[Principles of static perimetry from the perspective of the computer-assisted method].
Explore the source record for details and available documents.
Humans↗
SEARCH · Search PubMed
Results for “Computational methods”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Computer-assisted method development and optimization in high-performance liquid chromatography.
This paper reports the use of DryLab, a computer simulation software package, to assist in the development and optimization of a reversed-phase high-performance liquid chromatographic (HPLC) method for the separation of a model drug candidate and its degradation products. Prior to the optimization process, columns with various bonded phases are evaluated for their chromatographic performance using the sample of interest. Simultaneous optimization of two separation variables and the use of resolution maps to predict the optimal conditions are illustrated. Options to optimize column conditions (column length and flow-rate) to further reduce run time are briefly discussed. The accuracy of DryLab-predicted retention times and resolution is compared with experimental values. The DryLab software used in this study provided satisfactory predictions for the selected model, with average errors of less than 3.5 and 11.8% for retention time and resolution, respectively.
Chromatography, High Pressure Liquid↗
[Multiserial ECG-gated computed tomographic method: Evaluation of left ventricular volumes, wall thickness and wall motion].
The purpose of this study was to investigate the potential usefulness of multiserial ECG-gated computed tomography (CT) (GE CT/T 8800) for a quantitative assessment of left ventricular volume, wall thickness and wall motion in 15 patients with coronary heart disease. In order to obtain ideal left ventricular short-axis images, the gantry was tilted to the cephalad 15 degree with patients on the right lateral position. Five ECG-gated scans (5.6 sec for one scan) were performed in each patient with intravenous injection of contrast material (Urografin 76). Left ventricular volumes were computed by a modified Simpson's rule and segmental wall motion was analyzed at three levels (base, papillary muscle and apex) by tracing the endocardial outline at end-diastole and end-systole. Left ventricular systolic and diastolic volumes ( LVSV , LVDV ) had a good correlation with those measured by left ventriculography (LVG) (r = 0.75 and 0.66). Wall thickness of the interventricular septum and left ventricular posterior wall obtained by CT was correlated with those by M-mode echocardiography (r = 0.82 and 0.71). Comparative analysis of segmental wall motion by CT, two-dimensional (2 D) echocardiography and left ventriculography was done. The 2 D echocardiographic segments with normal and abnormal wall motion were accurately identified by CT, best at the papillary muscle level (91%), and less at the base (71%) and the apex (73%). Similarly, 85% of left ventriculographic segments could be detected by CT. In conclusion, ECG-gated computed tomography proved to be a useful method for evaluating left ventricular function in coronary heart disease.
Adult↗
The spectral-element method, Beowulf computing, and global seismology.
The propagation of seismic waves through Earth can now be modeled accurately with the recently developed spectral-element method. This method takes into account heterogeneity in Earth models, such as three-dimensional variations of seismic wave velocity, density, and crustal thickness. The method is implemented on relatively inexpensive clusters of personal computers, so-called Beowulf machines. This combination of hardware and software enables us to simulate broadband seismograms without intrinsic restrictions on the level of heterogeneity or the frequency content.
Journal Article↗
[Method of computing the effective doses and concentrations of chemical blastomogenic agents].
It is suggested to use the method of probit-analysis in Litchfield and Wilcockson modification for calculating effective blastomogenic doses and concentrations (BD16, BD50, BD84) of chemical blastomogenic agents belonging to different classes of chemical compounds, which carcinogenicity was studied experimentally on animals. The values of BD16, BD50 and BD84, functions of the angle of inclination of "S" and "tgalpha" are given for 8 chemical blastomogenic agents.
Animals↗
[Method for computing the milk losses from sterility in cows].
An attempt was made to work out a method and establish the indices in calculating the losses of milk due to sterility in cows, along with recording the level of productivity and the duration of the period of sterility. The differences were established between: 1. The size of the average daily milk yield per normative day (a day of the period between calvings of 365 days) and that per day of the actual period between calvings. 2. The average daily milk yield per normative day and that per day of the period of sterility. The milk losses calculated in both ways gave almost comparable results. It is , therefore, suggested when calculating the losses due to sterility to use the established indices of milk losses per sterility day (Table 2) at a varying milkiness of the cows and a varying length of the period between calvings, resp., the period of sterility.
Animals↗
Heart rate variability effects of an agonist or antagonists of the beta-adrenoceptor assessed with scatterplot and sequence analysis.
There is evidence that the processes regulating heart rate variations reflect non-linear complexity and show 'chaotic' determinism. Data analyses using non-linear methods may therefore reveal patterns not apparent with conventional statistical approaches. We have consequently investigated two non-linear methods, the Poincaré plot (scatterplot) and cardiac sequence (quadrant) analysis, and compared these with standard time-domain summary statistics, during a normal volunteer investigation of an agonist and antagonists of the cardiac beta-adrenoceptor. Under double-blind and randomized conditions (Latin square design), 12 normal volunteers received placebo, celiprolol (beta 1- and beta 2-adrenoceptor partial agonist), propranolol (beta 1- and beta 2-adrenoceptor antagonist), atenolol (beta 1-adrenoceptor antagonist) and combinations of these agents. Single oral doses of medication (at weekly intervals) were administered at 22:30 hours with sleeping heart rates recorded overnight. The long (SDNN, SDANN) and short-term (rmsSD) time-domain summary statistics were reduced by celiprolol--effects different from the unchanged or small increases after atenolol and propranolol alone. The Poincaré plot was constructed by plotting each RR interval against the preceding RR interval, but unlike previous descriptions of the method, an automated computer method, with a high level of reproducibility, was employed. Scatterplot length and area were reduced following celiprolol and different from the small increases after propranolol and atenolol. The geometric analysis of the scatterplots allowed width assessment (i.e. dispersion) at fixed RR intervals. Differences between the drugs were confined to the higher percentiles (i.e. 75% and 90% of scatterplot length: low heart rate). The long-term time-domain statistics (SDNN, SDANN) correlated best with scatterplot length and area whereas the short-term heart rate variability (HRV) indices (rmsSD), pNN50) correlated strongly with scatterplot width. Cardiac sequence analysis (differences between three adjacent beats; delta RR vs delta RRn+1) assessed the short-term patterns of cardiac acceleration and deceleration, four patterns are identified: +/+ (a lengthening sequencing), +/- or -/+ (balanced sequences), and finally -/- (a shortening sequence). A running count of events by quadrant, together with the average magnitude of the differences was computed. The beta-adrenoceptor partial agonist celiprolol increased acceleration sequences. The duration of beat-to-beat difference shortened after celiprolol; this contrasted with increased duration of beat-to-beat difference after propranolol and atenolol. These results demonstrated a shift towards sympathetic dominance after the beta-adrenoceptor partial agonist celiprolol contrasting in parasympathetic dominance after the beta-adrenoceptor antagonists propranolol and atenolol. These non-linear methods appear to be valuable tools to investigate HRV in health and in cardiovascular disease and to study the implications of alterations in autonomic control during therapeutic intervention.
Adrenergic beta-Agonists↗
The ToxCast program for prioritizing toxicity testing of environmental chemicals.
The U.S. Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS), and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources toward chemicals that likely represent the greatest hazard to human health and the environment. This chemical prioritization research program, entitled "ToxCast," is being initiated with the purpose of developing the ability to forecast toxicity based on bioactivity profiling. The proof-of-concept phase of ToxCast will focus upon chemicals with an existing, rich toxicological database in order to provide an interpretive context for the ToxCast data. This set of several hundred reference chemicals will represent numerous structural classes and phenotypic outcomes, including tumorigens, developmental and reproductive toxicants, neurotoxicants, and immunotoxicants. The ToxCast program will evaluate chemical properties and bioactivity profiles across a broad spectrum of data domains: physical-chemical, predicted biological activities based on existing structure-activity models, biochemical properties based on HTS assays, cell-based phenotypic assays, and genomic and metabolomic analyses of cells. These data will be generated through a series of external contracts, along with collaborations across EPA, with the National Toxicology Program, and with the National Institutes of Health Chemical Genomics Center. The resulting multidimensional data set provides an informatics challenge requiring appropriate computational methods for integrating various chemical, biological, and toxicological data into profiles and models predicting toxicity.
Animals↗
Small hepatocellular carcinomas undetected on two-phased incremental computed tomography. Angiographic and clinicopathologic findings.
RATIONALE AND OBJECTIVES: To elucidate the characteristic clinicopathologic features of hepatocellular carcinomas (HCCs) undetected on two-phased incremental computed tomography (CT). METHODS: Computed tomographic scans of 115 surgically resected small (< or = 3 cm) HCCs from 83 patients were performed 45 seconds and 6 minutes after the administration of contrast material. These scans were compared with corresponding angiographic and histopathologic findings. RESULTS: Eighty HCCs (70%) were depicted on the early images; 73 (63%) on the delayed images; and 89 (77%) using two-phased incremental CT. The small HCCs undetected on the early images but seen histologically had the following characteristics: (1) absence of a fibrous capsule, (2) well-differentiated tumor, (3) replacing growth patterns of the tumors, (4) lack of fatty metamorphosis and/or clear cell changes, (5) hypovascular on angiography. Those not seen on delayed images had the following characteristics: (1) absence of a fibrous capsule, (2) replacing growth patterns, and (3) presence of portal tracts in the tumors. CONCLUSIONS: The replacing growth pattern and the presence of portal tracts correlate with the undetectability on CT. For HCCs undetected on CT, treatment methods must be considered carefully, because the HCCs may be receiving transsinusoidal and portal blood supplies.
Adult↗
Computationally focusing the directed evolution of proteins.
Directed evolution has proven to be a successful strategy for the modification of enzyme properties. To date, the preferred experimental procedure has been to apply mutations or crossovers randomly throughout the gene. With the emergence of powerful computational methods, it has become possible to develop focused combinatorial searches, guided by computer algorithms. Here, we describe several computational methods that have emerged to aid the optimization of mutant libraries, the targeting of specific residues for mutagenesis, and the design of recombination experiments.
Algorithms↗
Determination of 0.1 to 1000 micro g/ml cadmium in a hydrometallurgical zinc refining process stream by a flow injection technique with computer controlled injection method.
A computer-controlled flow injection system was developed for the determination of cadmium in a hydrometallurgical zinc refining process stream. An anion-exchange method in acidic potassium iodide medium was used for the on-line separation of cadmium from the matrix zinc. 1-(4-Nitrophenyl)-3-(4-phenylazophenyl)triazene (Cadion) was used as the chromogenic reagent for the spectrophotometric detection of cadmium. In order to expand the dynamic range of the flow injection - spectrophotometry, a computer-aided time-based variable-volume injection method has been employed for the introduction of the sample into the flow injection system. Samples ranging from 0.56 to 350 microl can be delivered by controlling the time period of the sample introduction valve and the flow rate of the carrier solution. The system permits a throughput of 5 samples per hour. The reproducibility has been proven to be satisfactory with a relative standard deviation of less than 6.2% (sample injected: 0.56 microl of 850 microg Cd/ml; n=100) and 5.0% (350 microl of 0.14 microg Cd/ml; n=5). The determination limit was 20 microg Cd/ml with 0.56 microl sample injection and 0.05 microg Cd/ml with 350 microl sample injection (the absolute amount of cadmium injected into the system was 11 ng and 17.5 ng, respectively).
Journal Article↗
A general, computer-based method for study of the spatial distribution of muscle fiber types in skeletal muscle.
The present method provides detailed quantitative information on the spatial distribution of the muscle fiber types in skeletal muscle. This is accomplished by comparing the measured spatial distribution of the fiber types with a computer-simulated random pattern. The method is based on a registration of the absolute frequency for six principal categories of fiber contacts (I-I, I-IIA, I-IIB, IIA-IIA, IIA-IIB, IIB-IIB). A computer program was designed to simulate a random pattern of fibers. The simulations were performed with high accuracy with regard to fiber type proportion and the number of neighbouring fibers. The computer then calculated the frequency for each of the different categories of fiber contacts in the simulated random pattern. The measured distribution of fiber contacts could thus be compared to the simulated random pattern. In three bovine muscles studied, the spatial distribution of the muscle fiber types showed a similar pattern. The muscle fibers had a distinct tendency to be surrounded by fibers of a different type. In all three muscles the difference between the measured and the simulated random pattern was statistically significant (p less than 10(-3).
Animals↗
A computationally efficient method for accurately solving the EEG forward problem in a finely discretized head model.
OBJECTIVE: Solution of the forward problem using realistic head models is necessary for accurate EEG source analysis. Realistic models are usually derived from volumetric magnetic resonance images that provide a voxel resolution of about 1 mm3. Electrical models could, therefore contain, for a normal adult head, over 4 million elements. Solution of the forward problem using models of this magnitude has so far been impractical due to issues of computation time and memory. METHODS: A preconditioner is proposed for the conjugate-gradient method that enables the forward problem to be solved using head models of this magnitude. It is applied to the system matrix constructed from the head anatomy using finite differences. The preconditioner is not computed explicitly and so is very efficient in terms of memory utilization. RESULTS: Using a spherical head model discretized into over 4 million volumes, we have been able to obtain accurate forward solutions in about 60 min on a 1 GHz Pentium III. L2 accuracy of the solutions was better than 2%. CONCLUSIONS: Accurate solution of the forward problem in EEG in a finely discretized head model is practical in terms of computation time and memory. SIGNIFICANCE: The results represent an important step in head modeling for EEG source analysis.
Algorithms↗
A performance programmed method for computing inbreeding coefficients from large data sets for use in mixed-model analyses.
Coefficients of inbreeding are commonly used in mixed-model methods for forming inverses of Wright's numerator relationship matrix and transformation matrices used in variance component estimation and national cattle evaluation. Computation of exact coefficients of inbreeding from very large data sets has been believed to be too expensive or too difficult a task to perform. Approximate methods have been used instead. The effects of using approximation methods for inbred data that appear in national cattle data sets are demonstrated. An algorithm is given for the computation of inbreeding coefficients for large data sets. The algorithm feasibly computes inbreeding coefficients for large data sets even on small computing architectures.
Algorithms↗
Generator column determination of aqueous solubilities for non-ortho and mono-ortho substituted polychlorinated biphenyls.
Aqueous solubilities of four non-ortho and eight mono-ortho substituted PCBs were determined using a generator-column technique followed by subsequent off-line GC/ECD analysis of the aqueous solutions. The method is based on pumping water through a column containing glass beads coated with the congener being studied and has been used to measure solubilities at room temperature. The method circumvents many of the experimental difficulties encountered with the traditional shake-flask system. Aqueous solubility of 3,3',4,4'-tetrachlorobiphenyl determined by this procedure is compared with data obtained from the shake-flask method and the computational method. The precision of replicate measurements is better than +/- 6.5%. Aqueous solubilities determined for 12 congeners ranged from 6.07 x 10(-11) to 4.47 x 10(-9) mol/L and generally decreased with molecular weight and increased with degree of ortho-chlorine substitution within a molecular-weight class.
Chromatography, Gas↗
Utilizing logical relationships in genomic data to decipher cellular processes.
The wealth of available genomic data has spawned a corresponding interest in computational methods that can impart biological meaning and context to these experiments. Traditional computational methods have drawn relationships between pairs of proteins or genes based on notions of equality or similarity between their patterns of occurrence or behavior. For example, two genes displaying similar variation in expression, over a number of experiments, may be predicted to be functionally related. We have introduced a natural extension of these approaches, instead identifying logical relationships involving triplets of proteins. Triplets provide for various discrete kinds of logic relationships, leading to detailed inferences about biological associations. For instance, a protein C might be encoded within an organism if, and only if, two other proteins A and B are also both encoded within the organism, thus suggesting that gene C is functionally related to genes A and B. The method has been applied fruitfully to both phylogenetic and microarray expression data, and has been used to associate logical combinations of protein activity with disease state phenotypes, revealing previously unknown ternary relationships among proteins, and illustrating the inherent complexities that arise in biological data.
Algorithms↗
A semi-automated computer-assisted method for measuring bone loss adjacent to dental implants.
The purpose of this study was to develop a repeatable method for measurement of bone support around root form and blade implants suitable for use in high-quality but unstandardized radiographs. 10 phantoms were fabricated to simulate progressive osseous defects around implants. Radiographs were taken in triplicate and digitized. Specialized software was written which placed a grid of known dimensions over the implant so that the top and the bottom of the grid were at the neck and the base of the implant, respectively. The investigators selected the edge of the bone at each point where the grid intersected the implant and the software automatically detected the implant edge. The software also outlined and displayed the defect on the computer monitor. Measurements were performed 5 times and the standard deviation was taken as a measure of the repeatability of the method. Repeatability for blades and root forms was 0.19 +/- 0.07 mm and 0.08 +/- 0.03 mm, respectively. There was no significant difference in the ability to measure bone loss in the blade versus the root form (p = 0.17, NS). These results indicate that this semi-automated computer-assisted method for measuring bone loss around implants is repeatable and may be of value for clinical trials using either root form or blade implants.
Alveolar Bone Loss↗
Computational analysis of molecular basis of 1:1 interactions of NRG-1beta wild-type and variants with ErbB3 and ErbB4.
The neuregulin/ErbB system is a growth factor/receptor cascade that has been proven to be essential in the development of the heart and the sympathetic nervous system. However, the basis of the specificity of ligand-receptor recognition remains to be elucidated. In this study, the structures of NRG-1beta/ErbB3 and NRG-1beta/ErbB4 complexes were modeled based on the available structures of the homologous proteins. The binding free energies of NRG-1beta to ErbB3 and ErbB4 were calculated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) computational method. In addition, computational alanine-scanning mutagenesis was performed in the binding site of NRG-1beta and the difference in the binding free energies between NRG-1beta mutants and the receptors was calculated. The results specify the contribution of each residue at the interaction interfaces to the binding affinity of NRG-1beta with ErbB3 and ErbB4, identifying several important interaction residue pairs that are in agreement with previously acquired experimental data. This indicates that the presented structural models of NRG-1beta/ErbB3 and NRG-1beta/ErbB4 complexes are reliable and could be used to guide future studies, such as performing desirable mutations on NRG-1beta to increase the binding affinity and selectivity to the receptor and discovering new therapeutic agents for the treatment of heart failure.
Alanine↗