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PubMed1994

Experimental design for parameter estimation through sensitivity analysis.

Parameter estimates can be obtained by fitting a numerical simulation model to experimental data, but these estimates may be biased and/or imprecise because of noise in the experimental data. Appropriate choice of experimental conditions, such as exposure or substrate concentrations and sampling times, can minimize the effect of experimental noise on parameter estimates, thus reducing bias and improving precision. This article describes a technique for selecting experimental (initial) conditions and measurement times for optimal parameter estimation. The technique makes use of a user-supplied mathematical simulation model for the process under study with a set of "current" parameter values specified. These "current" parameter values are the best that can be obtained using all available experimental data and/or literature information at the time when design calculations are performed. Early in a modeling study, the "current" parameter values will be tentative--based on a relatively small amount of information. Later in a study, the "current" parameter values may be known to reasonable accuracy, but final confirmation is desired. The technique uses the simulation model to calculate a numerical index for each possible experimental design. The numerical index, or Information Index, is a measure of the response of a simulation model to changes in parameter values, described by Kalogerakis and Luus (1983, 1984). The experimental design with the greatest value of Information Index is the one under which parameters can be most precisely estimated. Computation of the Information Index, described in detail, can be somewhat complicated, depending on the software available. The results, however, are simple to interpret and provide valuable information on the quality of alternate proposed experiments. The technique is applicable to a broad range of dynamical systems. Its use is demonstrated by application to a simulation model being developed to describe the in vitro metabolism of benzene by mouse liver microsomes.

Animals↗

PubMedDate not supplied

Maximization of contrast-to-noise ratio to distinguish diffusion and microcirculatory flow.

Optimization of the contrast-to-noise ratio (CNR) is described for microcirculation magnetic resonance (MR) imaging techniques based on flow-compensated/flow-dephased sequences, both with and without even-echo rephasing. The authors present the most advantageous manner of applying flow-dephased gradients, such that dephasing is maximal while diffusion losses are minimal. The theoretical considerations include phase, diffusion, echo time, and bandwidth in the determination of the optimal parameters for microcirculation imaging. Studies in phantoms consisting of stationary and flowing copper sulfate in Sephadex columns demonstrate the validity of the calculations. Optimized in vivo images of a rat stroke model demonstrate the potential of the flow-compensated/flow-dephased technique and the importance of optimizing CNR.

Animals↗

PubMed1984

The electronic structure of Fe2+ in reaction centers from Rhodopseudomonas sphaeroides. III. EPR measurements of the reduced acceptor complex.

Electron paramagnetic resonance (EPR) spectra of the reduced quinone-iron acceptor complex in reaction centers were measured in a variety of environments and compared with spectra calculated from a theoretical model. Spectra were obtained at microwave frequencies of 1, 9, and 35 GHz and at temperatures from 1.4 to 30 K. The spectra are characterized by a broad absorption peak centered at g = 1.8 with wings extending from g approximately equal to 5 to g less than 0.8. The peak is split with the low-field component increasing in amplitude with temperature. The theoretical model is based on a spin Hamiltonian, in which the reduced quinone, Q-, interacts magnetically with Fe2+. In this model the ground manifold of the interacting Q-Fe2+ system has two lowest doublets that are separated by approximately 3 K. Both perturbation analyses and exact numerical calculations were used to show how the observed spectrum arises from these two doublets. The following spin Hamiltonian parameters optimized the agreement between simulated and observed spectra: the electronic g tensor gFe, x = 2.16, gFe, y = 2.27, gFez = 2.04, the crystal field parameters D = 7.60 K and E/D = 0.25, and the antiferromagnetic magnetic interaction tensor, Jx = -0.13 K, Jy = -0.58 K, Jz = -0.58 K. The model accounts well for the g value (1.8) of the broad peak, the observed splitting of the peak, the high and low g value wings, and the observed temperature dependence of the shape of the spectra. The structural implications of the value of the magnetic interaction, J, and the influence of the environment on the spin Hamiltonian parameters are discussed. The similarity of spectra and relaxation times observed from the primary and secondary acceptor complexes Q-AFe2+ and Fe2+Q-B leads to the conclusion that the Fe2+ is approximately equidistant from QA and QB.

Biophysical Phenomena↗

PubMedDate not supplied

Direct inference of the spectra of pericardial potentials using the boundary-element method.

New methods, based on Tikhonov regularization, were developed to infer the magnitude and phase of pericardial potentials directly. These methods were tested in an adult-male torso model using measured human epicardial potentials. With 1% noise added to body-surface potentials, regularization with an optimal parameter at each frequency from 1 to 100 Hz gave an average relative error (RE) in inferred spectral magnitudes of 0.44. Regularization with the composite-residual-smoothing-operator (CRESO) parameter increased the RE slightly to 0.47. With 10% additive noise, 10 mm overestimation of heart radius, and a 10 mm error in heart position, the average CRESO parameter from 1 to 100 Hz gave an average RE of 0.71. Performance was frequency dependent. The smallest REs occurred at low frequencies. With 1% noise, optimal regularization gave average REs of 0.20, 0.40, and 0.53 in the 1-15, 15-46, and 46-100 Hz bands, respectively. Direct inference of spectral magnitudes was more accurate than Fourier transformation of inferred time-domain waveforms. Results suggest that when heart size and location are not known, minimum REs in spectral estimates are found using an overestimated heart size and a regularization parameter which is the average value over the frequency band of interest.

Body Surface Potential Mapping↗

PubMed1991

Invited review: electrodiagnostic assessment and monitoring of motor unit changes in disease.

The motor unit characteristics change dynamically with disease. This is the basis for the use of neurophysiologic methods for diagnostic purposes and for long-term monitoring. A great variety of nerve conduction and EMG parameters are available to study the motor unit. They reflect different aspects of motor unit function. Therefore, the electromyographer must choose his technique and optimal parameters depending on the situation, type of condition, whether the purpose is diagnosis or monitoring, and so on. In this presentation the relationship between EMG parameters and physiologic and morphologic counterparts in some pathologic conditions will be discussed.

Electromyography↗

PubMed2000

Prediction of functional outcome by quantification of sestamibi and BMIPP after acute myocardial infarction.

Iodine-123 15-(p-iodophenyl)-3-R,S-methylpentadecanoic acid (BMIPP) can be used to image myocardial fatty acid regional distribution and utilisation with single-photon emission tomography (SPET). By visual analysis, a mismatching with regional uptake of BMIPP less than that of a perfusion tracer has been shown to predict myocardial viability and functional improvement after restoration of flow in patients with myocardial infarction. The current study aimed to evaluate a newly developed quantitative method of analysis of sestamibi and BMIPP uptake for the prediction of functional recovery after revascularization in patients with acute infarction. BMIPP and gated sestamibi SPET studies at rest were obtained before and >3 months after revascularization in 18 patients with recent infarction. A colour-coded polar map was generated from the comparison of sestamibi and BMIPP uptake. Depending on the relative distribution of the two tracers, different patterns of uptake were identified and their extent expressed as percentages of the surface of the whole left ventricle and of the three main coronary artery territories. At follow-up, recovery was defined as a > or =5% increase in ejection fraction compared with baseline. Receiver-operating characteristic curve analysis was performed to analyse the data. At baseline, significant correlations were found between ejection fraction and the % surface with decreased sestamibi or BMIPP uptake (r=-0.68, P= 0.001, and r=-0.72, P<0.0001, respectively). When combining both tracers, ejection fraction was significantly associated with the extent of myocardium showing decreased sestamibi uptake with lower BMIPP uptake (mismatching; r=-0.68, P=0.001). At follow-up, significant functional recovery was found in 13/18 patients. By ROC curve analysis, the optimal pattern of distribution predicting recovery was a mismatching with uptake of sestamibi <70% and uptake of BMIPP at least 10% lower. For this parameter, optimal cut-off of extent was 10% of the whole left ventricle surface (sensitivity 69%, specificity 80%, accuracy 72%) and 25% of the infarct-related arterial territory (sensitivity 77%, specificity 80%, accuracy 78%). The areas under the curve were 79% for the left ventricle surface and 72% for the individual arterial territories. These results suggest that in patients with acute infarction, quantitative analysis of sestamibi and BMIPP could offer an objective and reproducible method for estimating the severity of cardiac dysfunction and predicting the evolution of ejection fraction after revascularization.

Fatty Acids↗

PubMed1995

Picosecond neodymium:yttrium lithium fluoride (Nd:YLF) laser peripheral iridotomy.

PURPOSE: We evaluated the picosecond neodymium:yttrium lithium fluoride (Nd:YLF) laser for performing peripheral iridotomies of predetermined size and shape in various types of irides. METHODS: In the first part of the study, we determined operating parameters from performing 60 iridotomies in human cadaver eyes. Subsequently, using the parameters obtained in cadaver eyes, iridotomies were created in eyes of patients with primary angle-closure glaucoma. RESULTS: In the cadaver eyes, the optimal parameters were a rectangular cutting pattern of 0.3 x 0.3 mm, 500-microns cutting depth, 50-microns spot separation, 200 to 400 microJ of energy per pulse, 200 to 400 pulses per second, and no focal offset distance. In 18 eyes of 11 patients, iridotomies with well-defined margins and size were created. Minimal hemorrhage occurred intraoperatively in ten of 18 eyes (55.6%), which did not affect the outcome of the procedure. Increases of postoperative intraocular pressure at one hour averaged 3.5 +/- 5.1 mm Hg, with an increase of more than 10 mm Hg in three eyes (16.7%), and a maximum of 12 mm Hg. We observed no corneal or retinal damage. CONCLUSION: The picosecond Nd:YLF laser seems to be an effective instrument for reliably performing peripheral iridotomies of precise size and shape using low energy per pulse levels. This laser, unlike the argon laser, is successful independent of iris thickness or color and can easily make a larger iridotomy than is often possible with the Nd:YAG laser.

Adult↗

PubMed1995

Segmentation methods for volume determination with 111In/99Tcm SPET.

Objective determination of regions of interest (ROIs) is a prerequisite for the accurate quantification of radionuclide volume distributions in single photon emission tomographic (SPET) images. In this study, we compared four segmentation methods: fixed thresholding (FT), grey level histogram (GL), region growing (RG) and combined region growing and edge detection (RGE). For this purpose, an elliptical phantom containing two cylinders with varying volumes (8-360 ml) and activities of 111In and 99Tcm (2.9-37 kBq ml-1) was employed. Using these methods, the following correlation was observed between true and measured phantom volumes: 111In, r = 0.95 (FT), 0.73 (GL), 0.93 (RG) and 0.92 (RGE); 99Tcm, r = 0.85 (FT), 0.72 (GL), 0.85 (RG) and 0.89 (RGE). Volume determination with FT and RG was not sensitive to the cut-off frequency used in image filtering. A significant correlation was observed between spleen volumes measured with the different segmentation methods, except GL, when applied to the SPET images of 25 patients administered 111In-labelled platelets. On the basis of these results, FT and RG are recommended for the clinical determination of ROIs, although they can be difficult to apply if the signal-to-noise ratio is very low or highly variable, when a combination of different imaging modalities may be the only accurate solution to the segmentation problem. The RGE method can also produce accurate results, but estimation of parameters is laborious with this method. Before being applied clinically, all segmentation methods tested in this study require phantom measurements for the determination of optimal parameters.

Humans↗

PubMed1988

Application of the molecular replacement method to multidomain proteins. 1. Determination of the orientation of an immunoglobulin Fab fragment.

Multidomain proteins provide special problems in the application of the molecular replacement method of structure determination. The structure of the Fab fragment from the autoimmune poly(dT)-specific antibody HED10 has been determined using molecular replacement. An analysis of the effects of varying the model and the parameters used in the rotation function indicates that dividing the molecule into individual relatively rigid domains simplifies interpretation of the results, and that the optimal parameters depend on the molecule under study.

Antibodies↗

PubMed1980

Analysis of the urethral pressure profile using a mechanical model.

Using a model of the urethra designed to ensure a predictable pressure profile along its length, we investigated optimal parameters for gas and water profilometry. In gas profilometry, the response characteristics of the machine, attributable to the highly compressible nature of gas, were shown to be the most important determinants of accuracy. Gas and water profilometry have drawbacks that make clinical results inaccurate. However, if all measuring parameters are carefully recorded and considered when a pressure profile is analyzed, system error can be decreased from 62 to 5% by using the optimal pull and flow rates determined by this study.

Hydrostatic Pressure↗

PubMed2001

Backpropagation algorithm adaptation parameters using learning automata.

Despite of the many successful applications of backpropagation for training multi-layer neural networks, it has many drawbocks. For complex problems it may require a long time to train the networks, and it may not train at all. Long training time can be the result of the non-optimal parameters. It is not easy to choose appropriate value of the parameters for a particular problem. In this paper, by interconnection of fixed structure learning automata (FSLA) to the feedforward neural networks, we apply learning automata (LA) scheme for adjusting these parameters based on the observation of random response of neural networks. The main motivation in using learning automata as an adaptation algorithm is to use its capability of global optimization when dealing with multi-modal surface. The feasibility of proposed method is shown through simulations on three learning problems: exclusive-or, encoding problem, and digit recognition. The simulation results show that the adaptation of these parameters using this method not only increases the convergence rate of learning but it increases the likelihood of escaping from the local minima.

Algorithms↗

PubMed1999

Influence of helical CT parameters on spatial resolution in CT angiography performed with a subsecond scanner.

RATIONALE AND OBJECTIVES: In helical CT, the beam collimation, table feed (TF) per tube rotation, voltage, current, reconstruction increment, kernel, linear interpolation algorithm (LIA), and contrast are variable parameters. The purpose of this study was to determine which of these parameters are most important to minimize partial volume effects for improving spatial resolution in CT angiography. METHODS: Phantom vessel stenoses of different lengths (2, 8 mm) and diameters (0.5, 1, 2, 3, 4 mm) were scanned with helical CT using a constant tube rotation time of 0.75 sec and 42 selected combinations of the above-mentioned parameters. Orthogonal targeted maximum intensity projections of the stenoses were ordered according to the increase in blurring and noise in a consensus reading by two radiologists blinded to the parameters used. RESULTS: Three millimeters of collimation and TF in conjunction with a 180 degrees LIA and > 250 Hounsfield unit contrast density was considered the optimal parameter combination and enabled a continuous visualization of the stenoses down to 0.5 mm in diameter. A collimation of 1 or 2 mm and 5 mm was considered inferior to a collimation of 3 mm because of, respectively, noise and blurring. With 3 mm collimation, significant blurring occurred when a pitch larger than 1.5 was used. A 3 mm collimation with a pitch of 2 (6 mm TF) was found to be superior to a collimation of 5 mm in conjunction with a pitch of 1 (5 mm TF). With 5 mm collimation, the short stenoses could be visualized only when using a 180 degrees LIA and a TF per tube rotation smaller than 7 mm. Eight and 10 mm collimations failed to depict the short stenoses. CONCLUSIONS: Collimation had the most influence on image quality in CT angiography, followed by LIA, pitch, and contrast density. Decreasing the reconstruction increment to less than one third of the TF or increasing the voltage or current beyond standard values did not improve the delineation of the stenoses. For screening examinations, the authors recommend the use of 3 mm collimation, 180 degrees LIA, and a pitch of 2.

Angiography↗

PubMed2003

MOPED: method for optimizing physical energy parameters using decoys.

We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation parameters in the energy function EEF1, which consists of the CHARMM19 polar hydrogen force field augmented by a Gaussian solvation term. Although the published parameters for EEF1 correctly discriminate the native from decoys in the decoy sets of Levitt et al., they fail on several of the more difficult decoy sets of Baker et al. MOPED successfully finds improved parameters that allow EEF1 to discriminate native from decoy structures on all protein structures that do not have metals or prosthetic groups.

Algorithms↗

PubMed2001

Single-cell electroporation.

Using modified patch-clamp methodology, we demonstrated that it is possible to insert genes or other compounds routinely into single cells by electroporation. When the cell is indented by a small-tipped microelectrode, a voltage of 10 V or less in the pipette is divided by the pipette resistance and the series resistance of the cleft between the pipette tip and the cell surface. The voltage at the cell membrane can be high enough to cause localized dielectric breakdown of the membrane and create pores that allow compounds in the pipette to enter the cell. Rectangular pulses from 20 micros to more than 300 ms are effective, as are frequencies from DC to 5 kHz. The most significant parameter was the total time for which the voltage was applied. Pipette voltages of 2-10 V were required, with larger genes requiring larger voltages. With optimal parameters, transfection rates in excess of 80% were also possible routinely. This approach offers an effective alternative to intracellular pressure injection and iontophoresis for placing genes, drugs, and other compounds in cells. Because of the small size of the electrode tips, substances can be inserted in cells from almost any location on their surfaces. In addition, the small tips electroporated only a limited area and so did little cell damage.

Contrast Media↗

PubMed1988

Depth of intraspinal wire penetration during passage of sublaminar wires.

A major concern with the use of sublaminar wires for segmental spinal instrumentation is the risk of neurologic compromise associated with repeated passage of wires through the epidural space. Because of the inability to visualize the wire tip during its sublaminar passage, the surgeon is unable to appreciate the depth of wire penetration (DOWP). The purpose of this investigation was to determine, through direct measurement, the depth of intraspinal penetration during the passage of sublaminar wires. Using their model, the authors have been able to define the optimal parameters for safe wire passage. Careful attention to maintaining contact between the wire tip and the under-surface of the lamina, using a wire of optimal configuration, will result in minimal DOWP and reduce the possibility of neurologic compromise.

Adult↗

PubMed1977

[Image processing in pathology. III. Structure and use of an automatic morphometry system for recording morphometric features of nuclei (author's transl)].

UNLABELLED: An image processing system for morphological investigation of liver cell nuclei in biopsy specimens is demonstrated. The present study deals with the age dependence of normal hepatic nuclear areas. The results were compared with those of conventional methods. MATERIAL AND METHODS: The image processing system consists of a microscope, an image dissector and a computer (central processing unit, display, teletype, magnetic tape devices and line printer). 74 liver biopsies were investigated. They sshowed no signs of acute or chronic diseases. Paraffin sections of 4 micron in thickness were prepared and stained by Feulgen method. 8-10 biopsies were available for each decade from 1-8. 18,000 liver cell nuclei from all specimens were isolated and measured automatically. Using the image processing system and adequate computer programs 20 parameters of all isolated nuclei were gained (parameters of shape, size and structure of the nuclei). For sampling and processing of the information the following programs are developed: PROBE Program for investigation of optimal parameters of scanning and processing. SAMPL Program for scanning, object isolation, feature extraction and storage of data records. KORRL Program for investigation of correlations between the features of objects. LISTE Program for listing of data records. ULTRA Program for search of objects with extremal features. CODER Program for correction od data records. ADAPT Program for training of classificators. SCHAU Program for demonstration and checking of the classificator. MORPH Program for output of feature distributions and statistical parameters. Following object features were calculated and investigated: features of size: KOFL area within the object contour; KKFL minimal covex area of the object; ZKFL object area without holes; KONL length of the object contour.

Adolescent↗

PubMed1994

Biological evaluation of d2, an algorithm for high-performance sequence comparison.

A number of algorithms exist for searching sequence databases for biologically significant similarities based on the primary sequence similarity of aligned sequences. We have determined the biological sensitivity and selectivity of d2, a high-performance comparison algorithm that rapidly determines the relative dissimilarity of large datasets of genetic sequences. d2 uses sequence-word multiplicity as a simple measure of dissimilarity. It is not constrained by the comparison of direct sequence alignments and so can use word contexts to yield new information on relationships. It is extremely efficient, comparing a query of length 884 bases (INS1ECLAC) with 19,540,603 bases of the bacterial division of GenBank (release 76.0) in 51.77 CPU seconds on a Cray Y/MP-48 supercomputer. It is unique in that subsequences (words) of biological interest can be weighted to improve the sensitivity and selectivity of a search over existing methods. We have determined the ability of d2 to detect biologically significant matches between a query and large datasets of DNA sequences while varying parameters such as word-length and window size. We have also determined the distribution of dissimilarity scores within eukaryotic and prokaryotic divisions of GenBank. We have optimized parameters of the d2 program using Cray hardware and present an analysis of the sensitivity and selectivity of the algorithm. A theoretical analysis of the expectation for scores is presented. This work demonstrates that d2 is a unique, sensitive, and selective method of rapid sequence comparison that can detect novel sequence relationships which remain undetected by alternate methodologies.

Algorithms↗

PubMed1987

PEDA: a microcomputer program for parameter estimation and dosage adjustment in clinical practice.

PEDA, an integrated program in BASIC for implementation on microcomputers, has been developed for use in clinical practice to assist dosage adjustment for individual patients. A parameter optimization for individual patients is based on the principle of Bayes' theory and Maximum Likelihood Estimation, and utilizes a prior information on the distribution of population pharmacokinetic parameters, means and variances, as well as serum drug concentrations. The program can accommodate a one-compartment open linear model and a non-linear model at steady state (Michaelis-Menten model) and handle both uniform and non-uniform multiple dosage regimens mostly arising from clinical settings. Clinical examples which demonstrate the ability and the flexibility of the program are provided. The program may also be used as an aid for instruction in clinical pharmacokinetics.

Adult↗