MicroRNA–mRNA interaction network using TSK-type recurrent neural fuzzy network

MicroRNAs are short non-coding RNAs that can regulate gene expression during various crucial cell processes such as differentiation, proliferation and apoptosis. Changes in expression profiles of miRNA play an important role in the development of many cancers, including CRC. Therefore, the identification of cancer related miRNAs and their target genes are important for cancer biology research. In this paper, we applied TSK-type recurrent neural fuzzy network (TRNFN) to infer miRNA–mRNA association network from paired miRNA, mRNA expression profiles of CRC patients. We demonstrated that the method we proposed achieved good performance in recovering known experimentally verified miRNA–mRNA associations. Moreover, our approach proved successful in identifying 17 validated cancer miRNAs which are directly involved in the CRC related pathways. Targeting such miRNAs may help not only to prevent the recurrence of disease but also to control the growth of advanced metastatic tumors. Our regulatory modules provide valuable insights into the pathogenesis of cancer

Genetic algorithm based indicator sequence method for exon prediction

Considerable research effort has been devoted in predicting the exon regions of genes. The binary indicator (BI), Electron ion interaction pseudo potential (EIIP), Filter method are some of the methods. All these methods make use of the period three behavior of the exon region. Even though the method suggested in this paper is similar to above mentioned methods , it introduces a set of sequences for mapping the nucleotides selected by applying genetic algorithm and found to be more promising

Studies on the interaction of two level atoms with quantized electromagnetic field

The present study described about the interaction of a two level atom and squeezed field with time varying frequency. By applying a sinusoidal variation in the frequency of the field, the randomness in population inversion is reduced and the collapses and periodic revivals are regained. Quantum optics is an emerging field in physics which mainly deals with the interaction of atoms with quantised electromagnetic fields. Jaynes-Cummings Model (JCM) is a key model among them, which describes the interaction between a two level atom and a single mode radiation field. Here the study begins with a brief history of light, atom and their interactions. Also discussed the interaction between atoms and electromagnetic fields. The study suggest a method to manipulate the population inversion due to interaction and control the randomness in it, by applying a time dependence on the frequency of the interacting squeezed field.The change in behaviour of the population inversion due to the presence of a phase factor in the applied frequency variation is explained here.This study also describes the interaction between two level atom and electromagnetic field in nonlinear Kerr medium. It deals with atomic and field state evolution in a coupled cavity system. Our results suggest a new method to control and manipulate the population of states in two level atom radiation interaction,which is very essential for quantum information processing.We have also studied the variation of atomic population inversion with time, when a two level atom interacts with light field, where the light field has a sinusoidal frequency variation with a constant phase. In both coherent field and squeezed field cases, the population inversion variation is completely different from the phase zero frequency modulation case. It is observed that in the presence of a non zero phase φ, the population inversion oscillates sinusoidally.Also the collapses and revivals gradually disappears when φ increases from 0 to π/2. When φ = π/2 the evolution of population inversion is identical to the case when a two level atom interacts with a Fock state. Thus, by applying a phase shifted frequency modulation one can induce sinusoidal oscillations of atomic inversion in linear medium, those normally observed in Kerr medium. We noticed that the entanglement between the atom and field can be controlled by varying the period of the field frequency fluctuations. The system has been solved numerically and the behaviour of it for different initial conditions and different susceptibility values are analysed. It is observed that, for weak cavity coupling the effect of susceptibility is minimal. In cases of strong cavity coupling, susceptibility factor modifies the nature in which the probability oscillates with time. Effect of susceptibility on probability of states is closely related to the initial state of the system.