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At least 523 records · Page 29Linked to original sources
PubMed2006

Predicting calcium-binding sites in proteins - a graph theory and geometry approach.

Identifying calcium-binding sites in proteins is one of the first steps towards predicting and understanding the role of calcium in biological systems for protein structure and function studies. Due to the complexity and irregularity of calcium-binding sites, a fast and accurate method for predicting and identifying calcium-binding protein is needed. Here we report our development of a new fast algorithm (GG) to detect calcium-binding sites. The GG algorithm uses a graph theory algorithm to find oxygen clusters of the protein and a geometric algorithm to identify the center of these clusters. A cluster of four or more oxygen atoms has a high potential for calcium binding. High performance with about 90% site sensitivity and 80% site selectivity has been obtained for three datasets containing a total of 123 proteins. The results suggest that a sphere of a certain size with four or more oxygen atoms on the surface and without other atoms inside is necessary and sufficient for quickly identifying the majority of the calcium-binding sites with high accuracy. Our finding opens a new avenue to visualize and analyze calcium-binding sites in proteins facilitating the prediction of functions from structural genomic information.

Algorithms↗
PubMed2001

Event history graphs for censored survival data.

A compact graphical device for combining survival and time-varying covariate information is proposed. The proposed graph contains the Kaplan-Meier estimator for right-censored data and a simultaneous display of the behaviour of time-dependent covariate(s) and the lifetime for each subject in the sample. The observed levels of time-dependent covariates are possibly subjected to an initial dimension reduction or smoothing step to produce a continuous covariate function. Values of this function are plotted on a horizontal bar for the length of the lifetime of the subject. Covariate information for censored data is also incorporated. The union of the horizontal bars forms the Kaplan-Meier estimator of the survival function. Our graphical method is implemented with a new S-plus function and demonstrated in several applications.

Age Factors↗
PubMed1993

Acyclic directed graphs for automatic image analysis of lung parenchymal geometry.

We have developed a simple method for encoding pulmonary alveolar geometry suitable for morphometric analysis and modeling. The approach involves the use of 8-bit video microscopic images of lung which are thresholded to produce binary images. Each alveolar wall was thinned to its midline to produce a skeletonized image. We present an algorithm for converting such an image to an acyclic directed graph. Such a representation is quite suitable for mathematical treatment, lending itself to problems involving simulation or modeling. We present as an example application, the measurement of dihedral angles in rat lung using conventional histological sections.

Algorithms↗
PubMed1995

Uniqueness and multiplicity of steady states in monocyclic enzyme cascades: a graph-theoretic analysis.

Monocyclic enzyme cascades are important regulators of biochemical reactions in living cells. The reaction network may have either one steady state or many, depending on its structure. The occurrence of multiple steady states has important biological implications. A simple graph-theoretic method has been applied to five reaction mechanisms--which together cover many common monocyclic cascades--to determine which mechanisms generate just one steady state and which ones allow more than one state. It is shown that an unstable steady state in a multiplicity region can be usefully exploited and that in some cases transitions may occur between uniqueness and multiplicity regions. The possible effects of such transitions are discussed.

Animals↗
PubMed1999

Cytological, genetic and evolutionary functions of chiasmata based on chiasma graph analysis.

The nature of the chiasma as a cytological parameter for analysing cross-over was reexamined quantitatively by an improved chiasma graph method. It was reconfirmed in Mus platythrix (n =13) that interstitial chiasmata at diakinesis are distributed randomly and almost uniformly along bivalents except for the centromere and telomere regions. The size of these chiasma blank regions was consistently 0.8% of the total length of haploid autosomes in all chromosomes. There was a minimum value of chiasma interference distance between two adjacent chiasmata, which was constantly 1.8% in all chromosomes. The chiasma frequency at diakinesis was 20.1+/-2. 0 by the conventional method including terminal chiasmata. However, the primed in situ labeling technique revealed that terminal chiasmata were mostly telomere-telomere associations. From these data and also from recent molecular data we concluded that the terminal chiasma is cytologically functional for ensuring the normal disjunction of bivalents at anaphase I, but genetically non-functional for shuffling genes. The chiasma frequency excluding terminal chiasmata was 14.6+/-1.8. Reexamination of the chiasma frequency of 106 animal species revealed that the chiasma frequency increased linearly in proportion to the haploid chromosome number in spite of remarkable difference in their genome size. The increase in chiasma frequency would be evolution-adaptive, because gene shuffling is expected to be accelerated in species with high chromosome numbers.

Animals↗
PubMed2002

Gene mapping via the ancestral recombination graph.

We present a multilocus gene mapping method based on linkage disequilibrium, which uses the ancestral recombination graph to model the history of sequences that may harbor an influential variant. We describe the construction of a recurrence equation used to make inferences about the location of a trait-influencing mutation. We demonstrate how a Monte Carlo algorithm combined with a local importance sampling scheme can be used for mapping. We explain how to simulate the timing of events in the coalescent in the presence of recombination and mutation, which accomodates variable population size. We provide an example to illustrate the use of the method, which can be easily extended to more general situations. Although the method is computationally intensive and variation in the likelihood profiles can occur, the method offers a great deal of promise.

Chromosome Mapping↗
PubMed2005

Graph embedding to improve supervised classification and novel class detection: application to prostate cancer.

Recently there has been a great deal of interest in algorithms for constructing low-dimensional feature-space embeddings of high dimensional data sets in order to visualize inter- and intra-class relationships. In this paper we present a novel application of graph embedding in improving the accuracy of supervised classification schemes, especially in cases where object class labels cannot be reliably ascertained. By refining the initial training set of class labels we seek to improve the prior class distributions and thus classification accuracy. We also present a novel way of visualizing the class embeddings which makes it easy to appreciate inter-class relationships and to infer the presence of new classes which were not part of the original classification. We demonstrate the utility of the method in detecting prostatic adenocarcinoma from high-resolution MRI.

Adenocarcinoma↗
PubMed1995

Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece.

A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the 15N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.

Amino Acid Sequence↗
PubMed1980

The graph of loudness recruitment (ABLB-test).

The ABLB-test compares the subjective loudness in patients with unilateral sensorineural hearing loss. The graph of this comparison of loudness at different suprathreshold intensities is of interest for understanding the function of the hair cells.

Auditory Threshold↗
PubMed2001

New aspects of using the structural graph-grammar based techniques for recognition of selected medical images.

This report will describe the application of syntactic pattern recognition methods for analysis of morphology and recognition of pathologic symptoms of chronic diseases such as upper urinary tract disorders. Detection of these lesions will be assisted by the special graph-grammar developed in our institute for efficient analysis and recognition of such lesions. We present key points of methodology and practical results of its application.

Diagnostic Imaging↗
PubMed2005

A bond graph model of the cardiovascular system.

The study of the autonomic nervous system (ANS) function has shown to provide useful indicators for risk stratification and early detection on a variety of cardiovascular pathologies. However, data gathered during different tests of the ANS are difficult to analyse, mainly due to the complex mechanisms involved in the autonomic regulation of the cardiovascular system (CVS). Although model-based analysis of ANS data has been already proposed as a way to cope with this complexity, only a few models coupling the main elements involved have been presented in the literature. In this paper, a new model of the CVS, representing the ventricles, the circulatory system and the regulation of the CVS activity by the ANS, is presented. The models of the vascular system and the ventricular activity have been developed using the Bond Graph formalism, as it proposes a unified representation for all energetic domains, facilitating the integration of mechanic and hydraulic phenomena. In order to take into account the electro-mechanical behaviour of both ventricles, an electrophysiologic model of the cardiac action potential, represented by a set of ordinary differential equations, has been integrated. The short-term ANS regulation of heart rate, cardiac contractility and peripheral vasoconstriction is represented by means of continuous transfer functions. These models, represented in different continuous formalisms, are coupled by using a multi-formalism simulation library. Results are presented for two different autonomic tests, namely the Tilt Test and the Valsalva Manoeuvre, by comparing real and simulated signals.

Cardiovascular System↗
PubMed1981

Experiments with bar graph process supervision displays on VDUs.

Bar graph representations of process variables are compared with alternatives (stroke-type and 'T'-type, combined bar and stroke) in experiments with human subjects, using either an automatic slide projector or a closed-circuit TV system. The stroke-type appears to give superior results when used for detection of off-normal conditions.

Journal Article↗
PubMed1995

Molecular fragments associated with non-genotoxic carcinogens, as detected using a software program based on graph theory: their usefulness to predict carcinogenicity.

We assembled 390 chemicals with a structure non-alerting to DNA-reactivity (145 carcinogens and 245 non-carcinogens) for which rodent carcinogenicity data were available. These non-alerting chemicals were defined by the absence in their molecules of DNA-reactive (directly or after metabolic activation) alerting structures, as described by Ashby and coworkers (Mutat. Res., 204 (1988) 17-115; Mutat. Res., 223 (1989) 73-103; Mutat. Res., 257 (1991) 209-227; Mutat. Res., 286 (1993) 3-74). Using our software program based on graph theory we analyzed the compounds in order to estimate the program's ability to predict nonalerting carcinogens. Our software fragmented the structural formula of the chemicals into all possible fragments of contiguous atoms with size between 2 and 8 (non-hydrogen) atoms and learned about statistically significant fragments from a training set of chemicals. These fragments were used to predict carcinogenicity or lack thereof in a verification set of compounds. For 390 runs of the software program we used (n - 1) of the chemicals as a training set, to predict the excluded chemical at each run (as a test set). Using two different probability thresholds to select significant fragments (P = 0.05 and P = 0.125 1-tailed according to binomial distribution), we performed two analyses: in the better one (P = 0.05) 19% of the molecules tested lacked significant fragments, for the remaining 81% the observed level of accuracy of the prediction was 66.0% against an expected level of accuracy of 51.7%. The difference was highly significant (P < 0.0001). We also examined the more significant activating fragments (biophores) and discussed at length both their biological plausibility and the working hypothesis that additional alerting structures for carcinogenicity (not only those related to genotoxicity) can be detected using this type of SAR approach. This new class of alerting structures could identify subfamilies of congeneric analogs active through mechanisms of receptor mediated carcinogenesis.

Carcinogens↗
PubMed1978

Bond graphs and the exploitation of power conserving transformations.

Use is made of the guaranteed energy conservation property of any bond graph model (presuming that consistent energy variables are used). Thus power transformations are power conserving, and this property is exploited with respect to multiport transformers where many effort and flow variables may be involved. In these cases the relationship among the effort (flow) variables across the transformer may be easier to derive than the relationship among the flows (efforts). The power conserving nature of the transformer permits immediate derivation of the alternate variable relationship. This formulation procedure is applied to the reflex reaction of the arm.

Energy Metabolism↗
PubMed1992

Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques.

Using 3-D searching techniques based on algorithms derived from graph theory we have established a striking structural similarity between the structure of bovine carboxypeptidase A and that of the C-terminal domain of bovine leucine aminopeptidase. There is no significant sequence homology between the aminopeptidases and the carboxypeptidases but the strong structural relationship detected in this complex fold suggests that there may be a very remote divergent evolutionary relationship between these two enzyme classes.

Animals↗
PubMed1993

Three-dimensional structural resemblance between the ribonuclease H and connection domains of HIV reverse transcriptase and the ATPase fold revealed using graph theoretical techniques.

Using 3D searching techniques based on algorithms derived from graph theory, we have established two previously unreported structural similarities involving the ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT). First, we report that there is a strong similarity between the 3D folds of the RNase H domain of RT and the 'ATPase folds' of hexokinase, the 70 kDa heat-shock cognate protein and actin. Like RNase H, these enzymes are involved in nucleotide binding and metal ion-catalysed cleavage of a phosphodiester bond. Similarities of the folding motif and the position of the metal-binding site in these enzymes suggest possible functional analogies and evolutionary relationships with RNase H. Second, we find there is a strong resemblance between the folds of the RNase H domain and of the p66 and p51 'connection' domains of RT. It is possible that this striking similarity within the RT structure indicates a possible ancestral gene doubling event. The similarity may also indicate that the connection domains possess functional roles in addition to those previously suggested, and they may therefore represent a further target for the design of therapeutic agents.

Adenosine Triphosphatases↗
PubMed1985

Amino acid transport across the human blood-CSF barrier. An evaluation graph for amino acid concentrations in cerebrospinal fluid.

The correlation of cerebrospinal fluid (CSF)/serum concentration quotients was used as a method for identification of amino acids which are transported by a common carrier system across the blood-CSF barrier. Isoleucine, leucine, valine, phenylalanine, tyrosine and lysine were found to compete for the same carrier system. This group of amino acids in man was found to be different from the system described as a neutral amino acid carrier at the blood-brain barrier in rats. In man, methionine and tryptophan do not compete with the other neutral amino acids for the same carrier system. In contrast, lysine as a basic amino acid is found to be correlated with the same transport system as the five neutral amino acids. A graph for the evaluation of pathological amino acid concentrations in CSF is presented. Patients with a blood-CSF barrier dysfunction for proteins showed partly normal, partly increased, CSF/serum concentration quotients for the amino acids. Hydroxyproline could be identified as a constituent of the amino acid pool in CSF. For proline and hydroxyproline a special control system has to be suggested because of their smaller biological variance in CSF than in blood. Contrary to the other amino acids proline and hydroxyproline have a smaller biological variation in CSF than in serum.

Adolescent↗