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Kocarev L.,Macedonia Academy of science and Arts
PLoS ONE | Year: 2014

Complex networks have recently become the focus of research in many fields. Their structure reveals crucial information for the nodes, how they connect and share information. In our work we analyze protein interaction networks as complex networks for their functional modular structure and later use that information in the functional annotation of proteins within the network. We propose several graph representations for the protein interaction network, each having different level of complexity and inclusion of the annotation information within the graph. We aim to explore what the benefits and the drawbacks of these proposed graphs are, when they are used in the function prediction process via clustering methods. For making this cluster based prediction, we adopt well established approaches for cluster detection in complex networks using most recent representative algorithms that have been proven as efficient in the task at hand. The experiments are performed using a purified and reliable Saccharomyces cerevisiae protein interaction network, which is then used to generate the different graph representations. Each of the graph representations is later analysed in combination with each of the clustering algorithms, which have been possibly modified and implemented to fit the specific graph. We evaluate results in regards of biological validity and function prediction performance. Our results indicate that the novel ways of presenting the complex graph improve the prediction process, although the computational complexity should be taken into account when deciding on a particular approach. © 2014 Trivodaliev et al.

Makreski P.,Ss. Cyril and Methodius University of Skopje | Jovanovski S.,Ss. Cyril and Methodius University of Skopje | Pejov L.,Ss. Cyril and Methodius University of Skopje | Kloess G.,University of Leipzig | And 3 more authors.
Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy | Year: 2013

(Graph Presented) The arsenate hydroxyl-bearing minerals sarkinite and adamite were studied with vibrational spectroscopic (IR and Raman) and quantum theoretical methods. The observed IR bands in the higher (1100-600 cm -1) and especially lower (600-450 cm-1) frequency region of AsO4 vibrations could clearly discriminate between the studied analogues. The differences between their crystal structures are much pronounced in both IR and Raman OH-stretching regions. Namely, a single strong band is found in the case of orthorhombic adamite compared to four weaker bands observed in corresponding IR and Raman spectral regions of monoclinic sarkinite. Essentially all bands in the experimental spectra, collected at both room and liquid nitrogen temperature, were tentatively assigned. To support the tentative assignment of bands in the vibrational spectra of the mentioned minerals, periodic pseudopotential plane wave density functional theory calculations were carried out. Geometry optimizations of the 3D periodic systems included both optimizations of the atomic positions within the unit cell and of the unit cell itself. In most cases, the assignments were either supported or implied by the obtained theoretical data. It is worth mentioning that this is the first experimental and theoretical study of the vibrational spectra of the veryrare sarkinite mineral. © 2013 Elsevier B.V. All rights reserved.

Gutierrez J.,Columbia University | Rosoklija G.,Columbia University | Rosoklija G.,Macedonia Academy of Science and Arts | Murray J.,Mount Sinai School of Medicine | And 8 more authors.
Frontiers in Physiology | Year: 2014

Mechanisms underlying brain arterial remodeling are uncertain. We tested the hypothesis that arterial size and location are important determinants of arterial characteristics. We collected large and penetrating brain arteries from cadavers with and without HIV. Morphometric characterization was obtained from digital images using color-based thresholding. The association of arterial size and location with lumen diameter, media and adventitia area, media proportion, a wall thickness, wall-to-lumen ratio and stenosis was obtained with multilevel mixed models and a P value ≤ 0.05 was considered significant. We included 336 brains, in which 2279 large arteries and 1488 penetrating arteries were identified. We found that arterial size was significantly associated with all arterial characteristics studied of large and penetrating arteries with exception of arterial stenosis in large arteries. After adjusting for size, an independent association was found between lumen diameters, media and adventitia thickness with artery locations. Arterial stenosis was also associated with artery location in both large and penetrating arteries. In summary, significant effects of size and/or location were found in arterial characteristics typically used to define arterial remodeling. Brain arterial remodeling characteristics differ across arterial sizes and location, and these differences should be controlled for in future studies of brain arterial remodeling. © 2014 Gutierrez, Rosoklija, Murray, Chon, Elkind, Goldman, Honig, Dwork, Morgello and Marshall.

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