CAMBer: an approach to support comparative analysis of multiple bacterial strains

10.1109/BIBM.2010.5706549Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010121-12

Cost-sensitive decision tree ensembles for effective imbalanced classification

Real-life datasets are often imbalanced, that is, there are significantly more training samples available for some classes than for others, and consequently the conventional aim of reducing overall classification accuracy is not appropriate when dealing with such problems. Various approaches have been introduced in the literature to deal with imbalanced datasets, and are typically based on oversampling, undersampling or cost-sensitive classification. In this paper, we introduce an effective ensemble of cost-sensitive decision trees for imbalanced classification. Base classifiers are constructed according to a given cost matrix, but are trained on random feature subspaces to ensure sufficient diversity of the ensemble members. We employ an evolutionary algorithm for simultaneous classifier selection and assignment of committee member weights for the fusion process. Our proposed algorithm is evaluated on a variety of benchmark datasets, and is confirmed to lead to improved recognition of the minority class, to be capable of outperforming other state-of-the-art algorithms, and hence to represent a useful and effective approach for dealing with imbalanced datasets

lncRNAs-EZH2 interaction as promising therapeutic target in cutaneous melanoma

Melanoma is the most lethal skin cancer with increasing incidence worldwide. Despite a great improvement of diagnostics and treatment of melanoma patients, this disease is still a serious clinical problem. Therefore, novel druggable targets are in focus of research. EZH2 is a component of the PRC2 protein complex that mediates epigenetic silencing of target genes. Several mutations activating EZH2 have been identified in melanoma, which contributes to aberrant gene silencing during tumor progression. Emerging evidence indicates that long non-coding RNAs (lncRNAs) are molecular “address codes” for EZH2 silencing specificity, and targeting lncRNAs-EZH2 interaction may slow down the progression of many solid cancers, including melanoma. This review summarizes current knowledge regarding the involvement of lncRNAs in EZH2-mediated gene silencing in melanoma. The possibility of blocking lncRNAs-EZH2 interaction in melanoma as a novel therapeutic option and plausible controversies and drawbacks of this approach are also briefly discussed

The physiological concentration of ferrous iron (II) alters the inhibitory effect of hydrogen peroxide on CD45, LAR and PTP1B phosphatases

Hydrogen peroxide is an important regulator of protein tyrosine phosphatase activity via reversible oxidation. However, the role of iron in this reaction has not been yet elucidated. Here we compare the influence of hydrogen peroxide and the ferrous iron (reagent for Fenton reaction) on the enzymatic activity of recombinant CD45, LAR, PTP1B phosphatases and cellular CD45 in Jurkat cells. The obtained results show that ferrous iron (II) is potent inhibitor of CD45, LAR and PTP1B, but the inhibitory effect is concentration dependent. We found that the higher concentrations of ferrous iron (II) increase the inactivation of CD45, LAR and PTP1B phosphatase caused by hydrogen peroxide, but the addition of the physiological concentration (500 nM) of ferrous iron (II) has even a slightly preventive effect on the phosphatase activity against hydrogen peroxide