process models of channel gating mechanisms. We present a maximum likelihood algorithm for estimation of gating parameters from records where only a single channel is present. Computer simulated data for three different models of agonist receptor gated channels are used to demonstrate the performance of the procedure. Full details of the implementation of the algorithm are given for an example gating mechanism. The effects of omission of brief openings and closings from the single-channel data on parameter estimation are explored. A strategy for discriminating between alternative possible gating models, based upon use of the Schwarz criterion, is described. Omission of brief events is shown not to lead to incorrect model identification, except in extreme circumstances. Finally, the algorithm is extended to include channel gating models exhibiting multiple conductance levels.

Animals↗
PubMed1999

[Inverse problem identification of parameters in heat transfer processes of human body].

In order that the distortion of the relative skin temperatures which is accompanied with the physiological destruction of an organ in the abdominal cavity and its physical-physiological mechanism may be investigated, we adopt in this paper the mathematical model for heat transfer problems in human layered tissues and a perfect parametric identification approach-inverse problem method. By utilizing the extremum method and integrating with the experimental data of an artificial thermo-focus, this difficult biophysical problem is solved.

Algorithms↗
PubMed2005

[Parameter optimization of water quality model: implementation of genetic algorithm and its control parameters analysis].

Parameter identification plays an important role in environmental model application. As a commonly used global optimization method, genetic algorithm (GA) has very simple structure, the key related to whether a practical issue can be solved using GA or not is algorithm design and selection of the control parameters. Based on the feature of parameter optimization of water quality model, orthogonal test method was proposed for reviewing effects of different control parameters of GA on the performance of water quality parameter optimization. The results indicate that orthogonal method could identify key factors, and also provide possible optimized experiment plan. It is concluded that GA can be applied to the research on parameter identification of complicated water quality model.

Algorithms↗
PubMed1989

Placebo-controlled study on acute and subchronic effects of buspirone vs bromazepam utilizing psychomotor and cognitive assessments in healthy volunteers.

The acute and subchronic effects of orally administered buspirone (acute: 15 mg; subchronic: 5 mg t.i.d.; Day 7:5 mg) and bromazepam (acute: 6 mg; subchronic: 2 mg t.i.d.; Day 7: 2 mg) on psychomotor and cognitive parameters were explored vs placebo in a randomized, double-blind crossover design with three periods in 12 healthy male volunteers. The washout periods between active treatments lasted one week. Psychomotor and cognitive measurements were taken with the Oculodynamic Text (ODT), which is a computerized psychophysiological online testing device for the simultaneous measurement of electrooculographic and performance (signal identification) parameters. Subjective side effects were recorded with a symptom checklist (41 items) with regard to the first and seventh day of administration. Intradiurnal assessments were done at 0, +1, +3, and +5 hours post-dose on Days 1 and 7 of each of the three randomized treatment periods. Buspirone behaved placebo-like in the EOG and signal-identification parameters after acute and subchronic administration. After bromazepam the respective parameters were significantly impaired--acutely as well as subchronically. Acute and subchronic buspirone was significantly superior to bromazepam with regard to the majority of psychophysiological parameters. The incidence of acute side effects was higher for both active treatments than for placebo. With buspirone there were fewer acute and subchronic side effects than with bromazepam. The side effect profiles of the three preparations were different. With regard to all active treatments the incidence of side effects was lower on Day 7 after the subchronic dosing period--with a third of the subchronic dose--than after the first single administration.

Adult↗
PubMed2004

Model of head-neck joint fast movements in the frontal plane.

The objective of this work is to develop a model representing the physiological systems driving fast head movements in frontal plane. All the contributions occurring mechanically in the head movement are considered: damping, stiffness, physiological limit of range of motion, gravitational field, and muscular torques due to voluntary activation as well as to stretch reflex depending on fusal afferences. Model parameters are partly derived from the literature, when possible, whereas undetermined block parameters are determined by optimising the model output, fitting to real kinematics data acquired by a motion capture system in specific experimental set-ups. The optimisation for parameter identification is performed by genetic algorithms. Results show that the model represents very well fast head movements in the whole range of inclination in the frontal plane. Such a model could be proposed as a tool for transforming kinematics data on head movements in 'neural equivalent data', especially for assessing head control disease and properly planning the rehabilitation process. In addition, the use of genetic algorithms seems to fit well the problem of parameter identification, allowing for the use of a very simple experimental set-up and granting model robustness.

Adult↗
PubMed2000

Multiparameter brain tissue monitoring--correlation between parameters and identification of CPP thresholds.

Continuous monitoring of brain interstitial gas concentrations allows direct regional evaluation of the pathophysiology of cerebral tissues. We have incorporated the Paratrend 7 (P7) multiparameter sensor into our established multimodal monitoring of head injured patients, to investigate the relationship between brain and arterial pO2, pCO2, and pH, as well as defining thresholds for cerebral perfusion pressure (CPP). A P7 sensor was inserted into the brain tissue of 40 adult head injured patients via a modified Camino bolt or triple lumen bolt. A second sensor was placed in the femoral artery for continuous monitoring of blood gases. Data signals from 19 monitored parameters were collected onto computer at the bedside for up to 14 days. No complications were seen. For individual patients the changes in brain tissue parameters showed large variations over 24 hours and the relationship between parameters varied considerably both between patients and during the period of monitoring any one individual. Changes related to periods of arterial desaturation, cerebral hypoperfusion and therapeutic manoeuvres could be seen. Good correlation was seen between brain pCO2 and arterial pCO2 (r = 0.58). Poor correlation was seen between CPP and brain pO2, and between brain pO2 and ICP. However, by grouping values for intracranial pressure (ICP) and CPP, thresholds for brain tissue pO2 were identified in 16 patients where CPP fell below 60 mmHg. No patients where CPP was always > 60 mmHg showed a significant threshold for a drop in brain pO2 (n = 16). In conclusion, the P7 shows potential as a monitor of regional brain oxygenation and for detection of potentially damaging secondary insults. The results must be interpreted whilst considering catheter position, autoregulation and systemic arterial changes for each individual.

Adolescent↗
PubMed1988

Direct identification of parameters in a mathematical model describing conduction through the atrioventricular node.

Function of the atrioventricular node is assessed during intracardiac electrophysiology study by relating the output intervals A2H2 and H1H2 to the input A1A2, where A and H are, respectively, atrial and His bundle electrograms recorded by catheter. The H1H2 curves have been previously deduced from a model describing the A2H2 curves. Because of presence in a few cases of different behaviour of A2H2 and H1H2, this study aimed to establish a more suitable model of H1H2 independently of A2H2 for the particular case of a single transmission pathway. The two models were compared by calculation of standard error of the estimate. As a first approximation, the deduced model may be sufficient. However, the standard error of the estimate was less with the direct algorithm, which is therefore the more suitable for further development, particularly for recognition and modelling of conduction over multiple pathways through the atrioventricular node.

Adult↗
PubMed1997

Treatment of hairy cell leukaemia (HCL) with 2-chlorodeoxyadenosine (2-CdA): identification of parameters predictive of adverse effects.

2-chlorodeoxyadenosine (2-CdA) induces high complete remission (CR) rates in hairy cell leukaemia (HCL), but is associated with serious toxicities. Therefore we reviewed our experience with 2-CdA in 16 HCL patients, with special attention to adverse effects. One-third of patients presented severe neutropenic infections and/or required prolonged blood support. Patients with low tumour mass and moderate cytopenias were more likely to achieve CR, whereas those with high tumour burden and severe bone marrow impairment were at increased risk of severe infection and blood product requirements. All these unfavourable parameters may be corrected by short-term alpha-interferon (IFN) therapy. Therefore we suggest that patients with unfavourable presenting features might benefit from IFN therapy before 2-CdA.

Antineoplastic Agents↗