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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↗

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↗

[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↗

Optimization of rib surgery parameters for the correction of scoliotic deformities using approximation models.

BACKGROUND: As opposed to thoracoplasty (a cosmetic surgical intervention used to reduce the rib hump associated with scoliosis), experimental scoliosis has been produced or reversed on animals by rib shortening or lengthening. In a prior work (J. Orthop. Res., 20, pp. 1121-1128), a finite element modeling (FEM) of rib surgeries was developed to study the biomechanics of their correction mechanisms. Our aims in the present study were to investigate the influence of the rib surgery parameters and to identify optimal configurations. Hence, a specific objective of this study was to develop a method to find surgical parameters maximizing the correction by addressing the issue of high computational cost associated with FEM. METHOD OF APPROACH: Different configurations of rib shortening or lengthening were simulated using a FEM of the complete torso adapted to the geometry of six patients. Each configuration was assessed using objective functions that represent different correction objectives. Their value was evaluated using the rib surgery simulation for sample locations in the design space specified by an experimental design. Dual kriging (interpolation technique) was used to fit the data from the computer experiment. The resulting approximation model was used to locate parameters minimizing the objective function. RESULTS: The overall coverage of the design space and the use of an approximation model ensured that the optimization algorithm had not found a local minimum but a global optimal correction. The interventions generally produced slight immediate modifications with final geometry presenting between 95-120% of the initial deformation in about 50% of the tested cases. But in optimal cases, important loads (500-2000 N mm) were generated on vertebral endplates in the apical region, which could potentially produce the long-term correction of vertebral wedging by modulating growth. Optimal parameters varied among patients and for different correction objectives. CONCLUSIONS: Approximation models make it possible to study and find optimal rib surgery parameters while reducing computational cost.

Adolescent↗

Aorta in vivo parameter identification using an axial force constraint.

It was shown in a previous study by Stålhand et al. (2004) that both material and residual strain parameters for an artery can be identified noninvasively from an in vivo clinical pressure-diameter measurement. The only constraints placed on the model parameters in this previous study was a set of simple box constraints. More advanced constraints can also be utilized, however. These constraints restrict the model parameters implicitly by demanding the state of the artery to behave in a specified way. It has been observed in vitro that the axial force is nearly invariant to the pressure at the physiological operation point. In this paper, we study the possibility to include this behaviour as a constraint in the parameter optimization. The method is tested on an in vivo obtained pressure-diameter cycle for a 24-year-old human. Presented results show that the constrained parameter identification procedure proposed here can be used to obtain good results, and we believe that it may be applied to account for other observed behaviours as well.

Adult↗

Extraction of rye bran by supercritical carbon dioxide: influence of temperature, CO2, and cosolvent flow rates.

Process parameter optimization for the supercritical CO(2) extraction of rye bran to obtain alkylresorcinols (AR) was studied by carrying out a two-level fractional design experiment. Four parameters, temperature, CO(2) flow rate, cosolvent percentage, and extraction time, presumed to influence the extraction process, were analyzed. A tentative fractionation of the crude extract was also carried out and is discussed. The best extracts were achieved when the CO(2) flow rate and extraction time or temperature and cosolvent addition were kept high. It was found that temperature increase was not statistically significant within the range of the study performed, and the extraction time was thus the most important factor. A preliminary fractionation process in two cyclone separators yielded two fractions, one rich in AR components with higher molecular weights and the other rich in AR components with low molecular weight.

Carbon Dioxide↗

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↗

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↗

[Treatment of sulfanilamide production wastewater by resin adsorption technique].

According to the character of sulfanilamide production wastewater, in this paper, the recovery process of sulfanilamide, sodium nitrate in wastewater resulting from manufacturing sulfanilamide was developed by using macro porous resin. The conditions of the resin adsorption and desorption capacity were investigated and the optimal parameters were determined. The results of experiment indicated that this technique was suitable for removal of sulfanilamide from wastewater. About 86% COD removal was obtained under the optimized adsorption conditions, about 86% sulfanilamide and 95% sodium nitrate were recovered from wastewater for possible recycling to the manufacturing process and the recovered sulfanilamide's purity reached 99.8%. The adsorption capacity of resin remained constant during the repetition process of adsorption and desorption. This technique not only eliminates the environmental pollution but also obtain distinct economic benefit.

Adsorption↗

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↗

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↗

[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↗

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↗

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↗

Optimized acquisition and processing protocols for I-123 cardiac SPECT imaging.

BACKGROUND: Deconvolution of septal penetration (DSP) has been developed to improve quantification so as to allow the use of low-energy high-resolution collimators for iodine 123 cardiac single photon emission computed tomography (SPECT) imaging. The purpose of this study is to optimize its acquisition and processing protocols. METHODS AND RESULTS: Planar images of a 9-compartment phantom loaded with variable radioactive concentrations were acquired to derive optimal scatter compensation scaling factors for 20% and 15% photopeak energy window configurations, respectively. A cardiac phantom, loaded with high and low heart-to-calibration ratios (HCRs), respectively, was imaged with both configurations. Repeated acquisitions were done for medium-energy all-purpose collimators for comparison. Critical frequencies for Butterworth filtering were optimized by use of defect contrast and normal short-axis uniformity as selection indices. HCRs were calculated with planar projection and different reconstruction methods, respectively, and then compared with the true HCRs. SPECT produced more accurate HCRs than planar imaging. With the optimized parameters for scatter compensation and filtering, the 2 energy window configurations yielded similar results. Iterative reconstructions with DSP yielded more accurate HCRs than other reconstructions without DSP. CONCLUSION: The optimized protocols based on DSP show promise that quantification of I-123 cardiac SPECT imaging can be achieved with the widely available low-energy high-resolution collimators.

Algorithms↗

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↗

Time-variant parametric estimation of transient quadratic phase couplings during electroencephalographic burst activity.

OBJECTIVES: Electroencephalographic burst activity characteristic of burst-suppression pattern (BSP) in sedated patients and of burst-interburst pattern (BIP) in the quiet sleep of healthy neonates have similar linear and non-linear signal properties. Strong interrelations between a slow frequency component and rhythmic, spindle-like activities with higher frequencies have been identified in previous studies. Time-varying characteristics of BSP and BIP prevent a definite patternrelated analysis. A continuous estimation of the bispectrum is essential to analyze these patterns. Parametric bispectral approaches provide this opportunity. METHODS: The adaptation of an AR model leads to a parametric bispectrum by using the transfer function of the estimated AR filter. Time-variant parametric bispectral approaches require an estimation of AR parameters which consider higher order moments to preserve phase information. Accordingly, a time-variant parametric estimation of the bispectrum was introduced. Data driven simulations were performed to provide optimal parameters. BSP (12 patients) and BIP (6 neonates) were analyzed using this novel approach. RESULTS: Significant differences in the time course of burst pattern during BSP and burst-like pattern before the onset of BSP could be shown. A rhythmic quadratic phase coupling (period 10 sec) was identified during BIP in all neonates. CONCLUSION: Quadratic phase couplings during BSP increases in the time course depending on depth of sedation. The visually detected burst activity in BIP is only the temporarily observable EEG correlate of a hidden neural process. Time-variant bispectral approaches offer the possibility of a better characterization of underlying neural processes leading to improved diagnostic tools used in clinical routine.

Algorithms↗

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↗