Analyzing biological network parameters with CentiScaPe.

Summary: The increasing availability of large network datasets along with the progresses in experimental high-throughput technologies have prompted the need for tools allowing easy integration of experimental data with data derived form network computational analysis. In order to enrich experimental data with network topological parameters, we have developed the Cytoscape plug-in CentiScaPe. The plug-in computes several network centrality parameters and allows the user to analyze existing relationships between experimental data provided by the users and node centrality values computed by the plug-in.

Expression differences by continent of origin point to the immortalization process.

Analysis of recently available microarray expression data sets obtained from immortalized cell lines of the individuals represented in the HapMap project have led to inconclusive comparisons across cohorts with different ancestral continent of origin (ACOO). To address this apparent inconsistency, we applied a novel approach to accentuate population-specific gene expression signatures for the CEU [homogeneous US residents with northern and western European ancestry (HapMap samples)] and YRI [homogenous Yoruba people of Ibadan, Nigeria (HapMap samples)] trios. In this report, we describe how four independent data sets point to the differential expression across ACOO of gene networks implicated in transforming the normal lymphoblast into immortalized lymphoblastoid cells.

Integrin activation in the immune system.

Modulation of leukocyte adhesiveness is critical to leukocyte function during the immune response. A central paradigm in this phenomenon is represented by integrin activation, which is controlled by inside-out signal transduction mechanisms triggered by selectins, chemoattractants and TcR-bound Ag and facilitated by mechanochemical forces. Integrins are heterodimeric adhesive receptors differently expressed on all leukocyte subtypes.

Towards a computational method for imaging the extracellular potassium concentration during regional ischemia.

We investigate the possibility of using body surface potential maps to image the extracellular potassium concentration during regional ischemia. The problem is formulated as an inverse problem based on a linear approximation of the bidomain model, where we minimize the difference between the results of the model and observations of body surface potentials. The minimization problem is solved by a one-shot technique, where the original PDE system, an adjoint problem, and the relation describing the minimum, are solved simultaneously.

Synchronizing computer simulations with measurement data for a case of atrial flutter.

Atrial flutter is a common supraventricular tachycardia that can be treated using radiofrequency catheter ablation, a procedure that is guided by electroanatomical mapping systems. In this paper, we propose an algorithm for incorporating mapping data into computer simulations of atrial electrical activity with the purpose of creating a more accurate map of electrical activation. The algorithm takes as input the extracellular potential values recorded at a number of sites throughout the atria and estimates the activation time for the entire atrial domain.

A condition for setting off ectopic waves in computational models of excitable cells.

The purpose of this paper is to study the stability of steady state solutions of the Monodomain model equipped with Luo-Rudy I kinetics. It is well established that re-entrant arrhythmias can be created in computational models of excitable cells. Such arrhythmias can be initiated by applying an external stimulus that interacts with a partially refractory region, and spawn breaking waves that can eventually generate extremely complex wave patterns commonly referred to as fibrillation.