Detection of network communities with memory-biased random walk algorithms

WOS: 000426423600003Community structure and its detection in complex networks has been the subject of many studies in the recent years. Towards this goal, we have created a novel approach based on the analysis of the motion of a memory-biased random walker, i.e. an entity that traverses the network with some tendency to follow or avoid pathways it has previously traversed. We found that the walker tends to remain inside communities, that is, subsets of the network nodes which are more connected to each other, rather than to the rest of the network. Based on this trait of the MBRW we developed a method to detect communities and tested its performance on a range of networks with different levels of community structure. In all tested cases, the method proved to be at least as effective as Girvan-Newman or Infomap while outperforming them when communities were less well defined.Scientific and Technological Research Council of Turkey (TUBITAK) fellowship; Louis and Bessie Stein Family Fellowship for Exchanges with Israeli UniversitiesMesut Yucel was funded by the Scientific and Technological Research Council of Turkey (TUBITAK) fellowship. Uri Hershberg is a Stein fellow and the collaboration in this work was supported in part by the the Louis and Bessie Stein Family Fellowship for Exchanges with Israeli Universities

A generic model for diffusive dynamics of the substrate and fluorescein tagged enzyme in microfluidic platform

WOS: 000435585500023The aim of this study was to develop a model that describes enzymatic conversion in a microfluidic system along with convective and diffusive transport of substrate/product within the microchannels. Hence, a 1-D partial differential equation model based on Fick's Law was employed in order to describe the substrate/product concentration distributions within the system. Enzyme immobilized in PEO-inclusive/non-inclusive TEOS-based hydrogels were tagged with fluorescein and examined under confocal laser scanning microscopy to evaluate the distribution of the enzyme. The image processing analysis demonstrated that 88.2 +/- 5.9% of the PEO-inclusive gel fragment surface (pixelated) area was occupied by the enzyme-dye complex with an emission density of 29.92 +/- 1.07. Subsequent to ensuring the homogeneity throughout the microchannel, the effects of flow rate and the distance for a range of inlet substrate concentrations were considered in regards to various substrate concentrations and conversion rates. The developed model provided a quantification for the conversion of substrate into products and enhanced understanding of the transport phenomena in the hydrogel.Scientific and Technical Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [113M050]We acknowledge financial research support from the Scientific and Technical Research Council of Turkey (TUBITAK) 113M050 project. Additionally, we are grateful to Frank Bossler and Norbert Willenbacher for access to the Confocal Laser Scanning Microscopy at the Institute for Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology, Germany

Increased alkalotolerant and thermostable ribonuclease (RNase) production from alkaliphilic Streptomyces sp M49-1 by optimizing the growth conditions using response surface methodology

WOS: 000323223300008PubMed ID: 23532461Total of 171 alkaliphilic actinomycetes were evaluated for extracellular RNase production and Streptomyces sp. M49-1 was selected for further experiments. Fermentation optimization for RNase production was implemented in two steps using response surface methodology with central composite design. In the first step, the effect of independent fermentation variables including temperature, initial pH and process time were investigated. After identification of carbon and nitrogen sources affecting the production by one variable at a time method, concentrations of glucose and yeast extract and also inoculum size were chosen for the second central composite design. A maximum RNase activity was obtained under optimal conditions of 4.14 % glucose concentration, 4.63 % yeast extract concentration, 6.7 x 10(6) spores as inoculum size for 50 ml medium, 42.9 A degrees C, 91.2 h process time and medium initial pH 9.0. Optimum activity of the enzyme is achieved at pH 11 and temperature 60 A degrees C. The enzyme is highly stable at pH range 9.0-12.0 and at 90 A degrees C after 2 h. Statistical optimization experiments provide 2.25 fold increases in the activity of alkalotolerant and thermostable RNase and shortened the fermentation time compared to that of unoptimized condition. The members of Streptomyces can be promising qualified RNase producer for pharmaceutical industries.Ege UniversityEge University [09.MUH.078]This research was supported by The Research Fund of Ege University with 09.MUH.078 project number. The authors would like to thank Professor Murat Elibol (Department of Bioengineering, Faculty of Engineering, Ege University, Izmir, Turkey) for his valuable comments and suggestions during the preparation of this manuscript

Dipeptidyl peptidase IV production by solid state fermentation using alternative fungal sources

WOS: 000312424500007The present work was carried out for the production of dipeptidyl peptidase IV (DPP IV; EC 3.4.14.5) using Aspergillus, Penicillium, and Rhizopus strains under solid state fermentation conditions. Response surface methodology was applied for the optimization of the selected operational variables (corn flour, initial moisture content, and cultivation time) for DPP IV activity as the response. The optimal parameters of DPP IV activity for the independent variables, namely the amount of corn flour (% w/w), initial moisture content (% w/w), and cultivation time (days), were evaluated to be 2.44%, 60.85%, and 4.69 days, respectively, using Aspergillus awamori T116. The response for these results was also shown to be in very close agreement with the experimental data.TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [105T195]We thank Sevket Karacanci (PhD) for using the Design Expert software (version 7.1.6, Stat-Ease, Inc.). This study was supported by TUBITAK, project number 105T195

Interleukin-4, Interleukin-8 and E-selectin Levels in Intranasal Polyposis Patients with and without Allergy: A Comparative Study

Intranasal polyposis is a chronic inflammatory upper airway disease with unknown aetiology. Interleukin (IL)-4 and IL-8 play very significant roles in allergic events and infectious inflammation, respectively. In contrast, E-selectin is important in the initiation and organization of inflammation. In this study, levels of IL-4, IL-8 and E-selectin were measured in nasal mucosa specimens of intranasal polyposis patients with and without allergic rhinitis, and healthy controls. Healthy controls had significantly higher IL-4 levels than allergic patients and non-allergic patients; IL-4 levels were similar in allergic and non-allergic patients. Allergic and non-allergic patients had significantly higher IL-8 levels than healthy controls; IL-8 levels were comparable in allergic and non-allergic patients. E-selectin levels were similar in all groups. The infection-based theory, represented by IL-8, seems to be more likely than the allergy-based theory, represented by IL-4, for the pathogenesis of nasal polyposis

Interleukin-4, interleukin-8 and E-selectin levels in intranasal polyposis patients with and without allergy: a comparative study

Intranasal polyposis is a chronic inflammatory upper airway disease with unknown aetiology. Interleukin (IL)-4 and IL-8 play very significant roles in allergic events and infectious inflammation, respectively. In contrast, E-selectin is important in the initiation and organization of inflammation. In this study, levels of IL-4, IL-8 and E-selectin were measured in nasal mucosa specimens of intranasal polyposis patients with and without allergic rhinitis, and healthy controls. Healthy controls had significantly higher IL-4 levels than allergic patients and non-allergic patients; IL-4 levels were similar in allergic and non-allergic patients. Allergic and non-allergic patients had significantly higher IL-8 levels than healthy controls; IL-8 levels were comparable in allergic and non-allergic patients. E-selectin levels were similar in all groups. The infection-based theory, represented by IL-8, seems to be more likely than the allergy-based theory, represented by IL-4, for the pathogenesis of nasal polyposis

Optimization and mathematical modeling of mass transfer between Zostera marina residues and supercritical CO2 modified with ethanol

Supercritical CO2 extraction of phenolic compounds from Zostera marina residues was optimized by developing a mathematical model based on mass transfer balances. A linear driving force model was applied considering model parameters such as solute concentration on the surface of the solid (Cs) and in the supercritical fluid phase (Cf), film mass transfer coefficient (kf) and molecular diffusivity (DAB) and axial dispersion (Dax) coefficients. Henry's law was used to describe the equilibrium state of solid and fluid phases. The results of the proposed model were compared to that of the experimental data in terms of transport properties and extraction yield at various temperatures (303.15, 323.15, 353.15 K), pressures (15, 25, 35 MPa) and co-solvent mass ratios (0, 10, 20%). The optimum parameters were elicited as 25 MPa, 353.15 K and a co-solvent ratio of 20% yielding 77.22 μg g−1 dry feed. The model satisfactorily described the extraction yield which can be used for scale-up purposes