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PubMed2006

AliBaba: PubMed as a graph.

UNLABELLED: The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. AVAILABILITY: http://alibaba.informatik.hu-berlin.de/

Abstracting and Indexing↗

PubMed2006

Dense subgraph computation via stochastic search: application to detect transcriptional modules.

MOTIVATION: In a tri-partite biological network of transcription factors, their putative target genes, and the tissues in which the target genes are differentially expressed, a tightly inter-connected (dense) subgraph may reveal knowledge about tissue specific transcription regulation mediated by a specific set of transcription factors-a tissue-specific transcriptional module. This is just one context in which an efficient computation of dense subgraphs in a multi-partite graph is needed. RESULT: Here we report a generic stochastic search based method to compute dense subgraphs in a graph with an arbitrary number of partitions and an arbitrary connectivity among the partitions. We then use the tool to explore tissue-specific transcriptional regulation in the human genome. We validate our findings in Skeletal muscle based on literature. We could accurately deduce biological processes for transcription factors via the tri-partite clusters of transcription factors, genes, and the functional annotation of genes. Additionally, we propose a few previously unknown TF-pathway associations and tissue-specific roles for certain pathways. Finally, our combined analysis of Cardiac, Skeletal, and Smooth muscle data recapitulates the evolutionary relationship among the three tissues.

Algorithms↗

PubMed2003

Self-avoiding walks and connective constants in small-world networks.

Long-distance characteristics of small-world networks have been studied by means of self-avoiding walks (SAW's). We consider networks generated by rewiring links in one- and two-dimensional regular lattices. The number of SAW's u(n) was obtained from numerical simulations as a function of the number of steps n on the considered networks. The so-called connective constant, mu=lim(n-->infinity)u(n)/u(n-1), which characterizes the long-distance behavior of the walks, increases continuously with disorder strength (or rewiring probability p). For small p, one has a linear relation mu=mu(0)+ap, mu(0) and a being constants dependent on the underlying lattice. Close to p=1 one finds the behavior expected for random graphs. An analytical approach is given to account for the results derived from numerical simulations. Both methods yield results agreeing with each other for small p, and differ for p close to 1, because of the different connectivity distributions resulting in both cases.

Journal Article↗

PubMed2005

Influence of the link weight structure on the shortest path.

The shortest path tree rooted at a source to all other nodes is investigated in a graph with polynomial link weights tunable by the power exponent alpha. By varying alpha, different types of shortest path trees, in short alpha trees, appear. Especially, the alpha --> 0 regime that corresponds to heavily fluctuating link weights possesses a peculiar type of tree. The most important properties of this alpha --> 0 tree are derived in the asymptotic limit for large N. The application of the theoretical insights to real networks (such as the Internet) are discussed: steering flow by adjusting link weights (traffic engineering), sensitivity of link weights and modeling of the network by alpha trees.

Journal Article↗

PubMed1990

Graph-set analysis of hydrogen-bond patterns in organic crystals.

A method is presented based on graph theory for categorizing hydrogen-bond motifs in such a way that complex hydrogen-bond patterns can be disentangled, or decoded, systematically and consistently. This method is based on viewing hydrogen-bond patterns topologically as if they were intertwined nets with molecules as the nodes and hydrogen bonds as the lines. Surprisingly, very few parameters are needed to define the hydrogen-bond motifs comprising these networks. The methods for making these assignments, and examples of their chemical utility are given.

Chemical Phenomena↗

PubMed2005

Neurophysiological architecture of functional magnetic resonance images of human brain.

We investigated large-scale systems organization of the whole human brain using functional magnetic resonance imaging (fMRI) data acquired from healthy volunteers in a no-task or 'resting' state. Images were parcellated using a prior anatomical template, yielding regional mean time series for each of 90 regions (major cortical gyri and subcortical nuclei) in each subject. Significant pairwise functional connections, defined by the group mean inter-regional partial correlation matrix, were mostly either local and intrahemispheric or symmetrically interhemispheric. Low-frequency components in the time series subtended stronger inter-regional correlations than high-frequency components. Intrahemispheric connectivity was generally related to anatomical distance by an inverse square law; many symmetrical interhemispheric connections were stronger than predicted by the anatomical distance between bilaterally homologous regions. Strong interhemispheric connectivity was notably absent in data acquired from a single patient, minimally conscious following a brainstem lesion. Multivariate analysis by hierarchical clustering and multidimensional scaling consistently defined six major systems in healthy volunteers-- corresponding approximately to four neocortical lobes, medial temporal lobe and subcortical nuclei- - that could be further decomposed into anatomically and functionally plausible subsystems, e.g. dorsal and ventral divisions of occipital cortex. An undirected graph derived by thresholding the healthy group mean partial correlation matrix demonstrated local clustering or cliquishness of connectivity and short mean path length compatible with prior data on small world characteristics of non-human cortical anatomy. Functional MRI demonstrates a neurophysiological architecture of the normal human brain that is anatomically sensible, strongly symmetrical, disrupted by acute brain injury, subtended predominantly by low frequencies and consistent with a small world network topology.

Adult↗

PubMed2000

Channel- and layer-type anionic host structures in inclusion compounds of urea, tetraalkylammonium terephthalate/trimesate and water

New crystalline adducts of tetraalkylammonium terephthalate/trimesate with urea and water molecules result from hydrogen-bond directed assembly of complementary acceptors and donors, and the anionic host lattices are described using the graph-set notation to identify distinct hydrogen-bonding motifs and patterns. Tetra-n-butylammonium terephthalate-urea-water (1/6/2), C46H104N14O12 (1), triclinic, space group P1, a = 8.390 (2), b = 9.894 (2), c = 18.908 (3) A, alpha = 105.06 (2), beta = 94.91 (1), gamma = 93.82 (2)o, Z = 1, is composed of hydrogen-bonded terephthalate-urea layers, which are intersected by urea layers to generate a three-dimensional network containing large channels for accommodation of the cations. Tetraethylammonium terephthalate-urea-water (1/1/5), C25H58N4O10 (2), triclinic, P1, a = 9.432 (1), b = 12.601 (1), c = 14.804 (1) A, alpha = 79.98 (1), beta = 79.20 (1), gamma = 84.18 (1)o, Z = 2, has cations sandwiched between hydrogen-bonded anionic layers. Tetraethylammonium trimesate-urea-water (1/2/7.5), C35H86N7O15.5 (3), triclinic, P1, a = 13.250 (1), b = 14.034 (1), c = 15.260 (1) A, alpha = 72.46 (1), beta = 78.32 (1), gamma = 66.95 (1)o, Z = 2, manifests a layer-type structure analogous to that of (2). Tetra-n-propylammonium hydrogen trimesate-urea-water (1/2/5), C35H78N6O13 (4), orthorhombic, Pna2(1), a = 16.467 (3), b = 33.109 (6), c = 8.344 (1) A, Z = 4, features hydrogen trimesate helices in a three-dimensional host architecture containing nanoscale channels each filled by a double column of cations.

Journal Article↗

PubMed1982

Collection development using interlibrary loan borrowing and acquisitions statistics.

Libraries, especially those supporting the sciences, continually face the problem of selecting appropriate new books for their users. Traditional collection development techniques include the use of librarian or user subject specialists, user recommendations, and approval plans. These methods of selection, however, are most effective in large libraries and do not systemically correlate new book purchases with the actual demands of users served. This paper describes a statistical method for determining subject strengths and weaknesses in a library book collection in relation to user demand. Using interlibrary loan borrowing and book acquisition statistics gathered for one fiscal year from three health sciences libraries, the authors developed a way to graph the broad and narrow subject fields of strength and potential weakness in a book collection. This method has the advantages of simplicity, speed of implementation, and clarity. It can also be used over a period of time to verify the success or failure of a collection development program. Finally, the method has potential as a tool for use by two or more libraries seeking to improve cooperative collection development in a network or consortium.

Interlibrary Loans↗

PubMed2002

The use of polynomial neural networks for mortality prediction in uncontrolled venous and arterial hemorrhage.

BACKGROUND: The ability to rapidly and accurately triage, evacuate, and utilize appropriate interventions can be problematic in the early decision-making process of trauma care. With current methods of prehospital data collection and analysis, decisions are often based upon single data points. This information may be insufficient for reliable decision-making. To date, no studies have attempted to utilize data at multiple time points for purposes of enhancing prediction, nor have studies attempted to synthesize prediction models with data reflecting both large-vessel venous and arterial injuries. Therefore, we performed a retrospective study to examine the potential utility of dynamic neural networks in predicting mortality using highly discretized uncontrolled hemorrhagic shock data. METHODS: One hundred forty-three swine with either grade V liver injuries or 2.8-mm aortotomies had hemodynamic data collected every minute throughout injury and resuscitation. The independent variables used as inputs to the polynomial neural networks (PNNs) included systolic blood pressure and mean arterial pressure (MAP). These inputs were used to predict mortality in individual swine 1 hour after injury using data up to 20 minutes after injury. Survival models were compared based on discrimination power (DP), i.e., where specificity equals sensitivity, and area under the receiver operating characteristic (ROC) curve (c-statistic). The Hosmer-Lemeshow (H-L) statistic was used to measure model calibration. RESULTS: The best PNN model predicted mortality at 60 minutes utilizing data from injury to 20 minutes after injury. This model produced a ROC area of 0.919, a DP of 0.857, and a H-L value of 16.47. A DP of 0.857 means that 85.7% of the survivors are correctly predicted to survive, and 85.7% of the nonsurvivors are predicted to die. MAP of survivors and nonsurvivors were graphed for comparative purposes. As this graph illustrates, the use of MAP alone cannot discriminate survivors from nonsurvivors. CONCLUSION: This study demonstrates that PNN models can effectively harness the dynamic nature of uncontrolled hemorrhagic shock data, despite utilizing data from large-vessel arterial and venous injuries. Utilizing the dynamic nature of hemorrhagic shock data in PNNs may ultimately allow the development of novel decision assist devices.

Animals↗

PubMed1992

Direct injection analysis of carbamazepine and its active 10,11-epoxide metabolite in plasma by use of a semipermeable surface (SPS) silica column in LC.

A semipermeable surface (SPS) silica column was applied for the simultaneous determination of carbamazepine (CBZ) and its active 10,11-epoxide metabolite (EPO) in plasma following direct injection in LC. The SPS packing material consists of an ODS ligand as the hydrophobic inner phase and a polyoxyethylene network as the hydrophilic outer phase. When a 5-microliters portion of intact plasma was injected onto the column using a mobile phase of phosphate buffer (pH 7.1, ionic strength 0.1)-acetonitrile (4:1, v/v), the plasma proteins were size-excluded, whereas the drug and its metabolite were retained and separated both from each other and from other commonly co-administered drugs such as phenobarbital (PB) and phenytoin (DPH). The calibration graphs (peak area vs concentration) of CBZ, EPO and PB were linear over the therapeutic range of plasma concentration (r greater than 0.998) with good relative standard deviations (RSD less than 3.98%, n = 5). The recoveries from plasma were almost complete (greater than 96.6%). The analysis time was 17 min. The method as developed was applied in studies on the time course of plasma concentrations of unchanged CBZ and EPO after i.v. administration of CBZ to the rat.

Calibration↗

PubMedDate not supplied

Pattern completion through phase coding in population neurodynamics.

This article presents an alternative phase coding mechanism for Freeman's KIII model of population neurodynamics. Motivated by experimental evidence that supports the existence of a neural code based on synchronous oscillations, we propose an analogy between synchronization in neural populations and phase locking in KIII channels. An efficient method is proposed to extract phase differences across granule channels from their state-space trajectories. First, the scale invariance of the KIII model with respect to phase information is established. The phase code is then compared against the conventional amplitude code in terms of their bit-wise and across-fiber pattern recovery capabilities using decision-theoretic principles and a Hamming-distance classifier. Graph isomorphism in the Hebbian connections is exploited to perform an exhaustive evaluation of patterns on an 8-channel KIII model. Simulation results show that phase information outperforms amplitude information in the recovery of incomplete or corrupted stimuli.

Models, Neurological↗

PubMed1994

Measurement issues in research on social support and health.

STUDY OBJECTIVE: The aims were: (1) to identify methodological problems that may explain the inconsistencies and contradictions in the research evidence on social support and health, and (2) to validate a frequently used measure of social support in order to determine whether or not it could be used in multivariate analyses of population data in research on social support and health. DESIGN AND METHODS: Secondary analysis of data collected in a cross sectional survey of a multistage cluster sample of the population of the United States, designed to study relationships in behavioural, social support and health variables. Statistical models based on item response theory and graph theory were used to validate the measure of social support to be used in subsequent analyses. PARTICIPANTS: Data on 1755 men and women aged 20 to 64 years were available for the scale validation. RESULTS: Massive evidence of item bias was found for all items of a group membership subscale. The most serious problems were found in relationship to an item measuring membership in work related groups. Using that item in the social network scale in multivariate analyses would distort findings on the statistical effects of education, employment status, and household income. Evidence of item bias was also found for a sociability subscale. When marital status was included to create what is called an intimate contacts subscale, the confounding grew worse. CONCLUSIONS: The composite measure of social network is not valid and would seriously distort the findings of analyses attempting to study relationships between the index and other variables. The findings show that valid measurement is a methodological issue that must be addressed in scientific research on population health.

Adult↗

PubMed2006

Product code optimization for determinate state LDPC decoding in robust image transmission.

We propose a novel scheme for error-resilient image transmission. The proposed scheme employs a product coder consisting of low-density parity check (LDPC) codes and Reed-Solomon codes in order to deal effectively with bit errors. The efficiency of the proposed scheme is based on the exploitation of determinate symbols in Tanner graph decoding of LDPC codes and a novel product code optimization technique based on error estimation. Experimental evaluation demonstrates the superiority of the proposed system in comparison to recent state-of-the-art techniques for image transmission.

Algorithms↗

PubMed2006

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

BACKGROUND: Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets. DESCRIPTION: Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html CONCLUSION: The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.

Database Management Systems↗

PubMed1999

Mutual synchronization and clustering in randomly coupled chaotic dynamical networks.

We introduce and study systems of randomly coupled maps where the relevant parameter is the degree of connectivity in the system. Global (almost-) synchronized states are found (equivalent to the synchronization observed in globally coupled maps) until a certain critical threshold for the connectivity is reached. We further show that not only the average connectivity, but also the architecture of the couplings is responsible for the cluster structure observed. We analyze the different phases of the system and use various correlation measures in order to detect ordered nonsynchronized states. Finally, it is shown that the system displays a dynamical hierarchical clustering which allows the definition of emerging graphs.

Journal Article↗

PubMed2005

Piecewise-linear models of genetic regulatory networks: equilibria and their stability.

A formalism based on piecewise-linear (PL) differential equations, originally due to Glass and Kauffman, has been shown to be well-suited to modelling genetic regulatory networks. However, the discontinuous vector field inherent in the PL models raises some mathematical problems in defining solutions on the surfaces of discontinuity. To overcome these difficulties we use the approach of Filippov, which extends the vector field to a differential inclusion. We study the stability of equilibria (called singular equilibrium sets) that lie on the surfaces of discontinuity. We prove several theorems that characterize the stability of these singular equilibria directly from the state transition graph, which is a qualitative representation of the dynamics of the system. We also formulate a stronger conjecture on the stability of these singular equilibrium sets.

Genes, Regulator↗

PubMed2005

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

MOTIVATION: Determining protein function is one of the most important problems in the post-genomic era. For the typical proteome, there are no functional annotations for one-third or more of its proteins. Recent high-throughput experiments have determined proteome-scale protein physical interaction maps for several organisms. These physical interactions are complemented by an abundance of data about other types of functional relationships between proteins, including genetic interactions, knowledge about co-expression and shared evolutionary history. Taken together, these pairwise linkages can be used to build whole-proteome protein interaction maps. RESULTS: We develop a network-flow based algorithm, FunctionalFlow, that exploits the underlying structure of protein interaction maps in order to predict protein function. In cross-validation testing on the yeast proteome, we show that FunctionalFlow has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors. By comparing several methods that use protein interaction maps to predict protein function, we demonstrate that FunctionalFlow performs well because it takes advantage of both network topology and some measure of locality. Finally, we show that performance can be improved substantially as we consider multiple data sources and use them to create weighted interaction networks. AVAILABILITY: http://compbio.cs.princeton.edu/function

Algorithms↗

PubMed1996

Using concept maps on the World-Wide Web to access a curriculum database for problem-based learning.

Development of medical school curriculum databases continues to be challenging. Representation of the instructional unit is becoming increasingly difficult due to characteristics of the problem-based learning (PBL) curricula. Curriculum databases may be used to store materials for the PBL curricula, and also to provide a delivery mechanism for those materials. However, in order to take advantage of the curriculum database as a tool for PBL, methods for accessing the curriculum database that are better suited to the information needs of students, faculty, and administrators must be developed. Concept maps are directed graph representations of conceptual relationships, and may be used to represent the content of a curriculum database. In this paper, we describe a Web application that uses Java-based concept maps was the user interface to a curriculum database.

Computer Communication Networks↗