DEEN:a simple and fast algorithm for network community detection

\u3cp\u3eThis paper introduces an algorithm for network community detection called DEEN (Delete Edges and Expand Nodes) consisting of two simple steps. First edges of the graph estimated to connect different clusters are detected and removed, next the resulting graph is used for generating communities by expanding seed nodes. DEEN uses as parameters the minimum and maximum allowed size of a cluster, and a resolution parameter whose value influences the number of removed edges. Application of DEEN to the budding yeast protein network for detecting functional protein complexes indicates its capability to identify clusters containing proteins with the same functional category, improving on MCL, a popular state-of-the-art method for functional protein complex detection. Moreover, application of DEEN to two popular benchmark networks results in the detection of accurate communities, substantiating the effectiveness of the proposed method in diverse domains.\u3c/p\u3

Detection and aggregation of the antitumoral drug parietin in ethanol/water mixture and on plasmonic metal nanoparticles studied by surface-enhanced optical spectroscopy: Effect of pH and ethanol concentration

7 págs.; 7 figs.In the present paper, we have investigated the effect of ethanol in aqueous media, the pH and the presence of Ag nanoparticles (NPs) on the aggregation processes of the antitumoral anthraquinone parietin in aqueous media and on the metal surface. UV-visible absorption, fluorescence and Raman spectra of parietin were used for such purpose. The present study provides information about the deprotonation and molecular aggregation processes occurring in parietin under different environments: ethanol/water mixture and when adsorbed onto Ag nanoparticles. The effect of ethanol on the optical properties of parietin in alcohol-water mixtures was also investigated at different ethanol concentrations with the time. For the case of the adsorption and organization of parietin molecules on the surface of Ag NPs, special attention was paid to the use of surface-enhanced optical techniques, SEF (surface-enhanced fluorescence) and SERS (surface-enhanced Raman scattering), for the characterization of the parietin aggregates and the ionization of the molecule on the surface. In particular, we have studied the variation of the SEF signal with the pH, which depends on the molecular organization of the molecule on the surface. Furthermore, a detailed analysis of the SERS spectra at different pH was accomplished and the main Raman bands of the protonated, mono-deprotonated and di-deprotonated parietin were identified. Finally, the second ionization pK of parietin on metal NPs was deduced from the SERS spectra. © 2016 Elsevier B.V. All rights reservedThis work has been supported by the Spanish Ministerio de Economía y Competitividad (FIS2014-52212-R), by Structural funds of the EU (contracts: NanoBioSens (ITMS code: 26220220107, 50%), SEPO II (ITMS code: 26220120039), and CEVA II (ITMS code: 26220120040), by the contract APVV-0242-11, and the 7FP EU project CELIM(316310).Peer Reviewe

Catalytic Effects of Silver Plasmonic Nanoparticles on the Redox Reaction Leading to ABTS (center dot+) Formation Studied Using UV-visible and Raman Spectroscopy

10 págs.; 5 figs.; 1 schemeABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) is a compound extensively employed to evaluate the free radical trapping capacity of antioxidant agents and complex mixtures such as biological fluids or foods. This evaluation is usually performed by using a colourimetric experiment, where preformed ABTS radical cation (ABTS˙+) molecules are reduced in the presence of an antioxidant causing an intensity decrease of the specific ABTS˙+ UV-visible absorption bands. In this work we report a strong effect of silver plasmonic nanoparticles (Ag NPs) on ABTS leading to the formation of ABTS˙+. The reaction of ABTS with Ag NPs has been found to be dependent on the interfacial and plasmonic properties of NPs. Specifically, this reaction is pronounced in the presence of spherical nanoparticles prepared by the reduction of silver nitrate with hydroxylamine (AgH) and in the case of star-shaped silver nanoparticles (AgNS). On the other hand, spherical nanoparticles prepared by the reduction of silver nitrate with citrate apparently do not react with ABTS. Additionally, the formation of ABTS˙+ is investigated by surface-enhanced Raman scattering (SERS) and the assignment of the most intense vibrational bands of this compound is performed. The SERS technique enables us to detect this radical cation at very low concentrations of ABTS (∼2 μM). Altogether, these findings allow us to suggest the use of ABTS/Ag NPs-systems as reliable and easy going substrates to test the antioxidant capacity of various compounds, even at concentrations much lower than those usually used in the spectrophotometric assays. Moreover, we have suggested that ABTS could be employed as a suitable agent to investigate the interfacial and plasmonic properties of the metal nanoparticles and, thus, to characterize the nanoparticle metal systems employed for various purposes. This journal is©the Owner Societies 2016This work was supported by the Scientific Grant Agencies of the Ministry of the Education of Slovak Republic (APVV-15-0485 and VEGA 1/0929/16) and the 7FP EU project CELIM 316310. This work has also been financially supported by MINECO (Project FIS2014-52212-R). A. G.-L. acknowledges CSIC and FSE for a JAE-Pre PhD fellowship.Peer Reviewe