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At least 181 records · Page 10Linked to original sources
PubMed2005

Farm animal networks: unraveling the contact structure of the British sheep population.

The spatial and temporal dynamics of many farm animal diseases depend both on disease specific parameters and on the underlying contact structure between farms. Whilst many models for farm animal diseases focus on obtaining and estimating disease transmission parameters, relatively little attention has been given to modelling the underlying network of contacts. In this paper, we present an initial analysis of two relations underlying the contact network of individual sheep breeds in Great Britain. The first relation is based on geographical proximity and the second is based on attendance at agricultural shows. These relations are combined to give a risk-potential network that is based on these two levels of interaction. The structure of each network is investigated using techniques developed in graph theory and social network analysis.

Agriculture↗
PubMed2006

Use of social network analysis to characterize the pattern of animal movements in the initial phases of the 2001 foot and mouth disease (FMD) epidemic in the UK.

Aggregated movement data do not take into account the relative position of the units within a higher-level structure. Social network analysis (SNA) and graph theory provide a tool to organise and analyse relational data overcoming the limitations of standard methods where the position of individuals/observations does not affect the result of the analysis. Some recorded movements of cattle and sheep during the initial phase of the 2001 foot and mouth disease (FMD) outbreak in the UK, before the ban on animal movements was imposed, are analysed descriptively using SNA. With the data available, a directed dichotomized network with 653 nodes and 797 arches was analysed. Most of the 10 nodes with the highest betweenness (3 farms, 4 markets and 3 dealers) were identified as key players in the initial spread of the infection. Three groups of nodes with distinctive proportion of k < or = 2 neighbours would result in three different theoretical outbreak dimensions assuming that the infection is only disseminated by the movements included in the network: no spread, spread up to 7% and around 25%. There are three hierarchical clusters with 308, 215 and 130 nodes, respectively. Farms in cluster 1 appear to be more similar in their movement patterns to non-farm holdings than to farms in clusters 2 and 3. Relative betweenness, k-neighbours and structural equivalence using hierarchical clustering were able to identify key actors in the evolution of the initial phases of the FMD outbreak such as markets, dealers and farms with atypical movement patterns. Holdings with high betweenness, large number of k < or = 2 neighbours and with movement pattern as in cluster 1 should be targeted in disease control activities once primary actors like markets, dealers and slaughter houses have been contained.

Animals↗
PubMed2003

Recovery, visualization, and analysis of actin and tubulin polymer flow in live cells: a fluorescent speckle microscopy study.

Fluorescent speckle microscopy (FSM) is becoming the technique of choice for analyzing in vivo the dynamics of polymer assemblies, such as the cytoskeleton. The massive amount of data produced by this method calls for computational approaches to recover the quantities of interest; namely, the polymerization and depolymerization activities and the motions undergone by the cytoskeleton over time. Attempts toward this goal have been hampered by the limited signal-to-noise ratio of typical FSM data, by the constant appearance and disappearance of speckles due to polymer turnover, and by the presence of flow singularities characteristic of many cytoskeletal polymer assemblies. To deal with these problems, we present a particle-based method for tracking fluorescent speckles in time-lapse FSM image series, based on ideas from operational research and graph theory. Our software delivers the displacements of thousands of speckles between consecutive frames, taking into account that speckles may appear and disappear. In this article we exploit this information to recover the speckle flow field. First, the software is tested on synthetic data to validate our methods. We then apply it to mapping filamentous actin retrograde flow at the front edge of migrating newt lung epithelial cells. Our results confirm findings from previously published kymograph analyses and manual tracking of such FSM data and illustrate the power of automated tracking for generating complete and quantitative flow measurements. Third, we analyze microtubule poleward flux in mitotic metaphase spindles assembled in Xenopus egg extracts, bringing new insight into the dynamics of microtubule assemblies in this system.

Actins↗
PubMed2001

AI-based algorithms for protein surface comparisons.

Many current methods for protein analysis depend on the detection of similarity in either the primary sequence, or the overall tertiary structure (the Calpha atoms of the protein backbone). These common sequences or structures may imply similar functional characteristics or active properties. Active sites and ligand binding sites usually occur on or near the surface of the protein; so similarly shaped surface regions could imply similar functions. We investigate various methods for describing the shape properties of protein surfaces and for comparing them. Our current work uses algorithms from computer vision to describe the protein surfaces, and methods from graph theory to compare the surface regions. Early results indicate that we can successfully match a family of related ligand binding sites, and find their similarly shaped surface regions. This method of surface analysis could be extended to help identify unknown surface regions for possible ligand binding or active sites.

Algorithms↗
PubMed2002

Theoretical neuroanatomy and the connectivity of the cerebral cortex.

Over recent years, a wealth of neuroanatomical information on the pattern of interconnections between segregated areas of the cerebral cortex has become available. Here, we describe a set of structural measures, based on graph theory, which can be used to analyze these anatomical patterns. We describe relationships between these structural measures and measures based on patterns of functional connectivity, i.e. patterns of correlations in neural activity. We find that networks capable of producing highly complex functional dynamics share common structural motifs. These motifs are also found in cortical connection matrices, which are characterized by the existence of densely linked groups of areas, low potential wiring length, and a high abundance of reciprocal connections and short cycles. An analysis of cortical functional connectivity demonstrates the existence of functional clusters of highly interactive areas, producing highly complex dynamics. The combined structural and functional analysis outlined in this chapter provides insight into the large-scale functional organization of distributed cortical systems.

Animals↗
PubMed1998

Automatic three-dimensional reconstruction and characterization of articular cartilage from high-resolution ultrasound acquisitions.

Three-dimensional (3D) high-resolution ultrasonography has proved to be useful for in vitro assessment of cartilage remodeling due to osteoarthritis. The diagnosis is performed by computation of the mean thickness of the cartilage, which reveals hypertrophy or thinning, and by 3D reconstruction of the data, which provides essential information about the size, extent, and localization of the lesion. In both cases, preliminary segmention of the cartilage is necessary. This article proposes an algorithm for automatic segmentation of the cartilage from 3D ultrasonic acquisitions of the rat patella, which includes the detection of the cartilage surface and the cartilage/bone interface. The method was designed on the assumption of regularity and smoothness of the interfaces. The use of a global threshold was sufficient to separate the patella area from the background. The cartilage/bone interface was detected by selection of regions of interest (ROIs) encompassing the interface, followed by the detection of the interface within these ROIs using the graph theory. The method was applied to 162 samples. The detection accuracy was judged to be very good or good in 99% of the cases for the cartilage surface and in 86% of the cases for the cartilage/bone interface. The mean cartilage thickness value in the central part of the patella obtained from the automatic detection method was compared to that obtained manually. The coefficient of correlation between the two measurements was 0.92. These results show that our method is reliable. Thus, fast processing of a large number of acquisitions and a more complete analysis of the cartilage surface become possible.

Aging↗
PubMed2003

An efficient peak assignment algorithm for two-dimensional NMR correlation spectra of framework structures.

An algorithm is described for efficiently assigning the resonances in NMR spectra to the inequivalent atoms in the structure under study based on the information in two-dimensional NMR correlation experiments and the 'connectivities' known from the structure. The algorithm, which is based on basic graph theory concepts, finds all possible assignments sets which are consistent with the experimentally observed correlations and known connectivities in a very efficient manner. It is designed to deal with less than ideal experimental data in which there may be overlapping peaks and uncertainty about the presence or absence of correlation peaks. The algorithm was primarily developed for assigning the peaks in the high-resolution solid-state 29Si MAS NMR spectra of highly siliceous zeolites based on two-dimensional 29Si INADEQUATE spectra and is described using the zeolites ZSM-12 and ZSM-5 as working examples. Peak assignment for zeolite frameworks is particularly challenging since there is often little or no information to distinguish peaks from one another such as characteristic chemical shifts, relative intensities, or different relaxation times. The algorithm may be a useful tool for easily, reliably, and efficiently working out peak assignments from other types of correlation experiments on other types of systems and further examples are provided in the Supplementary material.

Algorithms↗
PubMedDate not supplied

A simple QSPR model for predicting soil sorption coefficients of polar and nonpolar organic compounds from molecular formula.

A quantitative structure-property relationship (QSPR) model is developed to predict the logarithm of the soil sorption coefficient of 82 organic compounds. The data set contains polar and nonpolar, saturated, unsaturated, aliphatic, aromatic, and polycyclic aromatic compounds covering a log K(oc) range from about 1 to 6 log units. The best correlation equation, containing only five constitutional descriptors (number of benzene rings, molecular weight, number of N, O, and S atoms), predicts log K(oc) with a squared correlation coefficient of 0.94, having a standard deviation, s, of 0.33. The model is validated with an external set of 43 compounds not included in the training set. The descriptors involved in the model can be obtained easily from the molecular formula without any further calculation; therefore, the model is ready to use by environmental scientists with no background in quantum chemistry or chemical graph theory or when no software is available.

Journal Article↗
PubMedDate not supplied

Are deterministic expert systems for computer-assisted structure elucidation obsolete?

Expert systems for spectroscopic molecular structure elucidation have been developed since the mid-1960s. Algorithms associated with the structure generation process within these systems are deterministic; that is, they are based on graph theory and combinatorial analysis. A series of expert systems utilizing 2D NMR spectra have been described in the literature and are capable of determining the molecular structures of large organic molecules including complex natural products. Recently, an opinion was expressed in the literature that these systems would fail when elucidating structures containing more than 30 heavy atoms. A suggestion was put forward that stochastic algorithms for structure generation would be necessary to overcome this shortcoming. In this article, we describe a comprehensive investigation of the capabilities of the deterministic expert system Structure Elucidator. The results of performing the structure elucidation of 250 complex natural products with this program were studied and generalized. The conclusion is that 2D NMR deterministic expert systems are certainly capable of elucidating large structures (up to about 100 heavy atoms) and can deal with the complexities associated with both poor and contradictory spectral data.

Expert Systems↗
PubMed2001

Three-dimensional aromaticity in polyhedral boranes and related molecules.

Chemical bonding models based on graph theory or tensor surface harmonic theory demonstrate the analogy between the aromaticity in two-dimensional planar polygonal hydrocarbons such as benzene and that in three-dimensional deltahedral borane anions of the type BnHn2- (6 < or = n < or = 12). Such models are supported both by diverse computational studies and experimental determinations of electron density distribution. Related methods can be used to study the chemical bonding in the boron polyhedra found in other structures including neutral binary boron hydrides, metallaboranes, various allotropes of elemental boron, and boron-rich solid-state metal borides.

Journal Article↗
PubMed1998

Quantitative analysis of the structural requirements for blockade of the N-methyl-D-aspartate receptor at the phencyclidine binding site.

Blockade of the N-methyl-D-aspartate receptor by uncompetitive antagonists has implications for symptomatic and neuroprotective therapy of various neuropsychiatric diseases. Since the three-dimensional (3D) structure of this ion channel is unknown, the structural requirements for uncompetitive inhibition were investigated by application of a three-step strategy: At first, Ki values were measured for a number of structurally diverse compounds at the phencyclidine (PCP) binding site in postmortem human frontal cortex. Second, a pharmacophore model was developed for this set of molecules employing a mathematical method called graph theory. The resulting pharmacophore provided a very good explanation for the ability of structurally diverse compounds to bind to the same binding site. Using the experimental data and the pharmacophore as a basis for the third step, a three-dimensional quantitative structure-activity relationship (3D-QSAR) applying comparative molecular field analysis (CoMFA) was performed. The QSAR proved to be highly consistent and showed good predictiveness for several additional molecules. The results give a deeper insight into the structural requirements for effective NMDA receptor antagonism and offer the opportunity for improved drug design. The study represents the first quantitative 3D-QSAR model for NMDA receptor blockade, and it comprises structurally very different molecules. That the alignment for a highly consistent CoMFA is based on an automated 3D pharmacophore analysis has important methodological implications.

Binding Sites↗
PubMed2005

Reaction route graphs. III. Non-minimal kinetic mechanisms.

The concept of reaction route (RR) graphs introduced recently by us for kinetic mechanisms that produce minimal graphs is extended to the problem of non-minimal kinetic mechanisms for the case of a single overall reaction (OR). A RR graph is said to be minimal if all of the stoichiometric numbers in all direct RRs of the mechanism are equal to +/-1 and non-minimal if at least one stoichiometric number in a direct RR is non-unity, e.g., equal to +/-2. For a given mechanism, four unique topological characteristics of RR graphs are defined and enumerated, namely, direct full routes (FRs), empty routes (ERs), intermediate nodes (INs), and terminal nodes (TNs). These are further utilized to construct the RR graphs. One algorithm involves viewing each IN as a central node in a RR sub-graph. As a result, the construction and enumeration of RR graphs are reduced to the problem of balancing the peripheral nodes in the RR sub-graphs according to the list of FRs, ERs, INs, and TNs. An alternate method involves using an independent set of RRs to draw the RR graph while satisfying the INs and TNs. Three examples are presented to illustrate the application of non-minimal RR graph theory.

Journal Article↗
PubMed2002

Identification of protein functions from a molecular surface database, eF-site.

A bioinformatics method was developed to identify the protein surface around the functional site and to estimate the biochemical function, using a newly constructed molecular surface database named the eF-site (electrostatic surface of Functional site. Molecular surfaces of protein molecules were computed based on the atom coordinates, and the eF-site database was prepared by adding the physical properties on the constructed molecular surfaces. The electrostatic potential on each molecular surface was individually calculated solving the Poisson-Boltzmann equation numerically for the precise continuum model, and the hydrophobicity information of each residue was also included. The eF-site database is accessed by the internet (http://pi.protein.osaka-u.ac.jp/eF-site/). We have prepared four different databases, eF-site/antibody, eF-site/prosite, eF-site/P-site, and eF-site/ActiveSite, corresponding to the antigen binding sites of antibodies with the same orientations, the molecular surfaces for the individual motifs in PROSITE database, the phosphate binding sites, and the active site surfaces for the representatives of the individual protein family, respectively. An algorithm using the clique detection method as an applied graph theory was developed to search of the eF-site database, so as to recognize and discriminate the characteristic molecular surfaces of the proteins. The method identifies the active site having the similar function to those of the known proteins.

Antibodies↗
PubMed2002

Similarity among nucleotide sequences.

In this work we report a simple way to measure the similarity between two nucleotide sequences by using graph theory and information theory. This method reported allows for theoretical comparisons of naturally occurring nucleotide sequences.

Algorithms↗
PubMed2003

A theoretical graph method for search and analysis of critical phenomena in biochemical systems. I. Graphical rules for detecting oscillators.

Sufficient conditions for existence of concentration oscillations of components of complex reactions are considered on the basis of graph theory. Graphical rules were developed for detecting oscillators in kinetic schemes of complex biochemical systems. The main types of topology and principles of construction of kinetic schemes of oscillators containing two, three, and four substances are considered. The resulting oscillators might be a part of the biochemical systems of the n-th order. Under certain conditions they were found to be capable of generating oscillations of the system components.

Biological Clocks↗
PubMed2003

Geometrical capillary network analysis.

BACKGROUND: Skin microcirculation, especially the superficial network, can be assessed by a computer capillary video microscope system. The study of morphology and dynamics of microcirculation must include all dynamic and cooperative processes between the capillaries. For characterizing capillary ensembles, the statistical and geometrical properties of the network need to be explored. METHODS: The microvaculature of the skin and the microcirculation were investigated by combining videocapillaroscopy (VCP) and image processing techniques based on computational geometry and graph theory. Our goal was to characterize the capillary network in noisy pictures of the scalp. Different geometric methods were developed, based on proximity parameters (distance and surface) in order to circumscribe and construct this network. RESULTS: By studying the distribution of these parameters, extreme values or outliers, which usually correspond to artifact subregions in the pictures could be eliminated. Different algorithms were developed and has been implemented in an image processing software (Capilab Toolbox). CONCLUSION: This computerized system is capable of real-time processings, increasing the quality of videocapillaroscope images and minimizing the disturbance of artifacts. The algorithms presented here are easy to implement and can process any kind of images of the skin, even in the scalp. In association with an example-based detection system, this method can be generalized to other stimuli in the same conditions.

Capillaries↗
PubMed2005

Evolutionary dynamics on graphs.

Evolutionary dynamics have been traditionally studied in the context of homogeneous or spatially extended populations. Here we generalize population structure by arranging individuals on a graph. Each vertex represents an individual. The weighted edges denote reproductive rates which govern how often individuals place offspring into adjacent vertices. The homogeneous population, described by the Moran process, is the special case of a fully connected graph with evenly weighted edges. Spatial structures are described by graphs where vertices are connected with their nearest neighbours. We also explore evolution on random and scale-free networks. We determine the fixation probability of mutants, and characterize those graphs for which fixation behaviour is identical to that of a homogeneous population. Furthermore, some graphs act as suppressors and others as amplifiers of selection. It is even possible to find graphs that guarantee the fixation of any advantageous mutant. We also study frequency-dependent selection and show that the outcome of evolutionary games can depend entirely on the structure of the underlying graph. Evolutionary graph theory has many fascinating applications ranging from ecology to multi-cellular organization and economics.

Biological Evolution↗
PubMed2005

Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism.

Qualitative theoretical approaches such as graph theory and stoichiometric analyses are beginning to uncover the architecture and systemic functions of complex metabolic reaction networks. At present, however, only a few, largely unproven quantitative concepts propose functional design principles of the global flux distribution. As operational units of function, molecular fluxes determine the systemic cell phenotype by linking genes, proteins and metabolites to higher-level biological functions. In sharp contrast to other 'omics' analyses, 'fluxome' analysis remained tedious. By large-scale quantification of in vivo flux responses, we identified a robust flux distribution in 137 null mutants of Bacillus subtilis. On its preferred substrate, B. subtilis has suboptimal metabolism because regulators of developmental programs maintain a 'standby' mode that invests substantial resources in anticipation of changing environmental conditions at the expense of optimal growth. Network rigidity and robustness are probably universal functional design principles, whereas the standby mode may be more specific.

Acetyl Coenzyme A↗