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PubMed1996

A large-scale processing of kinetic data files with derivation of the inhibitory constant Ki: an application to proline isomerases.

An integral system of algorithms (file preprocessor + the adapted KORE program + the Powell non-linear least-squares minimizer) named KINMIN is described. This system was applied to simultaneously process a large number of kinetic data files for cis/trans isomerization of Xaa-Pro bonds in synthetic peptides catalysed by peptidylproline cis/trans isomerases which can be inhibited by nanomolar concentrations of the immunosuppressive compounds cyclosplorin-A, FK506 or rapamycin. The system allows preprocessing of kinetics data files and derives from them the first-order rate constants which are used to optimize the inhibitory constant Ki of each inhibitor. The KINMIN program may be also applied to derive Ki for other sets of enzymes and their inhibitors.

Algorithms↗
PubMed1993

CBEIA: programs for simulation of ELISA experiments and affinity determination.

Two computer programs for the analysis of results of enzyme immunoassays are presented. CBEIA-C simulates ELISA experiments based on competition between immobilized and soluble antibody for a soluble antigen (or vice versa). CBEIA-S simulates the formation of a ternary complex of immobilized antibody, antigen and soluble antibody. The programs provide a more reliable basis for affinity determination than linearized plots. Results obtained by the application of these programs are described in the accompanying paper on pp. 129-133).

Antibody Affinity↗
PubMed2002

Non-linear pharmacokinetics of irinotecan in mice.

Irinotecan (CPT-11) is a topoisomerase I inhibitor used in the treatment of metastatic colorectal cancer. Its conversion by carboxyl esterases is necessary to form the active metabolite SN-38. The aims of the study were to evaluate the linearity of CPT-11 pharmacokinetics and the influence of the schedule of administration of CPT-11 in mice, using a population pharmacokinetic approach with the NON-linear Mixed Effects Model (NONMEM) program. Mice were treated using two doses and two schedules of administration [10 mg/kg/day (dailyx5)x2 or 50 mg/kg/day on days 1 and 12]. Plasma concentrations of both CPT-11 and SN-38 were determined by HPLC. A pharmacokinetic model based on both immediate conversion of CPT-11 to SN-38 for a fraction of the administered dose and saturable process for the remaining fraction fitted the data well. Refinements of the model allowed us to evaluate both the impacts of the dose and the schedule of administration on the pharmacokinetic parameters. We conclude that the pharmacokinetics of CPT-11 is not linear in mice. Extrapolation of both pharmacokinetic and pharmacodynamic preclinical results to humans may be limited by species particularities for this drug.

Animals↗
PubMed2005

Localization and speech-identification ability of hearing-impaired listeners using phase-preserving amplification.

OBJECTIVE: The purpose of these experiments was to determine the ability of hearing-impaired listeners to localize and to identify speech in noise using phase-preserving and non-phase-preserving amplification. DESIGN: These abilities were measured 4 times over each of two 16-week periods, using a randomized, single-blinded, within-subject crossover design. Listeners were fitted bilaterally, using the National Acoustic Laboratories linear frequency-gain characteristic with a digital hearing aid programmed in one of two ways: (1) with a linear-phase filter and (2) with filters designed to compensate for the magnitude and phase anomalies caused by the hearing aid fitting, thus preserving interaural phase. Listeners identified a word and its location in background noise with a speech-shaped spectrum. RESULTS: Immediately after fitting, both hearing aid programs reduced the listeners' ability to localize the speech in noise. The phase-preserving processing had a less detrimental effect on localization ability immediately after fitting. After 3 weeks, performance improved such that, for localization in noise, there was no detrimental effect of amplification and no difference between the two processing strategies. Over 16 weeks, speech understanding in noise improved. Speech understanding for phase-preserving processing was slightly and significantly better than linear-phase processing at 16 weeks. CONCLUSIONS: Localization ability using phase-preserving amplification does not differ from localization ability using traditional non-phase-preserving amplification after just 3 weeks of use. Listeners quickly acclimated to altered spatial cues. Phase-preserving amplification provided a 2.3% advantage for speech intelligibility in noise after 16 weeks.

Aged↗
PubMed2004

A shockwave approach for web-based clinical motion analysis.

Advances in Internet connectivity and personal multimedia computing have created opportunities for integrating simple motion analysis into clinical practice. The Macromedia Shockwave environment provides tools for creating media-rich software that runs within a Web browser. For this project, clinical motion analysis software was created using Shockwave that can load digital video clips of a client's motion, step/shuttle/play through the clip, superimpose a grid over the video image, measure relative joint angles, scale to a linear factor, measure distances, and measure average velocities. After installing the Shockwave and Quicktime video plug-ins, the Motion Analysis Tools-Shockwave program runs directly from a Web page hyperlink. Program testing involved comparing angle measurements, linear distances, stride length, and walking speed among six video clips. The first three clips were of a transtibial prosthesis being carried through the field of view (640 x 480, 320 x 240, 320 x 240 enlarged to 640 x 480). The second set of three clips was of a metal square carried through the field of view. Average root mean square errors were 2.0 degrees for angle measures and 1.2 cm for length measures. Stride length standard deviation was 4.6 cm (mean length = 212.1 cm). Average walking speed standard deviation was 0.015 m/s (mean speed = 1.15 m/s). The test results were consistent with video motion analysis results and within an acceptable range for clinical design-making. This Web-based motion analysis approach provides a useful tool for ubiquitous, quantitative, clinical gait analysis.

Decision Support Techniques↗
PubMed1995

PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure--activity relationships in protein families.

A new version of the program PROANAL is described. A multiple linear regression analysis of the protein structure--activity relationship allows one to investigate the combinations of protein sites and factors influencing the activity. The program also provides the possibility to seek out protein sites, conservative or variable in variations of physicochemical characteristics, and regions with high or low values of these characteristics. PROANAL2 may be useful in the simulation of protein-engineering experiments and in the search of a number of protein regions such as functional sites, secondary structures, solvent-exposed regions, T- and B-cell antigenic determinants, etc.

Algorithms↗
PubMed1996

Quality assurance for abdominal CT: a rapid, computer-assisted technique.

OBJECTIVE: Maintaining high standards in a large CT imaging department with multiple scanners, a large technical and clerical staff, and a rotating staff of radiologists is an ongoing challenge. We undertook a project to design and implement a simple, rapidly performed computer-assisted system of quality assurance (QA) for use in abdominal CT. In our project, we also analyzed the results of that QA system. MATERIALS AND METHODS: We graded 1810 abdominal CT studies done in a 50-week period, using a three-point scale to indicate the quality of the following five parameters of technical quality: IV contrast enhancement, oral contrast opacification, window settings and artifacts, conformity to radiologists' protocol, and completeness and accuracy of header and scout data. In addition, a parameter reflecting performance of the film library and clerical staff was similarly graded. To provide a measure of peer review for radiologists, any disagreements with prior CT study reports were recorded when comparison studies were reviewed in the process of CT interpretation. A commercially available spreadsheet and database software program was tailored to allow rapid, easily performed data entry and analysis. Tables and graphs showing performance of technologists and film library and clerical staff were generated. This customized program was made available on the radiology department computer network. Results generated by the program were further analyzed with linear regression models. RESULTS: Our QA system was successfully integrated into the routine operation of the abdominal CT division. During the first 11.5 months of operation, the system reflected improvement in each of the technical parameters with a statistically significant improvement in the combined average technical score (from 1.15 to 1.68 on a scale of 0-2; p < .0001). The "Throughout Speed/Old Exams" parameter for performance of the film library and clerical staff, which was analyzed separately from the technical parameters, also improved significantly (from 1.3 to 1.8; p < .02). Improvements were statistically significant, even when we controlled for potential variations in quality among different CT scanners and variations among the radiologists who rated the quality of the examination. Thirty-eight disagreements with previous scan interpretations (5% of all scan comparisons) were recorded for evaluation at peer review conferences. CONCLUSION: The ability to monitor performance continuously using a rapid, computer-assisted system has effected measurable improvement in our CT service. Technologist and film library and clerical staff performance improved for all parameters studied. Deficiencies were revealed and trends demonstrated. The QA system allowed us to identify disagreements in interpretation of CT examinations for subsequent peer review by radiologists. Our QA software program has been made available on the Internet as freeware to licensed Excel users via anonymous file transfer protocol at Internet Protocol 134.192.6.110.

Administration, Oral↗
PubMedDate not supplied

Prediction of surface and interior regions in proteins--Part I: Linear tripeptide sequences identify structural boundaries in proteins.

Previously, using an IBM or compatible program called SurfacePlot, it was shown that amino acid parameters of hydrophilicity, accessibility and flexibility could successfully predict linear accessible or surface regions observed in the x-ray structure of proteins. In addition, these surface regions defined the boundaries of secondary structure regions in proteins. In this paper we show that tripeptides containing the polar residues G K S D E N P T A R and Q also predict surface regions of proteins. Although tripeptides containing these residues predicted 91% of the observed accessible regions, the combination of polar tripeptide predictions with SurfacePlot predictions significantly reduced overpredictions (36% to 17%) and improved accuracy from 71% to 83% while maintaining an 86% prediction rate of observed x-ray-defined linear accessible regions. This new program also predicted 86% of beta-turn regions. The data indicated that not all beta-turns are highly exposed to solvent and that beta-turns should not be used as the sole criteria for defining surface regions.

Algorithms↗
PubMed1991

SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis.

Recently, novel technologies for isolation of nucleic acid molecules with specific biological activities have been reported. In each case, the enrichment process involves repeated rounds of selection from complex mixtures of nucleic acid sequences, followed by polymerase chain reaction (PCR) amplification of ligand sequences that function in the desired manner. Particular variations in experimental conditions can dramatically alter the outcome of these processes. In this study, we use mathematical analysis and computer simulation to predict which variations have the greatest impact and to develop strategies and guidelines for enhanced effectiveness. First, we perform reconstruction tests to demonstrate that a mathematical description based on equilibrium binding is sufficient to explain the high levels of enrichment attained in the laboratory after just a few rounds. Then, we show the expected enrichment for an extensive range of conditions; and, finally, we determine the optimum protein and nucleic acid concentrations to use for maximum enrichment, while also ensuring a high likelihood of recovering even the rare molecule that binds well. The strategies and guidelines for enhanced effectiveness are generally applicable to processes for systematic enrichment of DNA, RNA or peptide ligands and have been implemented in an interactive simulation program for integrated non-linear optimization of enrichment using any target of interest.

Biological Evolution↗
PubMed2005

MaP peptides: programming the self-assembly of peptide-based mesoscopic matrices.

We describe an approach that utilizes nonlinear peptides to direct the assembly of previously reported Self-Assembling Fibers (SAFs). The SAF system comprises two complementary linear peptides, SAF-p1 and SAF-p2a, which combine to form exclusively linear, nonbranched fibers. The Matrix-Programming (MaP) peptides described herein are based on these peptides: they comprise two or three half-peptide blocks derived from the SAF peptides, which are conjugated via dendritic hubs. Different MaP peptides coassembled with the standard SAF peptides to form specific structures, such as hyperbranched networks, polygonal matrices, and regularly segmented and terminated fibers. The role of each half-peptide block in dictating the different features has been elucidated. This provides a strong basis for designing new peptide-based nanostructured materials from the bottom up.

Circular Dichroism↗
PubMedDate not supplied

[Evaluation of the Malnourished Children's Recuperation Program in the town of Embu, located in the Metropolitan Area of São Paulo].

The objective of this study is to assess the anthropometric evolution of children who had been assisted by the Malnourished Children's Recuperation Program in the town of Embu, as well as to analyze some variables that interfered in this evaluation. The study included 233 children aged under five, enrolled in the program from January 1984 to December 1985. 201 (86,3%) were undernourished grade II and 32 (13,7%) grade III, according to Gomez. The percentage increase of Weight in relation to Age (W/A) and Height in relation to Age (H/A) - outcome variables, in the first and last examinations in the program - were analyzed, using the multiple linear regression. Younger children and in worse nutritional conditions showed higher W/A and H/A increases. Low birth weight, more frequent examinations, and longer stay in the program were associated to lower W/A increases. The presence of chronical pathologies jeopardized the H/A rate increases. This result strengthens the importance of developing programs for the assistance of undernourished children, due to higher risk of morbi-mortality in this group, mainly in younger children and with worse nutritional conditions.

English Abstract↗
PubMed1994

31P-magnetic resonance spectroscopy of the rabbit masseter muscle.

Dynamic biochemical changes in the masseter muscle were studied in 14 New Zealand adult male rabbits by 31P-nuclear magnetic resonance (NMR) spectroscopy. NMR spectra were obtained during rest and electrical stimulation of the muscle in the anaesthetized animal at 33 recording sessions. Electrical stimulation was applied by a pair of copper wires placed separately with hypodermic needles into the muscle. NMR spectra were acquired with a 2 x 3 cm, double-turn, copper transmit/receive coil. Sixteen spectra were averaged over 30 s to obtain averaged spectra continuously during a 30-min recording. The spectra were processed automatically using a non-linear 'least-squares' fitting program on the spectrometer. A Lorentzian line shape was assumed for the peaks, and values of peak height, area and chemical shifts were generated. Each averaged spectrum consisted of five peaks: inorganic phosphate (Pi), creatine phosphate (PCr), and three peaks related to ATP. Data were analysed as to absolute changes in Pi and PCr, in the ratio of Pi/PCr, and the shift of Pi to PCr to estimate pH. Several protocols were used in which ranges of frequency, intensity and duration of electrical stimulation were tested. The protocol for detailed studies involved stimulating the muscle twice at 5 Hz for 3 min separated by a 3-min rest period, then stimulating twice at 50 Hz for 3 min separated by a rest period. During contraction of the muscle, there was a significant increase in the Pi/PCr ratio (p < 0.05) as compared to the resting level. The ratio reached a plateau over a 3-min contraction using 5-Hz stimulation, then increased significantly more with the 50-Hz stimulation but decayed during the 3 min. Sustained stimulation with 50 Hz for 15-45 min evoked an initial sharp change in Pi/PCr, which then reached a steady plateau that remained over the entire stimulation. These findings indicate that the rabbit masseter muscle is relatively fatigue resistant in maintaining a steady-state equilibrium in the relation of Pi to PCr.

Adenosine Triphosphate↗
PubMed1985

Computerized analysis of enzyme cascade reactions using continuous rate data obtained with an ELISA reader.

Two programs have been written which permit analysis of multiple continuous-rate enzyme-cascade assays conducted with the use of an ELISA spectrophotometer and a synthetic chromogenic substrate. Because the product of the first reaction functions as the enzyme in the second reaction, production of chromophore continuously accelerates and it is the rate of acceleration which serves to measure the rate of the initial reaction in the system. The first program determines the rate of acceleration using linear regression to analyze the reaction curves as a function of the square of time. The second program, using a Simplex algorithm, determines the parameters which establish the assay standard curve by fitting the rate data to the Hill equation. Used together, these programs facilitate the analysis of many kinetic experiments conducted simultaneously.

Chromogenic Compounds↗
PubMed1984

Ventricular size in patients with presenile dementia of the Alzheimer's type.

The computed tomograms (CTs) of eight mild to moderately impaired patients with presenile dementia of Alzheimer's type (aged 53 to 64 years) were compared with scans of ten healthy age-matched controls. Two computer programs and a variety of linear measurements were used to analyze the CTs. A single computerized measure of fluid volume on the slice at the maximum width of the bodies of the lateral ventricles correctly predicts the group membership of 88.89% of the subjects. Computerized measures on other CT slices do not increase discrimination between the groups. Easily performed linear measures correctly predict the group membership of 78.9% of the subjects. Computerized measures of ventricular size may provide highly valuable information for the diagnosis of Alzheimer's disease in the presenile age range.

Aged↗
PubMed1984

CT density numbers in patients with senile dementia of the Alzheimer's type.

The computed tomograms (CTs) of 13 mild to moderately impaired patients with senile dementia of the Alzheimer's type (aged 65 to 82 years) were compared with CTs of 18 healthy age-matched controls. Two computer programs and a variety of linear measurements were used to analyze the CTs. A measure of the mean CT density number of the brain tissue on the slice at the maximum width of the bodies of the lateral ventricles correctly predicts the group membership of 77.42% of the subjects. The addition of a second computerized variable, the fluid volume on the slice at the maximum width of the third ventricle, increased discriminating power to 93.55%. The CT density numbers may provide highly valuable information for the diagnosis of Alzheimer's disease in the senile age range.

Aged↗
PubMedDate not supplied

Estimation problem due to multiple solutions in pharmacokinetic curve fitting to two-compartment model and its avoidance.

A size of error in observed data for fitting curves and an estimation problem due to multiple solutions in a two-compartment model were studied by using two different non-linear least-squares regression programs, SALS and NONLIN. It was found that bolus intravenous data have generally 5-10 per cent errors and oral data contain 10-25 per cent errors against the fitted data with respect to total 151 data sets of 11 different drugs. Parameters of five drugs reported in references were used to obtain simulated concentrations at the sampling times, and five different data sets containing 25 per cent normally distributed random errors as a coefficient of variation were generated using each data set of these simulated concentration. In the two-compartment model with tri-exponential equations, unreasonable estimates were occasionally observed, resulting in reversed relative values to the theoretical ones of L/M, L/N, M/N or Ka/alpha, which are analogous to the well-known flip-flop phenomenon in the one-compartment model, when number of parameters to be estimated is not less than five or errors of data exceed about 10 per cent. In an attempt to avoid such unreasonable values, initial estimates for curve fitting was successfully obtained by using a microcomputer program SIMPLEX based on a simplex method. On the basis of these results, some problems in curve fitting of plasma drug concentration data are discussed.

Models, Statistical↗
PubMed1984

Pharmacokinetics of vincristine, vinblastine, and vindesine in rhesus monkeys.

The pharmacokinetics of vincristine, vindesine, and vinblastine following IV bolus doses of 0.05 mg, 0.10 mg, and 0.20 mg/kg body weight, respectively, were studied in adult male rhesus monkeys. The alkaloid concentrations were determined by a sensitive radioimmunoassay. Pharmacokinetic data were analyzed by a non-linear least-square regression program NONLIN, and the data fit a two-compartment open model. The average terminal half-lives of vincristine, vinblastine, and vindesine in the serum were 189, 152, and 175 min, respectively. The areas under the alkaloid concentration-time curve from 0 to infinity for these drugs for a 1-mg dose were as follows: vincristine, 26,572 nM x min; vinblastine, 16,745 nM x min; and vindesine, 12,708 nM x min. The clearance rate (ml/min/kg) for vincristine (4.8) was slightly lower than that for vinblastine (7.0) or vindesine (7.8). The apparent volumes of distribution for vincristine, vinblastine, and vindesine were, respectively, 1.3, 1.5, and 1.9 l/kg body weight. In the two-compartment open model, the transfer rate constant from compartment 2 to compartment 1 (k21) was lower than the other rate constants (k120 and k12) for each of the alkaloids. The total average excretion of the alkaloids over a 4-day period in urine and feces for vincristine, vinblastine, and vindesine were, respectively, 36.7%, 18.2%, and 25.3% of the injected dose. These data indicate avid tissue retention of the Catharanthus alkaloids in this non-human primate. The similarities between these pharmacokinetic parameters and those previously reported for man suggest that the rhesus monkey is an ideal animal model in which to study the pharmacologic properties of these alkaloids.

Animals↗
PubMed1979

Application of ferrokinetic investigation for differential diagnosis in bone marrow hypoplasia and their clinical relevance.

In this study, erythropoietic activity of bone marrow has been evaluated by ferrokinetics. For that purpose, the data of radioiron disappearance from plasma and its ultimate incorporation in red blood cells after the injection of about 10 muCi of 59Fe tagged autologous plasma, were analysed and fitted to the sum of three exponentials, using a non-linear least square SAAM-25 program on UNIVAC-1108 computer. A function representing time-activity relationship, was constructed. The functional physiological model of iron metabolism, proposed by Cavill and Ricketts, was used to calculate various ferrokinetic parameters in terms of coefficients and exponents of the time-activity function. After identifying the parameters that could be used as indices of erythropoietic activity of bone marrow, the study was repeated in six patients after they had undergone myelostimulative therapy. A distinct correlation was found between ferrokinetic observations and clinical and biochemical findings. It has been demonstrated that in histologically diagnosed cases with bone marrow hypoplasia, a further differentiation between pure aplasia and those with hypoplasia together with ineffective erythropoiesis was possible. This discrimination which is clinically very important, is only possible by means of kinetic investigations.

Adult↗