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PubMed2002

[Applications of informatics in anesthesiology: anesthesia graphics].

Computerization has brought radical changes to anesthesiology. Quality of care, management, cost control, training, research, safety and privacy have all improved. The anesthesiologist has been freed from repetitive clerical tasks and is able to make better use of time. A graphic display of anesthesia is only one of the many computer applications available as a consequence of links created among monitoring, continuous infusion and intelligent alarm systems, automatic data collection, network monitoring and the availability of bibliographic information (through Internet connection). The computer graphic display of anesthesia is more precise, legible, complete and reliable (during critical events, in substitutions of anesthesiologists or for research) than the traditional graph. One of the greatest problems of computer graphing today--besides start-up costs--is that of inserting comments on monitoring artifacts, given that the graph is a legally valid medical document.

Anesthesiology↗
PubMed2003

Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes.

Algorithms↗
PubMed2006

Statistics of cycles in large networks.

The occurrence of self-avoiding closed paths (cycles) in networks is studied under varying rules of wiring. As a main result, we find that the dependence between network size and typical cycle length is algebraic, (h) proportional to Nalpha, with distinct values of for different wiring rules. The Barabasi-Albert model has alpha=1. Different preferential and nonpreferential attachment rules and the growing Internet graph yield alpha<1. Computation of the statistics of cycles at arbitrary length is made possible by the introduction of an efficient sampling algorithm.

Journal Article↗
PubMed1998

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.

MOTIVATION: Although a large amount of information on the structure, function and properties of biomolecules is becoming available, it is difficult to understand the relationship between them. Thus, we have attempted to create an integrated relational database, search and visualization tool, 3DinSight, to help researchers to gain insight into their relationship. RESULTS: We have gathered data on the structure, function and properties of biomolecules, and implemented them into a relational database system. The structural data contain several subset data such as protein homologues, protein-DNA complex, in order to enable searching within a specific class of data. The functional data include motif sequence and mutation data of proteins. Also, various amino acid properties are implemented as a relational table. The World Wide Web (WWW) interfaces enable users to carry out various kinds of searches among these data. The locations of motif sequences and mutations are automatically mapped on the structure, and visualized in three-dimensional (3D) space by interactive viewers, VRML (Virtual Reality Modeling Language) and RasMol. In the case of VRML, the mapped 3D objects are hyper-linked to the corresponding document data. Also, amino acid properties, linked with structure, functional and mutation sites, can be displayed as graph plots. AVAILABILITY: 3DinSight is freely accessible through the Internet (http://www.rtc.riken.go.jp/3DinSight.h tml). CONTACT: sarai@rtc.riken.go.jp

Computer Communication Networks↗
PubMed1988

PROPHET--a national computing resource for life science research.

PROPHET is a national computing resource tailored to meet the data management and analysis needs of life scientists working in a wide variety of disciplines, ranging from pharmacology to molecular biology. The PROPHET system offers a fully integrated graphics-oriented environment designed for the manipulation and analysis of tabular data, graphs, molecular structures, biological simulation models, and protein and nucleic acid sequences, and it includes access to molecular structure and sequence databases.

Computer Communication Networks↗
PubMed2005

Dynamic rewiring in small world networks.

We investigate equilibrium properties of small world networks, in which both connectivity and spin variables are dynamic, using replicated transfer matrices within the replica symmetric approximation. Population dynamics techniques allow us to examine the order parameters of our system at total equilibrium, probing both spin and graph statistics. Of these, interestingly, the degree distribution is found to acquire a Poisson-like form (both within and outside the ordered phase). Comparison with Glauber simulations confirms our results satisfactorily.

Journal Article↗
PubMed2002

Small-world view of the amino acids that play a key role in protein folding.

We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as nucleation centers for protein folding. By constructing graphs corresponding to protein structures we show that they have the "small-world" feature of having a limited set of vertices with large connectivity. These vertices correspond to the key residues that play the role of "hubs" in the network of interactions that stabilize the structure of the transition state.

Amino Acids↗
PubMed2004

Lattice scale-free networks with weighted linking.

Recently, models of the scale-free (SF) networks on lattices were investigated, which consider the influence of the embedded space on the networks. Since a lot of real networks exist on the 2D global surface, it is helpful to discuss these models. In this paper, based on the lattice SF networks model, a linking weight is added, thus an additional parameter which can control the clustering coefficient is introduced. Depending on the linking weight, the properties of the model change smoothly from the lattice SF model to the SF random graphs.

Journal Article↗
PubMed1997

Image analysis based grading of bladder carcinoma. Comparison of object, texture and graph based methods and their reproducibility.

The possibility that computerized image analysis could increase the reproducibility of grading of bladder carcinoma as compared to conventional subjective grading made by pathologists was investigated. Object, texture and graph based analysis were carried out from Feulgen stained histological tissue sections. The object based features were extracted from gray scale images, binary images obtained by thresholding the nuclei and several other images derived through image processing operations. The textural features were based on the spatial gray-tone co-occurrence probability matrices and the graph based features were extracted from the minimum spanning trees connecting all nuclei. The large numbers of extracted features were evaluated in relation to subjective grading and to factors related to prognosis using multivariate statistical methods and multilayer backpropagation neural networks. All the methods were originally developed and tested on material from one patient and then tested for reproducibility on entirely different patient material. The results indicate reasonably good reproducibility for the best sets of features. In addition, image analysis based grading showed almost identical correlation to mitotic density and expression of p53 protein as subjective grading. It should thus be possible to use this kind of image analysis as a prognostic tool for bladder carcinoma.

Humans↗
PubMed2004

Time-reversal-based SU(2) x Sn scalar invariants as (Lie Algebraic) group measures: a structured overview of generalised democratic-recoupled, uniform non-Abelian [AX]n NMR spin systems, as abstract [Formula: see text] chain networks.

The physics of dual group scalar invariants (SIs) as (Lie algebraic) group measures (L-GMs) and its significance to non-Abelian NMR spin systems motivates this overview of uniform general-2n [AX](2n) spin evolution, which represents an extensive addendum to Corio's earlier (essentially restricted) view of Abelian spin system SU(2)-based SI-cardinalities. The [Formula: see text] values in [J. Magn. Reson., 134 (1998) 131] arise from strictly linear recoupled time-reversal invariance (TRI) models. In contrast, here we discuss the physical significance of an alternative polyhedral combinatorics approach to democratic recoupling (DR), a property inherent in both the TRI and statistical sampling. Recognition of spin ensemble SIs as being L-GMs over isomorphic algebras is invaluable in many DR-based NMR problems. Various [AX]n model spin systems, including the [AX]3 bis odd-odd parity spin system, are examined as direct applications of these L-GM- and combinatorial-based SI ideas. Hence in place of /SI/=15 (implied by Corio's [Formula: see text] approach), the bis 3-fold spin system cardinality is seen now as constrained to a single invariant on an isomorphic product algebra under L-GMs, in accord with the subspectral analysis of Jones et al. [Canad. J. Chem., 43 (1965) 683]. The group projective ideas cited here for DR (as cf. to graph theoretic views) apply to highly degenerate non-Abelian problems. Over dual tensorial bases, they define models of spin dynamical evolution whose (SR) quasiparticle superboson carrier (sub)spaces are characterised by SIs acting as explicit auxiliary labels [Physica, A198 (1993) 245; J. Math. Chem., 31 (2002) 281]. A deeper [Formula: see text] network-based view of spin-alone space developed in Balasubramanian's work [J. Chem. Phys., 78 (1983) 6358] is especially important, (e.g.) in the study of spin waves [J. Math. Chem., 31 (2002) 363]. Beyond the specific NMR SIs derived here, there are DR applications where a sporadic, still higher, 2n-fold regular uniform spin ensemble exhibits a topological FG duality to some known modest /SI/(2i<2n) cardinality--in principle providing for the (sparce) existence of other /SI/(2n) DR-based values.

Algorithms↗
PubMed2000

Aromatic clusters: a determinant of thermal stability of thermophilic proteins.

A number of factors have been elucidated as responsible for the thermal stability of thermophilic proteins. However, the contribution of aromatic interactions to thermal stability has not been systematically studied. In the present investigation we used a graph spectral method to identify aromatic clusters in a dataset of 24 protein families for which the crystal structures of both the thermophilic and their mesophilic homologues are known. Our analysis shows a presence of additional aromatic clusters or enlarged aromatic networks in 17 different thermophilic protein families, which are absent in the corresponding mesophilic homologue. The additional aromatic clusters identified in the thermophiles are smaller in size and are largely found on the protein surface. The aromatic clusters are found to be relatively rigid regions of the surface and often the additional aromatic cluster is located close to the active site of the thermophilic enzyme. The residues in the additional aromatic clusters are preferably mutated to Leu, Ser or Ile in the mesophilic homologue. An analysis of the packing geometry of the pairwise aromatic interaction in the additional aromatic clusters shows a preference for a T-shaped orthogonal packing geometry. The present study also provides new insights for protein engineers to design thermostable and thermophilic proteins.

Enzyme Stability↗
PubMed2026

Infra-low-frequency neurofeedback alters EEG network efficiency: exploratory evidence from healthy volunteers.

Infra-Low-Frequency Neurofeedback (ILF-NFB) combines classic frequency-band (FB) and infra-low-frequency (ILF) EEG components in implicit training protocols and is increasingly applied in clinical contexts. Yet, the neurophysiological mechanisms underlying ILF-NFB remain to be further elucidated. In this randomized, sham-controlled and double-blind study, we explored the online impact of a one-session ILF-NFB application on EEG correlates in healthy participants (39 analyzed datasets). Continuous 31-channel EEG was recorded during verum and sham feedback in a double-blind, randomized crossover design. In this exploratory analysis approach, functional connectivity was estimated using the debiased weighted phase-lag index (dwPLI) and analyzed with graph-theoretical measures. The results revealed higher global efficiency during verum compared to sham in the Beta1 band (12-15 Hz), reaching significance in the primary comparison but not surviving Bonferroni correction across the five tested bands; block-wise follow-ups showed a significant verum-sham difference in the first half of the neurofeedback session and a directionally consistent pattern in the second half. The Condition&#x202f;&#xd7;&#x202f;Block interaction was not significant. No consistent differences were observed in other frequency bands, nor for betweenness centrality. While preliminary, these exploratory results point to possible network-level effects during ILF-NFB and motivate further confirmatory work in extended training protocols and clinical populations.

Humans↗
PubMed1996

On the dimensionality of cortical graphs.

We propose to use a random-graph model of cortex as a tabula-rasa state, to be contrasted with various types of regular connectivity patterns. Key in our analysis is the notion of graph-theoretic dimensionality, closely linked to that of graph diameter. Our discussion focuses on patterns of synfire type, and on the synfire-superposition model proposed in previous papers.

Cerebral Cortex↗
PubMed2000

ELDONET--European Light Dosimeter Network. Structure and functions of the ELDONET server.

The European Light Dosimeter Network (ELDONET) project has been designed with the purpose of establishing an efficient system to monitor solar radiation in Europe, in as many as possible locations. This paper describes the structure of the server that collects and processes the data acquired by the different stations belonging to the network, and makes them freely available on the Internet to the scientific community. The server is able to receive data either via FTP from the Internet or via modem and to process them looking for errors or inconsistencies. Moreover, it automatically generates graphs, Web-pages and FTP archives. The server has been active for some years in testing mode and is now fully operative.

Computer Storage Devices↗
PubMed2006

Naphthalene-1,3-diol.

The molecules of the title compound, C10H8O2, are linked by two O-H...O hydrogen bonds, which form infinite chains with a graph-set descriptor of C6. These chains are linked into puckered (100) sheets of R4(4)(8) and R4(4)(24) rings. Adjacent sheets are connected by weak C-H...pi and pi-pi interactions into a continuous three-dimensional network.

Journal Article↗
PubMed2003

Resilience to damage of graphs with degree correlations.

The existence or nonexistence of a percolation threshold on power law correlated graphs is a fundamental question for which a general criterion is lacking. In this work we investigate the problems of site and bond percolation on graphs with degree correlations and their connection with spreading phenomena. We obtain some general expressions that allow the computation of the transition thresholds or their bounds. Using these results we study the effects of assortative and disassortative correlations on the resilience to damage of networks.

Journal Article↗
PubMed2005

Accuracy and scaling phenomena in Internet mapping.

It was recently argued that sampling a network by traversing it with paths from a small number of sources, as with traceroutes on the Internet, creates a fundamental bias in observed topological features like the degree distribution. We examine this bias analytically and experimentally. For Erdo s-Re nyi random graphs with mean degree c, we show analytically that such sampling gives an observed degree distribution P(k) approximately k(-1) for k less, similarc, despite the underlying distribution being Poissonian. For graphs whose degree distributions have power-law tails P(k) approximately k(-alpha), sampling can significantly underestimate alpha when the graph has a large excess (i.e., many more edges than vertices). We find that in order to accurately estimate alpha, one must use a number of sources which grows linearly in the mean degree of the underlying graph. Finally, we comment on the accuracy of the published values of alpha for the Internet.

Journal Article↗
PubMed2006

A framework toward restoration of writing order from single-stroked handwriting image.

Restoration of writing order from a single-stroked handwriting image can be seen as the problem of finding the smoothest path in its graph representation. In this paper, a 3-phase approach to restore a writing order is proposed within the framework of the Edge Continuity Relation (ECR). In the initial, local phase, in order to obtain possible ECRs at an even-degree node, a neural network is used for the node of degree 4 and a theoretical approach is presented for the node of degree higher than 4 by introducing certain reasonable assumptions. In the second phase, we identify double-traced lines by employing maximum weighted matching. This makes it possible to transform the problem of obtaining possible ECRs at odd-degree node to that at even-degree node. In the final, global phase, we find all the candidates of single-stroked paths by depth first search and select the best one by evaluating SLALOM smoothness. Experiments on static images converted from online data in the Unipen database show that our method achieves a restoration rate of 96.0 percent.

Algorithms↗