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At least 1,657 records · Page 92Linked to original sources
PubMed1995

Simulation study comparing interval estimates for the recombination fraction.

Three interval estimation procedures were evaluated to determine the method which provides the most accurate estimates for the recombination fraction, 0. The lod-0.83 support interval, the jackknife confidence interval, and the confidence interval based on estimated asymptotic standard error were compared by calculating the coverage probabilities of each. Family data that were simulated under the model of a single fully penetrant, dominant disease locus at some distance, 0, from fully informative matings were used. Comparisons were based on 1,000 random samples of size 20,60, and 100 families. In addition, a methodology for obtaining prediction intervals for 0 was developed. This procedure is of practical use and does not require asymptotic assumptions based on large sample theory. The results provide an a priori idea about precision of the estimates, as well as empirical interval estimates of 0. Graphs of the authors' Monte Carlo intervals are presented for these simulations. Investigators studying different traits, however, could condition specifically on the family structure and distribution of the disease they are investigating and obtain similar graphs.

Chi-Square Distribution↗
PubMed1997

Quantitative graphical description of portocentral gradients in hepatic gene expression by image analysis.

The liver consists of numerous repeating, randomly oriented, more or less cylindrical units, the lobules. Although enzyme-histochemical or microbiochemical assays accurately reflect zonal differences in lobular enzyme content, their results cannot be directly compared to biochemical assays. This is because section-based assays typically sample along a linear portocentral column of cells, even though periportal regions contribute substantially more to hepatic volume than pericentral regions. We have developed a time-efficient approach that depends on image analysis to determine the prevalence of hepatocytes (pixels) with a defined cellular concentration of a particular gene product (absorbance), and that generates a graph with the average absorbance per hepatocyte on the ordinate and the percentage of hepatocytes with absorbances in each of a predetermined range of absorbances incrementally summed on the abscissa. The direction of the gradient is read directly from the section. The gradient is a graphical representation of the two-dimensional distribution pattern of the gene product between the portal tracts and the central veins. The total surface area underneath the resulting graph represents the integrated absorbance and is equivalent to the outcome of a biochemical assay. The typical linear portocentral gradient can be derived from that representing the two-dimensional distribution if we assume that liver lobules are uniformly cylindrical or prismatic. The analysis, therefore, yields a quantitative description of the relation between the enzymatic phenotype of hepatocytes and their position on a normalized portocentral radius. We have used the procedure to compare portocentral gradients of different enzymes in the same liver and of the same enzyme in different livers. In addition, bipolar portocentral gradients of the same enzyme in the same liver were analyzed.

Animals↗
PubMed1991

Drug dose prediction with flexible test doses.

This article presents the first known practical method to apply one-compartment pharmacokinetic modeling to prediction of doses for drugs from one or more blood-drug concentrations, without requiring approximations or a computer. It should be useful for regulating doses of orally administered CNS drugs whose effects develop over a day or more, e.g., lithium, antidepressants, and anticonvulsants. Pharmacokinetic calculations for sequences of one, two, and three test doses are condensed into graphs that can be rapidly applied for clinical purposes. These graphs account for dose division, blood sampling time, and drug elimination rate; they show that the ratio of the steady-state day-mean drug level to the test-drug blood level is independent of the half-life if the test level is about a day after the last test dose. The calculations show the same value as experimental measurements for the ratio between steady-state serum lithium level and serum lithium level measured after a test dose. A rational strategy for drug-loading doses is discussed.

Central Nervous System Agents↗
PubMed2002

Qmd-plot: a graphical utility for rapid preliminary analysis of time series of fluctuating data, developed in the context of molecular dynamics simulations.

Qmd-plot is a utility to obtain rapid information about past or on-going simulations, or real-time data collections, in the form of graphs of recorded variables (x, y, ...), as x-y plots or as a function of simulated or real time. Time series records in the data file must be named. Variable names and their locations in the data file are initially unknown to the program, but are identified in a first scan, in which header records are located on the basis of a predefined key (that can be changed interactively). The names of the time series are then presented in an interactive menu, from which the user can repeatedly specify a graph to be viewed. Qmd-plot has been developed in the context of molecular dynamics simulations. We give examples of time series and x-y plots made from output of the sigma program. Qmd-plot code is a Java application; source and class files can be obtained free from the authors.

Journal Article↗
PubMed2004

Modification of the Wiener index 4.

A novel topological index W(F) is defined by the matrices X, W, and L as W(F) = XWL. Where L is a column vector expressing the characteristic of vertices in the molecule; X is a row vector expressing the bonding characteristics between adjacent atoms; W is a reciprocal distance matrix. The topological index W(F), based on the distance-related matrix of a molecular graph, is used to code the structural environment of each atom type in a molecular graph. The good QSPR/QSAR models have been obtained for the properties such as standard formation enthalpy of inorganic compounds and methyl halides, retention indices of gas chromatography of multiple bond-containing hydrocarbons, aqueous solubility, and octanol/water partition of benzene halides. These models indicate that the idea of using multiple matrices to define the modified Wiener index is valid and successful.

Journal Article↗
PubMed2005

Graphical approach to analyzing DNA sequences.

Recently, we proposed a 2D graphical representation of DNA sequence [J Comput Chem 25(2004) 1364-1368]. Based on this representation, we outline one approach to search optimal alignment. We also can judge the mutations between bases and an unknown sequence based on its graph and a known sequence's graph.

Algorithms↗
PubMed2002

Spectrophotometric determination of leukocytes in blood.

The determination of leukocyte concentration in human blood depending on the detection of oxidized o-dianisidine in acidic solution is studied. The oxidation of o-dianisidine was carried out by peroxidase enzymes found in leukocytes. The reaction was stopped by the addition of 4N H(2)SO(4) to the solution, and a very stable, colored o-dianisidine derivative was obtained. The calibration graph was plotted with the recorded absorbance values at 400 nm assigned to the y-axis, and leukocyte counts in 1-mL blood samples to the x-axis. The equation of the calibration graph was y=0.0025 x +0.0904, with a correlation coefficient of R=0.994. The coefficient of variation and P-value of the method were 4.00% and 0.05%, respectively.

Dianisidine↗
PubMedDate not supplied

Biparietal diameter and menstrual age in the black population attending Edendale Hospital.

The relationship between fetal biparietal diameter measured by echography and menstrual age for blacks was studied. Predicted values and their confidence limits are presented in tables and graphs. The biparietal diameter was significantly smaller from 28 weeks than American and European studies, demonstrating that a composite graph was not applicable to the Zulus. The echographic results were checked at term by external cephalometry. Occipitofrontal circumference and birth weights for newborns were found similar to other studies. The smaller BPD in late pregnancy could be explained by the head's shape. The new charts are valuable in assessing fetal growth in African blacks.

Birth Weight↗
PubMed1982

Change of digastric muscle length in feeding rabbits.

An experiment was undertaken to measure directly the changing length of a jaw muscle during feeding in four intact, unanesthetized New Zealand White rabbits. Metal markers were implanted to define the anterior and posterior ends of the single belly of the digastric muscle and fluoroscopic images were recorded on videotape while the animals fed on pelleted chow and carrot. Graphs of muscle length versus incisor separation were obtained by making measurements of single frames of the videotape record. The graphs revealed that when pelleted chow was being chewed the length of the digastric muscle changed by no more than 9% of its greatest length; during the latter part of the closing stroke it changed very little. Incising and chewing carrot caused the digastric muscle to change in length continuously throughout the chewing cycle; incising carrot resulted in a 13% change in the length of the digastric muscle. The velocity of shortening is slightly less than one muscle length per second.

Animals↗
PubMedDate not supplied

Multicenter trial of automated border detection in cardiac MR imaging.

The purpose of the present study was to evaluate the robustness of a method of automated border detection in cardiac magnetic resonance (MR) imaging. Thirty-seven short-axis spin-echo cardiac images were acquired from three medical centers, each with its own image-acquisition protocol. Endo- and epicardial borders and areas were derived from these images with a graph-searching-based method of edge detection. Computer results were compared with observer-traced borders. The method accurately defined myocardial borders in 36 of 37 images (97%), with excellent agreement between computer- and observer-derived endocardial and epicardial areas (correlation coefficients, .94-.99). The algorithm worked equally well for data from all three centers, despite differences in image-acquisition protocols, MR systems, and field strengths. These data suggest that a method of computer-assisted edge detection based on graph-searching principles yields endocardial and epicardial areas that correlate well with those derived by an independent observer.

Adult↗
PubMed1980

Cost evaluation of alternative pharmaceutical tableting processes by simulation.

A simulation model and a subsequent computer program were developed as experimentation methods for evaluating tableting processes with respect to cost. These methods also allow estimation of the various times involved in a tableting operation (e.g., the processing time). The model was programmed in FORTRAN using the GASP IV simulation language. After verification of the program, experiments were run that involved comparing different levels of specific input variables to determine which variable had an effect on the cost-time relationships of a particular processing method. Among the possible input variables chosen for evaluation were the drying method, the type of tableting machine, the batch size, the labor rate, and the operation of the equipment in the process. An analysis of variance was made, and three separate regression equations were developed that described the relationship between the input variables and the dependent variables of processing cost and time. Graphs were developed from the regression equations by manipulating them through series of different independent variables. These graphs then were used in determining minimum costs and times, breakeven points, and rates of change, as well as in simple evaluation of processes through graphic representation. By using the simulation program to run experiments and then by analyzing them, results can be obtained to help in making intelligent decisions about the cost-time relationships of a particular tableting procedure before it is implemented.

Chemistry, Pharmaceutical↗
PubMed1993

Hydrogen-bond patterns of dialkylpyridone iron chelators and their 1:1 formic acid solvates: description, prediction, and role in crystal packing.

The crystal structures (determined from single-crystal X-ray diffraction studies) and hydrogen-bond patterns of three crystalline 1,2-dialkyl-3-hydroxy-4-pyridones and their 1:1 formic acid solvates are elucidated. The primary hydrogen-bond connectivities observed are explained by a model that predicts that the best donor bonds to the best acceptor. Relative hydrogen-bond donating and accepting abilities of the functional groups observed in these compounds are evaluated by a combination of pKas, energy calculations, resonance arguments, and crystallographic evidence. The primary (O--H ... O) hydrogen-bond patterns are described by graph set notation, and brief explanations of the graph set assignments are also included. A total of 17 secondary (C--H ... O) hydrogen bonds are also observed in these six structures. Correlations are drawn between the observed C--H ... O hydrogen bonds and the molecular packing. The possible role of these secondary hydrogen bonds in influencing molecular packing is discussed.

Crystallography, X-Ray↗
PubMed2006

Longitudinal study of the motor response to levodopa in Parkinson's disease.

In this prospective study of 34 patients with Parkinson's disease, measurements of the short duration levodopa motor response have been performed in defined off states at 3 yearly intervals over a mean period of 11.4 years from the point of commencement of levodopa treatment. Twenty-two patients were still available for study; 10 had died and 2 were lost to follow-up. The levodopa motor response amplitude increases over the first 5 years of treatment, and thereafter, on and off scores worsen in parallel with conservation of the response. Patients who developed motor fluctuations within the first 5 years of treatment had, on average, a stronger response to levodopa with significantly better on phase motor function (P = 0.003). Although the proportion of "midline" motor disability (affecting gait, balance, and cranial motor function) increases with time, these deficits do not actually become unresponsive to levodopa. Patients who developed dementia had a significantly more rapid decline in motor function. The latest graph of serial scores for the whole cohort shows an upward curving or exponential increase in motor disability after the first decade of treatment. Applying a notional untreated disability line to this graph--an estimate of the disability that would have accrued if drugs had never been given--we suggest that the long-duration response to levodopa eventually runs down with disease progression.

Adult↗
PubMed1995

Measurements of tissue blood flow by the hydrogen clearance technique (HCT): a comparative study including laser Doppler flowmetry (LDF) and the Erlangen micro-lightguide spectrophotometer (EMPHO).

The purpose of this study was to compare the hydrogen clearance technique (HCT) with two different, well-established techniques, i.e., the laser Doppler flowmetry (LDF) and the Erlangen micro-lightguide spectrophotometer (EMPHO), for tissue blood flow measurements in an experimental setting. For the animal experiments, we chose a rat model for arterial and venous flap thrombosis, using the epigastric groin flap. Forty male dark Aguty rats were included in the study. The animals were divided into eight groups, each with a different vascular thrombotic model. HCT was used to collect 1,467 measurements, and 2,934 graphs were recorded; 27 measurements (54 graphs) had to be discarded due to faulty electrode placements and electronic noise. In 19 of the 27 discarded measurements the cause of failure was moving of the awaking animal with disruption of the decay signal. The LDF and EMPHO measurements were performed continuously during each measuring phase. Simple and multiple linear regression and paired t-tests were used to compare the three techniques. The reproducibility of registered blood flow values in phases 1, 3, 6 and 7 varied between 7.8% and 13.6% which is in about the same range as LDF and EMPHO. We could not find a significant difference between the three techniques in this regard. The correlation coefficient for HCT and LDF was r = 0.89. For HCT and EMPHO we found r = 0.67. Sensitivity and specificity values for HCT were both 1.0 in detecting arterial and venous flap thrombosis; for LDF we found values of 0.89 and 0.92, respectively. Sensitivity and specificity values for EMPHO were 0.92 and 0.95, respectively. After careful evaluation of three different techniques (HCT, LDF, and EMPHO) for measurements of local tissue blood flow we came to the conclusion that HCT must be favoured as a reliable tool for quantitative measurement of local tissue blood flow and early diagnosis of arterial and venous flap thrombosis.

Animals↗
PubMed1994

Internal temperature calibration for 1H NMR spectroscopy studies of blood plasma and other biofluids.

A method for temperature calibration of human blood plasma and cerebrospinal fluid (CSF) samples inside a high resolution NMR spectrometer is presented. This calibration is based on the temperature dependence of the chemical shift difference between the water signal and that from the H-1 proton of endogenous alpha-glucose or, in some circumstances, beta-glucose. This dependence can be fitted using a second-order polynomial equation and functions for both human blood plasma and human CSF are given. Similar graphs could easily be generated for other fluids. The blood plasma calibration appears to be accurate to +/- 0.9 K in test samples. The use of the blood plasma calibration graph has also been evaluated using the 1H NMR spectra of CSF and shown to overestimate the CSF internal temperature by ca 1.3 K. This approach should have a general applicability to blood plasma and CSF samples from normal and pathological situations or from other species, because there are unlikely to be large changes in ionic strength or pH even in disease states. Knowledge of the exact internal temperature of plasma samples is likely to be of particular importance in the investigation of lipid and lipoprotein interactions because of the significant temperature dependence of lipid and lipoprotein NMR linewidths in such samples.

Body Fluids↗
PubMed2002

Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model.

By Monte Carlo simulations, we explored the effect of single mutations on the thermodynamics and kinetics of the folding of a two-dimensional, energetically frustrated, hydrophobic protein model. Phi-Value analysis, corroborated by simulations beginning from given sets of judiciously chosen initial contacts, suggests that the transition state of the model consists of a limited region of the native structure, that is, a folding nucleus. It seems that the most important contacts in the transition state (large and positive Phi) are not the ones with the highest contact order, because in this case the entropic cost of their formation would be too high, but exactly the ones that decrease the entropic cost of difficult contacts, reducing their effective contact order. Mutations of internal monomers involved in high-order contacts were actually the ones resulting in the fastest kinetics (and Phi < 0), indicating they tend to make low order, non-native contacts of low entropic cost that stabilize the unfolded state with respect to the transition state. Folding acceleration by other non-native interactions was also observed and a simple general mechanism is proposed according to which non-native contacts can act indirectly over the folding nucleus, "chelating" out potentially harmful contacts. The polymer graph of our model, which facilitates the visualization of effective contact orders, successfully suggests the relative kinetic importance of different contacts and is reasonably consistent with analogous graphs for the well characterized family of SH3 domains.

Computer Simulation↗
PubMed2004

A unified representation of multiprotein complex data for modeling interaction networks.

The protein interaction network presents one perspective for understanding cellular processes. Recent experiments employing high-throughput mass spectrometric characterizations have resulted in large data sets of physiologically relevant multiprotein complexes. We present a unified representation of such data sets based on an underlying bipartite graph model that is an advance over existing models of the network. Our unified representation allows for weighting of connections between proteins shared in more than one complex, as well as addressing the higher level organization that occurs when the network is viewed as consisting of protein complexes that share components. This representation also allows for the application of the rigorous MinMaxCut graph clustering algorithm for the determination of relevant protein modules in the networks. Statistically significant annotations of clusters in the protein-protein and complex-complex networks using terms from the Gene Ontology indicate that this method will be useful for posing hypotheses about uncharacterized components of protein complexes or uncharacterized relationships between protein complexes.

Algorithms↗
PubMed2005

Evolution and similarity evaluation of protein structures in contact map space.

Prediction of fold from amino acid sequence of a protein has been an active area of research in the past few years, but the limited accuracy of existing techniques emphasizes the need to develop newer approaches to tackle this task. In this study, we use contact map prediction as an intermediate step in fold prediction from sequence. Contact map is a reduced graph-theoretic representation of proteins that models the local and global inter-residue contacts in the structure. We start with a population of random contact maps for the protein sequence and "evolve" the population to a "high-feasibility" configuration using a genetic algorithm. A neural network is employed to assess the feasibility of contact maps based on their 4 physically relevant properties. We also introduce 5 parameters, based on algebraic graph theory and physical considerations, that can be used to judge the structural similarity between proteins through contact maps. To predict the fold of a given amino acid sequence, we predict a contact map that will sufficiently approximate the structure of the corresponding protein. Then we assess the similarity of this contact map with the representative contact map of each fold; the fold that corresponds to the closest match is our predicted fold for the input sequence. We have found that our feasibility measure is able to differentiate between feasible and infeasible contact maps. Further, this novel approach is able to predict the folds from sequences significantly better than a random predictor.

Amino Acid Sequence↗