Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Spatial structure and prediction of Land use change considering development projects in urban promotion districts

n this paper, the actual conditions and the change structure of land use by using mesh data are studied in urban promotion area in a local hub city of Fukuoka, Japan. Firstly, all meshes are classified into 15 patterns based on distribution of land use. Then, transition probability models are made out based on the change of these 15 patterns. The Change structure of land use in an area depends on whether development projects are carried out or not. Therefore, all of the meshes are divided into two groups, and different transition probability models are proposed. Finally, a prediction method of land use is proposed under the consideration of the changing structure of meshes. Though our proposed approach is a macroscopic forecasting method of land use, it is useful to evaluate the effects of urban policies for development projects.

Properties of energetic-particle continuum modes destabilized by energetic ions with beam-like velocity distributions

Properties of energetic-particle continuum modes (EPMs) destabilized by energetic ions in tokamak plasmas were investigated using a hybrid simulation code for magnetohydrodynamics and energetic particles. The energetic ions are assumed to have beam-like velocity distributions for the purpose of clarifying the dependence on energetic ion velocity. It was found that for beam velocities lower than the Alfv?n velocity, the unstable modes are EPMs while the toroidal Alfv?n eigenmodes are unstable for the beam velocities well above the Alfv?n velocity. The EPMs destabilized by the copassing energetic ions and those destabilized by the counterpassing energetic ions differ in primary poloidal harmonics and spatial locations. The frequencies of the EPMs are located close to the shear Alfv?n continuous spectrum when they are compared at the spatial peak locations of the primary poloidal harmonic or compared at the spatial tails if the primary poloidal harmonic is m=1. The frequencies of the EPMs were carefully compared with the energetic-ion orbital frequencies. It was found that the frequencies of the EPMs are in good agreement with the energetic-ion orbital frequencies with a correction for the toroidal circulation frequency. This demonstrates that the energetic-ion orbital frequency determines the EPM frequency

Production of overdense plasmas by launching 2,45 GHz electron cyclotron waves in a helical device

For production of low temperature plasmas with low collisionality, 2.45GHz microwave power up to 20kW is injected perpendicularly to the toroidal field at very low toroidal field BtComment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Physical Modelling of Breaking Tidal Bores: Comparison with Prototype Data

A tidal bore is a hydraulic jump in translation, propagating upstream as the tide turns to rising and the flood flow advances in a funnel-shaped river mouth under spring tide conditions. This study focused on the unsteady turbulence induced by a breaking tidal bore. Detailed free-surface and velocity measurements were conducted with a high temporal resolution using non-intrusive free-surface measurement probes and acoustic Doppler velocimetry sampled at 200Hz. The laboratory data were systematically compared with an earlier series of field measurements conducted in the breaking bore of the Sélune River (France). Key findings include the agreement, in terms of dimensionless instantaneous free-surface and velocity data, between laboratory and field observations as well as the existence of a transient recirculation region near the bed