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At least 1,423 records · Page 79Linked to original sources
PubMed2005

A family of metrics for biopolymers based on counting independent sets.

We introduce a new family of metrics for graphs of fixed size, based on counting-independent sets. Our definition is simpler and easier to calculate than the edge ideal metric family defined by Llabrés and Rosselló without loosing any of its abstract properties. We contrast them on some examples with graphs that represent protein secondary and three-dimensional (3D) structures. We conclude that although the edge ideal metrics are faster to calculate on some sparse graphs, in general, the independent set metrics are more tractable.

Algorithms↗
PubMed2004

A digital reference model of the human bronchial tree.

In-vitro preparations of the human lung combined with high-resolution tomography can be used to derive precise models of the human lung. To develop an abstract graph representation, specially adapted image processing algorithms were applied to segment and delineate the bronchi. The graph thus obtained contains topological information about spatial coordinates, connectivities, diameters and branching angles of 1453 bronchi up to the 17th Horsfield order. The graph was analyzed for statistical and fractal properties and was compared with current models. Results indicate a model that exhibits asymmetry and multifractal properties. This newly established reference model is an important step forward in geometrical accuracy of the bronchial tree representation that will improve both analysis of lung images in clinical imaging and the realism of functional simulations.

Adult↗
PubMed2006

Spectrophotometric and tristimulus analysis of the colors of subcutaneous bleeding in living persons.

The colorimetric patterns of color changes of skin bruises were examined in adult male Japanese volunteers wounded by a sharp pinch on the inside of the upper arm and forearm. In most cases the non-traumatic area near the bruise could be used for the control skin. By using a colorimeter, tristimulus and spectrophotometric methods were available to objectively analyze the skin discoloration. On the L*a*b* color space analysis, Deltab*, the difference between the lesion and control area, was useful to judge whether a bruise was recent or older. When it showed a minus value, the bruise was diagnosed as recent within 2 days. The temporal course of Deltab* changes may be a good indication of the time of bruising as measured in days, however, in actual forensic analysis situations, it is difficult to measure changes in the skin area on a living person over several days. It was hard to perform further age analyses on older bruises especially where only one or two measurements had been taken. On spectrophotometric analysis, clear differences of spectral reflectance curves in some wavelength regions were observed in recent, older and nearly healed lesions as compared with controls. The characteristics of new bruises had a peak point around 500-520 nm of the green area and absorbed light remarkably in the green, yellow and orange wavelength regions (approximately 520-640 nm). On older lesions, reflectance in the blue and one portion of the green wavelength region (440-520 nm) remained unchanged or further reduced before approximately ending similarly to the control curve. Nearly healed injuries showed slight reductions of reflectance over wide wavelength regions, but the curves were close to that of control skin. These reflectance graph patterns could cope with the temporal sequence of color changes of a bruise. As individual reflectance graph patterns depended on particular factors, such as the degree of bruising, it was difficult to correspond the patterns of all bruises to the date of bruising. However, if two measurements were taken at 1 or 2 days, their validity for classifying into recent, older and nearly healed bruises, might be shown by comparing patterns of both curves patterns including the control area. Some indices using reflectance values on certain wavelengths were not very useful to pinpoint the time of bruising. On spectrophotometric analysis, the evaluation of the age of a bruise needs to be done by a comparison of reflectance graph patterns in wide wavelengths in visible light regions.

Adult↗
PubMed2005

New probabilistic graphical models for genetic regulatory networks studies.

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an independence graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions may be preserved. The results of our proposed models were compared with several other commonly used models, and our models have shown to give superior performance. Additionally, we found the same common limitations in the prediction of genetic regulatory networks when using only DNA microarray data.

Algorithms↗
PubMed2004

Candidates for novel RNA topologies.

Because the functional repertiore of RNA molecules, like proteins, is closely linked to the diversity of their shapes, uncovering RNA's structural repertoire is vital for identifying novel RNAs, especially in genomic sequences. To help expand the limited number of known RNA families, we use graphical representation and clustering analysis of RNA secondary structures to predict novel RNA topologies and their abundance as a function of size. Representing the essential topological properties of RNA secondary structures as graphs enables enumeration, generation, and prediction of novel RNA motifs. We apply a probabilistic graph-growing method to construct the RNA structure space encompassing the topologies of existing and hypothetical RNAs and cluster all RNA topologies into two groups using topological descriptors and a standard clustering algorithm. Significantly, we find that nearly all existing RNAs fall into one group, which we refer to as "RNA-like"; we consider the other group "non-RNA-like". Our method predicts many candidates for novel RNA secondary topologies, some of which are remarkably similar to existing structures; interestingly, the centroid of the RNA-like group is the tmRNA fold, a pseudoknot having both tRNA-like and mRNA-like functions. Additionally, our approach allows estimation of the relative abundance of pseudoknot and other (e.g. tree) motifs using the "edge-cut" property of RNA graphs. This analysis suggests that pseudoknots dominate the RNA structure universe, representing more than 90% when the sequence length exceeds 120 nt; the predicted trend for <100 nt agrees with data for existing RNAs. Together with our predictions for novel "RNA-like" topologies, our analysis can help direct the design of functional RNAs and identification of novel RNA folds in genomes through an efficient topology-directed search, which grows much more slowly in complexity with RNA size compared to the traditional sequence-based search.

Algorithms↗
PubMed2004

Network analysis of protein structures identifies functional residues.

Identifying active site residues strictly from protein three-dimensional structure is a difficult task, especially for proteins that have few or no homologues. We transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges. We found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values. Residues with high closeness values interact directly or by a few intermediates with all other residues of the protein. Combining closeness and surface accessibility identified active site residues in 70% of 178 representative structures. Detailed structural analysis of specific enzymes also located other types of functional residues. These include the substrate binding sites of acetylcholinesterases and subtilisin, and the regions whose structural changes activate MAP kinase and glycogen phosphorylase. Our approach uses single protein structures, and does not rely on sequence conservation, comparison to other similar structures or any prior knowledge. Residue closeness is distinct from various sequence and structure measures and can thus complement them in identifying key protein residues. Closeness integrates the effect of the entire protein on single residues. Such natural structural design may be evolutionary maintained to preserve interaction redundancy and contribute to optimal setting of functional sites.

Allosteric Site↗
PubMed2005

Learning protein secondary structure from sequential and relational data.

We propose a method for sequential supervised learning that exploits explicit knowledge of short- and long-range dependencies. The architecture consists of a recursive and bi-directional neural network that takes as input a sequence along with an associated interaction graph. The interaction graph models (partial) knowledge about long-range dependency relations. We tested the method on the prediction of protein secondary structure, a task in which relations due to beta-strand pairings and other spatial proximities are known to have a significant effect on the prediction accuracy. In this particular task, interactions can be derived from knowledge of protein contact maps at the residue level. Our results show that prediction accuracy can be significantly boosted by the integration of interaction graphs.

Animals↗
PubMed2006

Network analysis of Danish cattle industry trade patterns as an evaluation of risk potential for disease spread.

Trade patterns of animal movements in a specific industry are complex and difficult to study because there are many stakeholders, premises that are heterogeneously spread over the country, and a highly dynamic flow of animals exists among them. The Danish cattle industry was defined as a network of animal movements and graph theory was used to analyse the movements of cattle within this network. A premise was defined as a farm, an abattoir or a market. These premises constituted the network nodes in the graph and the animal movements between them were the links. In this framework, each premise had a sub-network of other premises to which it was linked by these animal movements. If no movement of animals were registered for a specific farm, then the sub-network for that premise consisted of only that premise. Otherwise, the sub-network linked the premise of interest to all premises from which and to which animals were moved, as long as there was a path linking animal movements to that specific premise. This approach allowed visualization and analyses of four levels of organization that existed in Denmark animal registers: (1) the animal that was moved, (2) the movements of all animals between two premises, (3) the specific premise network, and (4) the overall industry network. When contagious animals are moved from one premise to another, then to a third and so forth, these movements create a path for potential transfer of pathogens. The paths within which pathogens are present identify the transmission risks. A network of animal movements should provide information about pathogen transmission and disease spread. The network of the Danish cattle industry network was a directed scale-free graph (the direction of a movement was known), with an in-degree power of 2 an out-degree power of 1.46, consisted of 29,999 nodes, and 130,265 movements during a 6-month period. The in clustering coefficient was calculated to be 0.52 for the inward direction (movement to), while it was 0.02 for the outward direction (movement from). In Denmark, the cattle movements between premises demonstrated a large degree of heterogeneity. This heterogeneity in movements between farms should be used to evaluate the risk potential of disease transmission for each premise and must be considered when modelling disease spread between premises. The objective of this research was to describe the network of animal movements and not just the animal movements per se.

Animals↗
PubMed2005

Backward simulation of ancestors of sampled individuals.

If the population is large and the sampling mechanism is random, the coalescent is commonly used to model the haplotypes in the sample. Ordered genotypes can then be formed by random matching of the derived haplotypes. However, this approach is not realistic when (1) there is departure from random mating (e.g., dominant individuals in breeding populations or monogamy in humans), or (2) the population is small and/or the individuals in the sample are ascertained by applying some particular non-random sampling scheme, as is usually the case when considering the statistical modeling and analysis of pedigree data. For such situations, we present here a data generation method where an ancestral graph with non-overlapping generations is first generated backwards in time, using ideas from coalescent theory. Alleles are randomly assigned to the founders, and subsequently the gene flow over the entire genome is simulated forwards in time by dropping alleles down the graph according to recombination model without interference. The parameters controlling the mating behavior of generated individuals in the graph (degree of monogamy) can be tuned in order to match a particular demographic situation, without restriction to simple random mating. The performance of the approach is illustrated with a simulation example. The software (written in C-language) is freely available for research purposes at http://www.rni.helsinki.fi/~dag/.

Female↗
PubMed1997

Visual search and the detection of abnormal readings in graphical displays.

Two experiments evaluated the properties of polygon displays and bar graphs as fault indicator for systems with many parameters. A modified visual search paradigm was used to test the effectiveness of different display configurations to be check-read for the presence of abnormal ('target') readings. Whether the task was to detect the occurrence of a single abnormal (off-limits) parameter or count the number of abnormal parameters, both displays yielded response times and error rates that were independent of the total number (from 4 to 16) of displayed parameters. When the task was fault detection, the subjects performed equally well with both types of displays. When the task was counting the number of abnormalities, performance with the bar graph was independent of the number of abnormalities but performance with the polygon display was poorer overall and deteriorated with larger numbers of abnormalities. The results contradict either the proximity-compatibility hypothesis of Wickens or the traditional classification of polygons and bar graphs as typical integral and separable displays, respectively. The results are best characterized in terms of the similarity relations between and among 'target' and 'nontarget' parameters.

Adolescent↗
PubMed1998

Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns.

Hydropathy plots are often used in place of missing physical data to model transmembrane proteins that are difficult to crystallize. The sequential maxima of their graphs approximate the number and locations of transmembrane segments, but potentially useful additional information about sequential hydrophobic variation is lost in this smoothing procedure. To explore a broader range of hydrophobic variations without loss of the transmembrane segment-relevant sequential maxima, we utilize a sequence of linear decompositions and transformations of the n-length hydrophobic free energy sequences, Hi, i = 1...n, of proteins. Constructions of hydrophobic free energy eigenfunctions, psil, from M-lagged, M x M autocovariance matrices, CM, were followed by their all-poles, maximum entropy power spectral, Somega(psil), and Mexican Hat wavelet, Wa,b(psil), transformations. These procedures yielded graphs indicative of inverse frequencies, omega-1, and sequence locations of hydrophobic modes suggestive of secondary and supersecondary protein structures. The graphs of these computations discriminated between Greek Key, Jelly Role, and Up and Down categories of antiparallel beta-barrel proteins. With these methods, examples of porins, connexins, hexose transporters, nuclear membrane proteins, and potassium but not sodium channels appear to belong to the Up and Down antiparallel beta-barrel variety.

Carrier Proteins↗
PubMed1997

Modulation of the cardiac baroreflex following reversible blockade of the parabrachial nucleus in the rat.

The parabrachial nucleus (PBN) has a prominent anatomical connection with the nucleus of the solitary tract as well as other central baroreflex centres which suggests a role for the PBN in the regulation of this cardiovascular reflex. This study examined the effects of a reversible, bilateral blockade of the PBN on the cardiac baroreflex. Male Sprague-Dawley rats were anesthetized with sodium butabarbitol and instrumented to monitor blood pressure and heart rate and for the intravenous administration of drugs. The cardiac baroreflex was evoked using bolus intravenous injections of phenylephrine (PE) and sodium nitroprusside (NaNp) at various doses and a graph of baroreflex sensitivity was constructed. Bilateral microinjections of the reversible anesthetic, lidocaine (5%, 300 nl), into the PBN did not significantly change baseline blood pressure or heart rate when compared to microinjections of saline (0.9%, 300 nl) into the PBN. The pressor or depressor responses evoked by bolus injections of PE or NaNp, respectively, were not significantly affected by the bilateral pretreatment of the PBN with lidocaine when compared to saline controls. However, approximately 30 min following lidocaine injection, the amplitudes of both the evoked-reflex bradycardia and reflex tachycardia were significantly increased by approximately 98%. The cardiovascular responses to various doses of PE and NaNp were graphed and baroreflex sensitivity curves were constructed. This graph showed an increased slope of the baroreflex sensitivity curve following lesions of the PBN. Reflex changes in heart rate returned to pre-lidocaine injection levels after approximately 2 h. The results of the present investigation suggest that the PBN participates in the modulation of the cardiac baroreflex which in turn suggests a role for this nucleus in the central integration of cardiovascular reflex function.

Analysis of Variance↗
PubMed1999

An overview of quality control practices in Ontario with particular reference to cholesterol analysis.

BACKGROUND: The Laboratory Proficiency Testing Program (LPTP) assesses the analytical performance of all licensed laboratories in Ontario. The LPTP Enzymes, Cardiac Markers, and Lipids Committee conducted a "Patterns of Practice" survey to assess the in-house quality control (QC) practices of laboratories in Ontario using cholesterol as the QC paradigm. DESIGN AND METHODS: The survey was questionnaire-based seeking information on statistical calculations, software rules, review process and data retention, and so on. Copies of the in-house cholesterol QC graphs were requested. A total of 120 of 210 laboratories were randomly chosen to receive the questionnaires during 1995 and 1996; 115 laboratories responded, although some did not answer all questions. RESULTS: The majority calculate means and standard deviations (SD) every month, using anywhere from 4 to >100 data points. 65% use a fixed mean and SD, while 17% use means calculated from the previous month. A few use a floating or cumulative mean. Some laboratories that do not use fixed means use a fixed SD. About 90% use some form of statistical quality control rules. The most common rules used to detect random error are 1(3s)/R4s while 2(2s)/4(1s)/10x are used for systematic errors. About 20% did not assay any QC at levels >5.5 mmol/L. CONCLUSIONS: Quality control data are reviewed daily (technologists), weekly and monthly (supervisors/directors). Most laboratories retain their QC records for up to 3 years on paper and magnetic media. On some QC graphs the mean and SD, QC product lot number, or reference to action logs are not apparent. Quality control practices in Ontario are, therefore, disappointing. Improvement is required in the use of clinically appropriate concentrations of QC material and documentation on QC graphs.

Chemistry, Clinical↗
PubMed1984

RECFIT: a microcomputer-based nonlinear regression curve-fitting package for the quantitative resolution of beta-adrenoceptor subtypes and estimation of nonspecific binding.

A dedicated nonlinear regression based curve-fitting packages has been developed for quantitative analysis of beta-adrenoceptor subtypes. A feature of this package is the provision to obtain initial parameter estimates using a conversational graphical technique where the user is prompted for parameter estimates, and the resulting curve is displayed over the data. Data are then fitted to a one- or two-binding site model with user-selected weighting and constraints on the parameters. A novel feature is the provision to estimate the nonspecific binding component in the assays as a parameter in the model. The printout for each model consists of the parameters and their standard deviations, estimates of the goodness of fit, an analysis of residuals, and a graph of the data points overlayed with the fitted curve. The nonlinear regression algorithm is based on that of Gauss-Newton. When unweighted, the values determined by RECFIT are essentially the same as those found using the BMDPAR programs on an ICL 2976 mainframe computer. The implementation is reasonably efficient; a typical run for a two-site fit, using nine data points and estimating nonspecific binding, took a total time of about 8 min, excluding data entry and derivation of initial estimates, 4 min for the fitting, 30 sec for graph generation, and 2-3 min for printing of the graph and data.

Binding Sites↗
PubMed2003

Ancestral processes for non-neutral models of complex diseases.

We consider non-neutral models for unlinked loci, where the fitness of a chromosome or individual is not multiplicative across loci. Such models are suitable for many complex diseases, where there are gene-interactions. We derive a genealogical process for such models, called the complex selection graph (CSG). This coalescent-type process is related to the ancestral selection graph, and is derived from the ancestral influence graph by considering the limit as the recombination rate between loci gets large. We analyse the CSG both theoretically and via simulation. The main results are that the gene-interactions do not produce linkage disequilibrium, but do produce dependencies in allele frequencies between loci. For small selection rates, the distributions of the genealogy and the allele frequencies at a single locus are well-approximated by their distributions under a single locus model, where the fitness of each allele is the average of the true fitnesses of that allele with respect to the distribution of alleles at other loci.

Genetic Predisposition to Disease↗
PubMed2001

What defines a view?

At a given instant we see only visible surfaces, not an object's complete 3D appearance. Thus, objects may be represented as discrete 'views' showing only those features visible from a limited range of viewpoints. We address how to define a view using Koenderink's (Koenderink & Van Doorn, Biol. Cybernet. 32 (1979) 211.) geometric method for enumerating complete sets of stable views as aspect graphs. Using objects with known aspect graphs, five experiments examined whether the perception of orientation is sensitive to the qualitative features that define aspect graphs. Highest sensitivity to viewpoint changes was observed at locations where the theory predicts qualitative transitions, although some transitions did not affect performance. Hypotheses about why humans ignore some transitions offer insights into mechanisms for object representation.

Discrimination, Psychological↗
PubMed1998

A comparison of two computer-based face identification systems with human perceptions of faces.

The performance of two different computer systems for representing faces was compared with human ratings of similarity and distinctiveness, and human memory performance, on a specific set of face images. The systems compared were a graph-matching system (Lades M, Vorbrüggen JC, Buhmann J, Lage J, von der Malsburg C, Würtz RP, Konen W. IEEE., Trans Comput 1993;42:300-311.) and coding based on principal components analysis (PCA) of image pixels (Turk M, Pentland A. J Cognitive Neurosci 1991;3:71-86.). Replicating other work, the PCA-based system produced very much better performance at recognising faces, and higher correlations with human performance with the same images, when the images were initially standardised using a morphing procedure and separate analysis of 'shape' and 'shape-free' components then combined. Both the graph-matching and (shape + shape-free) PCA systems were equally able to recognise faces shown with changed expressions, both provided reasonable correlations with human ratings and memory data, and there were also correlations between the facial similarities recorded by each of the computer models. However, comparisons with human similarity ratings of faces with and without the hair visible, and prediction of memory performance with and without alteration in face expressions, suggested that the graph-matching system was better at capturing aspects of the appearance of the face, while the PCA-based system seemed better at capturing aspects of the appearance of specific images of faces.

Adult↗
PubMed2003

Vibrational Markovian modelling of footprints after the interaction of antibiotics with the packaging region of HIV type 1.

The design of novel anti-HIV compounds has now become a crucial area for scientists working in numerous interrelated fields of science such as molecular biology, medicinal chemistry, mathematical biology, molecular modelling and bioinformatics. In this context, the development of simple but physically meaningful mathematical models to represent the interaction between anti-HIV drugs and their biological targets is of major interest. One such area currently under investigation involves the targets in the HIV-RNA-packaging region. In the work described here, we applied Markov chain theory in an attempt to describe the interaction between the antibiotic paromomycin and the packaging region of the RNA in Type-1 HIV. In this model, a nucleic acid squeezed graph is used. The vertices of the graph represent the nucleotides while the edges are the phosphodiester bonds. A stochastic (Markovian) matrix was subsequently defined on this graph, an operation that codifies the probabilities of interaction between specific nucleotides of HIV-RNA and the antibiotic. The strength of these local interactions can be calculated through an inelastic vibrational model. The successive power of this matrix codifies the probabilities with which the vibrations after drug-RNA interactions vanish along the polynucleotide main chain. The sums of self-return probabilities in the k-vicinity of each nucleotide represent physically meaningful descriptors. A linear discriminant function was developed and gave rise to excellent discrimination in 80.8% of interacting and footprinted nucleotides. The Jackknife method was employed to assess the stability and predictability of the model. On the other hand, a linear regression model predicted the local binding affinity constants between a specific nucleotide and the antibiotic (R(2)=0.91, Q(2)=0.86). These kinds of models could play an important role either in the discovery of new anti-HIV compounds or the study of their mode of action.

Anti-HIV Agents↗