ZDOG: zooming in on dominating genes with mutations in cancer pathways

Background Inference of cancer-causing genes and their biological functions are crucial but challenging due to the heterogeneity of somatic mutations. The heterogeneity of somatic mutations reveals that only a handful of oncogenes mutate frequently and a number of cancer-causing genes mutate rarely. Results We develop a Cytoscape app, named ZDOG, for visualization of the extent to which mutated genes may affect cancer pathways using the dominating tree model. The dominator tree model allows us to examine conveniently the positional importance of a gene in cancer signalling pathways. This tool facilitates the identification of mutated “master” regulators even with low mutation frequency in deregulated signalling pathways. Conclusions We have presented a model for facilitating the examination of the extent to which mutation in a gene may affect downstream components in a signalling pathway through its positional information. The model is implemented in a user-friendly Cytoscape app which will be freely available upon publication. Availability Together with a user manual, the ZDOG app is freely available at GitHub (https://github.com/rudi2013/ZDOG). It is also available in the Cytoscape app store (http://apps.cytoscape.org/apps/ZDOG) and users can easily install it using the Cytoscape App Manager.

A Hybrid Framework Combining Genetic Algorithm with Iterated Local Search for the Dominating Tree Problem

Given an undirected, connected and edge-weighted graph, the dominating tree problem consists of finding a tree with minimum total edge weight such that for each vertex is either in the tree or adjacent to a vertex in the tree. In this paper, we propose a hybrid framework combining genetic algorithm with iterated local search (GAITLS) for solving the dominating tree problem. The main components of our framework are as follows: (1) the score functions D s c o r e and W s c o r e applied in the initialization and local search phase; (2) the initialization procedure with restricted candidate list (RCL) by controlling the parameter to balance the greediness and randomness; (3) the iterated local search with three phases, which is used to intensify the individuals; (4) the mutation with high diversity proposed to perturb the population. The experimental results on the classical instances show that our method performs much better than the-state-of-art algorithms.

The Effect of Pyrogenic Successionon Breeding Birds of Shelter Belts in the North-Western Part of the Azov Sea Region

The effect of the pyrogenic factor on the avifauna of shelter belts in the north-western part of the Azov Sea region, Ukraine is considered basing on results of the research carried out in 2001–2018. The breeding bird community of shelter belts is composed of 50 species, of them different types of shelter belts support 14–46 species. Changes in the species composition of breeding birds are analysed in subsequent years aft er the fires. The recovery of bird communities is progressing at a slow pace following the regeneration of tree-shrub vegetation and development of consortial relations of birds with dominating tree-shrub species and rook (Corvus frugilegus) colonies. It is established that the vegetation pyrogenic succession is accompanied by deep qualitative and quantitative changes in the structure of breeding avian communities in shelter belts of different type.

Evaluation of green area in the squares of Ulan-Ude city

Research on green area in Ulan-Ude has not been carried out since the moment of planting in 1970. The researchers didn’t study hardy-shrub species and factors of their strengthening and weakening. The research aims at evaluation of green areas in the mini-parks of UlanUde. The authors assess green areas in all mini-parks of the city and define species composition of hardy-shrub species and their condition. The researchers found out 23 species of trees and shrubs used in landscaping of Ulan-Ude. The identified species belong to 12 families and 23 genera. The largest number of species belongs to Rosaceae-7 species, the smallest number of hardy-shrub species belong to Cornaceae, Adoxaceae, Oleaceae and Ulmaceae. The researchers observed hardy-shrub species and found out that trees predominate (56.3%) the shrubs (43.5 %). Dominating tree species in the mini-parks are the balsamifera (L.) and Ulmus pumila (L.). The bushes commonly observed are Caragana arborescens (Lam.). The vital state of tree and shrubbery plantings is generally characterized as medium-stable, damaged, ranging from stable, healthy to unstable, severely damaged. The range of tree and shrubbery plantings used in gardening of Ulan-Ude is completed. The conducted research revealed that the main factors of lower resistance of green area in the city mini parks are seen as damaged development of the crown and drying of branches, mechanical damages of a trunk; stripping of bark and small deformations and cracks in a trunk, damages in axial escape and the crown related to high density of landings, curvature of a trunk and break of boughs of trees and bushes as a result of influence of wind or anthropogenic activity; careless attitude to requirements of cutting trees and bushes; twisting of leaves, modification of shoots, colorful Gauls due to attacks on them aphids; the presence of bacterial diseases in balsamic poplar; infectious pathologies of trunks and leaves.