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Results for “parameter optimization”

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At least 325 records · Page 18Linked to original sources

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↗

PubMed1994

Stochastic motif extraction using hidden Markov model.

In this paper, we study the application of an HMM (hidden Markov model) to the problem of representing protein sequences by a stochastic motif. A stochastic protein motif represents the small segments of protein sequences that have a certain function or structure. The stochastic motif, represented by an HMM, has conditional probabilities to deal with the stochastic nature of the motif. This HMM directly reflects the characteristics of the motif, such as a protein periodical structure or grouping. In order to obtain the optimal HMM, we developed the "ilerative duplication method" for HMM topology learning. It starts from a small fully-connected network and iterates the network generation and parameter optimization until it achieves sufficient discrimination accuracy. Using this method, we obtained an HMM for a leucine zipper motif. Compared to the accuracy of a symbolic pattern representation with accuracy of 14.8 percent, an HMM achieved 79.3 percent in prediction. Additionally, the method can obtain an HMM for various types of zinc finger motifs, and it might separate the mixed data. We demonstrated that this approach is applicable to the validation of the protein database; a constructed HMM has indicated that one protein sequence annotated as "leucine-zipper like sequence" in the database is quite different from other leucine-zipper sequences in terms of likelihood, and we found this discrimination is plausible.

Algorithms↗

PubMed2002

Modeling acidogenic and sulfate-reducing processes for the determination of fermentable fractions in wastewater.

The biochemical acidogenic potential (BAP) of a wastewater is the maximum concentration of volatile fatty acids (VFAs) that can be measured at the end of an anaerobic fermentation test. A model was constructed to describe the acidogenic reactions occurring during BAP tests and to divide the BAP into organic fractions. The model was calibrated with a set of specific experiments highlighting the role of sulfate-reducing bacteria on acidogenic processes, which description was necessary for correct parameter identification. The model could describe acidogenic fermentation processes, with or without sulfate reduction, at 20 degrees C, for 13 wastewaters of different origin, composition, and settleability using the same optimized parameters. A simplified version of the model, without sulfate reduction, was able to describe VFA production by the adjustment of only three variables: readily fermentable organic matter (Sf), anaerobically hydrolyzable organic matter (Xf), and heterotrophic acidogenic biomass (Xha), which proved to be coherent with the experimental BAP value. The combination of the BAP test and the model developed in this study resulted in a new reliable tool to characterize wastewater under anaerobic conditions. As VFAs are the main substrates for phosphate-accumulating organisms (PAOs), the use of organic fractions VFA, Sf, Xf, and Xha in wastewater treatment plant modeling could improve the predictability and optimization of enhanced biological phosphorus removal (EBPR) processes.

Bacteria, Anaerobic↗

PubMed1993

[The choice of the optimal regimen for apheresis of the low-density lipoproteins in patients with familial hypercholesterolemia by using mathematical modelling].

The study was undertaken to enhance the effectiveness of a low-density lipoprotein apheresis procedure by using the mathematical approach to choosing an individual sorption regimen for each patient when the cholesterol concentration given by a physician was achieved in the shortest time. The experimental estimation of time course of changes in plasma cholesterol levels at the column inlet and outlet during low-density lipoprotein apheresis allowed the optimal parameters of the procedure to be calculated. The adequacy of the proposed methods to the real data was examined by the paired t-test (p < 0.0001). The optimal regimen was chosen for 5 patients with familial hypercholesterolemia. It is shown that the optimization of the regime will reduce the time of the procedure to 47 min, by removing the same amount of a substance.

Adolescent↗

PubMed1991

Receiver operating characteristic curves of fetal, umbilical and uteroplacental blood velocity waveforms as predictors of fetal outcome.

The maximum blood flow velocity waveforms (FVW) were recorded by a pulsed Doppler ultrasound from the fetal aorta, umbilical artery and arcuate artery in 142 pregnancies suspected of intrauterine growth retardation (IUGR) according to ultrasound fetometry. The FVW were analysed for pulsatility index (PI) and Blood Flow Class (BFC). The aim of the study was to find the optimal parameter and cut-off level for predicting the outcome of pregnancy. Receiver operating characteristic curves were used for the analysis. The umbilical artery PI and BFC shows the strongest relationship to IUGR. The optimal cut-off point was found at 2 SD above the mean PI of the normal population. The aortic PI had a relatively low predictive value for IUGR, but the absence of aortic end-diastolic velocities (BFC 2 and 3) was the best parameter for predicting fetal distress. The arcuate artery PI had low predictive capacity for fetal outcome. The data indicate that the absence of diastolic velocities in the fetal aorta and the umbilical artery PI, with the cut-off level of 2 SD above the mean for the normal population, are the best and comparable blood flow parameters, which can be used for monitoring fetuses suspected of IUGR.

Blood Flow Velocity↗

PubMed1977

The effect of intravaginal electrical stimulation on the feline urethra and urinary bladder. Electrical parameters.

Intravaginal electrical stimulation (IVS) in cats caused urethral closure and bladder inhibition. The aim was to ascertain the electrical parameters most appropriate for these effects. Minimum voltage was used as main criterion to select an effective, non-destructive stimulation when the shape, frequency and duration of the pulses were systematically varied. Urethral closure was achieved at minimum voltage (3 V) with alternating pulses at a frequency of 50 Hz and a pulse duration of 1.5 ms. Corresponding optimal parameters for bladder inhibition were: alternating pulses, 10 Hz and 1.5 ms. Minimum voltage was 1 V. Moreover, the positions of the electrodes were of significance for the responses. The clinical implications of these findings are that: 1)more differentiated treatment of incontinence could be achieved by adapting the stimulation parameters to the cause of incontinence, and 2) specific electrode positions would probably give optimal responses.

Animals↗

PubMed1998

Development of an improved cloning vector and transformation system in Amycolatopsis mediterranei (Nocardia mediterranei).

A versatile plasmid cloning vector pRL60 carrying kanamycin/neomycin resistance (km/neo), erythromycin resistance (ermE) and alpha-amylase (alpha-amy) marker genes that replicates in various Amycolatopsis mediterranei strains and Escherichia coli has been constructed. This cloning vector has been derived from a hybrid plasmid pRL50, which was developed by cloning ermE from pIJ4026 into a pRL1 derivative pULAM2. While cloning ermE into the BamHI site of pULAM2, only a hybrid plasmid pRL50 with an additional copy of pULAM2 was selected. Thus pRL50 (18.7 kb) contained two copies each of the km/neo, alpha-amy, and one copy of ermE. When pRL50 was transformed into A. mediterranei DSM 40773 through electroporation and selected under erythromycin resistance, the plasmid underwent a spontaneous deletion of 8.5 kb fragment resulting in the formation of plasmid pRL60. pRL60 (10.2 kb) is a shuttle vector between A. mediterranei and E. coli with three marker genes: km/neo, ermE and alpha-amy. ermE is expressed in A. mediterranei thus allowing good selection of transformants. The alpha-amy gene of pRL60 is also expressed in A. mediterranei DSM 40773 and its activity can be easily detected on starch containing medium after iodine staining. Most critical parameters evaluated for electrotransformation using pRL60 in A. mediterranei were growth phase, electrical field strength, pulse length, pretreatment of mycelia with lysozyme and use of salt free water. At optimized parameters, a transformation efficiency of 4.0 x 10(4) transformants/microg DNA was reproducibly achieved for A. mediterranei DSM 40773. pRL60 could also be transformed into A. mediterranei DSM 43304, DSM 46095, MTCC-17 and in mutants F1/24 and T-195, (derived from an industrial strain of A. mediterranei N813). The alpha-amy of pRL60 conferred an amylolytic phenotype to all these strains. With the development of pRL60 and a reproducible transformation protocol, the application of recombinant DNA techniques to these industrial microorganisms has now become feasible.

Actinobacteria↗

PubMed1996

Evaluation of an optimized system for random amplified polymorphic DNA (RAPD)-analysis for genotypic mapping of Candida albicans strains.

A simple, rapid, and cost-effective protocol has been developed for a PCR-based molecular typing method for Candida albicans, which includes the use of a commercially available medium (Chelex 100 Resin) for DNA extraction and a single set of two arbitrarily chosen oligonucleotide (10 nt length) primers for random amplified DNA(RAPD)-analysis. The optimized parameters for the amplification components and conditions for the selected primer combination have been determined to avoid artifactual variation (absence/presence of bands) in RAPD banding patterns in repeated assays. The optimized RAPD-assay consistently generated DNA-patterns of 33 genetically unrelated C. albicans isolates that contained ten polymorphic markers in the non-artifactual banding patterns. The intralaboratory reproducibility of RAPD patterns was efficient and consistent provided the optimized amplification conditions were rigidly controlled. Interlaboratory reproducibility was tempered by slight variations in time of cyclers of different thermocyclers. In comparison, the RAPD assay was almost equal to restriction enzyme analysis (REA) (Eco RI digested chromosomal DNA) in discrimination, and the RAPD assay was able to group isolates of C. albicans that were untypable by REA. The protocol outlined for an optimized RAPD-assay of C. albicans has the potential to be widely useful epidemiological screening tool that can be easily applied in the clinical laboratory.

Candida albicans↗

PubMed1991

Two-parameter mobile phase optimization for the simultaneous high-performance liquid chromatographic determination of dopamine, serotonin and related compounds in microdissected rat brain nuclei.

A new high-pressure liquid chromatography method with electrochemical detection is described that allows the simultaneous determination of dopamine, serotonin, 3,4-dihydroxyphenylacetic acid, 3-methoxy-4-hydroxyphenylacetic acid, 5-hydroxytryptophan and 5-hydroxyindoleacetic acid in microdissected nuclei from individual rat brains. No sample pre-treatment steps are required. Resolution and analysis time were optimized by a simple limited optimization procedure, involving two-parameter factorial design.

3,4-Dihydroxyphenylacetic Acid↗

PubMed2000

Simulated molecular evolution in a full combinatorial library.

BACKGROUND: The Darwinian concept of 'survival of the fittest' has inspired the development of evolutionary optimization methods to find molecules with desired properties in iterative feedback cycles of synthesis and testing. These methods have recently been applied to the computer-guided heuristic selection of molecules that bind with high affinity to a given biological target. We describe the optimization behavior and performance of genetic algorithms (GAs) that select molecules from a combinatorial library of potential thrombin inhibitors in 'artificial molecular evolution' experiments, on the basis of biological screening results. RESULTS: A full combinatorial library of 15,360 members structurally biased towards the serine protease thrombin was synthesized, and all were tested for their ability to inhibit the protease activity of thrombin. Using the resulting large structure-activity landscape, we simulated the evolutionary selection of potent thrombin inhibitors from this library using GAs. Optimal parameter sets were found (encoding strategy, population size, mutation and cross-over rate) for this artificial molecular evolution. CONCLUSIONS: A GA-based evolutionary selection is a valuable combinatorial optimization strategy to discover compounds with desired properties without needing to synthesize and test all possible combinations (i.e. all molecules). GAs are especially powerful when dealing with very large combinatorial libraries for which synthesis and screening of all members is not possible and/or when only a small number of compounds compared with the library size can be synthesized or tested. The optimization gradient or 'learning' per individual increases when using smaller population sizes and decreases for higher mutation rates.

Algorithms↗