Vertex importance extension of betweenness centrality algorithm

Variety of real-life structures can be simplified by a graph. Such simplification emphasizes the structure represented by vertices connected via edges. A common method for the analysis of the vertices importance in a network is betweenness centrality. The centrality is computed using the information about the shortest paths that exist in a graph. This approach puts the importance on the edges that connect the vertices. However, not all vertices are equal. Some of them might be more important than others or have more significant influence on the behavior of the network. Therefore, we introduce the modification of the betweenness centrality algorithm that takes into account the vertex importance. This approach allows the further refinement of the betweenness centrality score to fulfill the needs of the network better. We show this idea on an example of the real traffic network. We test the performance of the algorithm on the traffic network data from the city of Bratislava, Slovakia to prove that the inclusion of the modification does not hinder the original algorithm much. We also provide a visualization of the traffic network of the city of Ostrava, the Czech Republic to show the effect of the vertex importance adjustment. The algorithm was parallelized by MPI (http://www.mpi-forum.org/) and was tested on the supercomputer Salomon (https://docs.it4i.cz/) at IT4Innovations National Supercomputing Center, the Czech Republic.808726

High-level production of violacein by the newly isolated Duganella violaceinigra str. NI28 and its impact on Staphylococcus aureus

A violacein-producing bacterial strain was isolated and identified as a relative of Duganella violaceinigra YIM 31327 based upon phylogenetic analyses using the 16S rRNA, gyrB and vioA gene sequences and a fatty acid methyl ester (FAME) analysis. This new strain was designated D. violaceinigra str. NI28. Although these two strains appear related based upon these analyses, the new isolate was phenotypically different from the type strain as it grew 25% faster on nutrient media and produced 45-fold more violacein. When compared with several other violacein producing strains, including Janthinobacterium lividum, D. violaceinigra str. NI28 was the best violacein producer. For instance, the crude violacein yield with D. violaceinigra str. NI28 was 6.0 mg/OD at 24 hours, a value that was more than two-fold higher than all the other strains. Finally, the antibacterial activity of D. violaceinigra str. NI28 crude violacein was assayed using several multidrug resistant Staphylococcus aureus. Addition of 30 mu M crude violacein led to a 96% loss in the initial S. aureus population while the minimum inhibitory concentration was 1.8 mu M. Consequently, this novel isolate represents a phenotypic variant of D. violaceinigra capable of producing much greater quantities of crude violacein, an antibiotic effective against multidrug resistant S. aureusopen

Benchmarking the Self-Assembly of Surfactin Biosurfactant at the Liquid–Air Interface to those of Synthetic Surfactants

The adsorption of surfactin, a lipopeptide biosurfactant, at the liquid–air interface has been investigated in this work. The maximum adsorption density and the nature and the extent of lateral interaction between the adsorbed surfactin molecules at the interface were estimated from surface tension data using the Frumkin model. The quantitative information obtained using the Frumkin model was also compared to those obtained using the Gibbs equation and the Langmuir–Szyszkowski model. Error analysis showed a better agreement between the experimental and the calculated values using the Frumkin model relative to the other two models. The adsorption of surfactin at the liquid–air interface was also compared to those of synthetic anionic, sodium dodecylbenzenesulphonate (SDBS), and nonionic, octaethylene glycol monotetradecyl ether (C14E8), surfactants. It has been estimated that the area occupied by a surfactin molecule at the interface is about 3- and 2.5-fold higher than those occupied by SDBS and C14E8 molecules, respectively. The interaction between the adsorbed molecules of the anionic biosurfactant (surfactin) was estimated to be attractive, unlike the mild repulsive interaction between the adsorbed SDBS molecules

Regulation of Pax6 by CTCF during Induction of Mouse ES Cell Differentiation

Pax6 plays an important role in embryonic cell (ES) differentiation during embryonic development. Expression of Pax6 undergoes from a low level to high levels following ES cell differentiation to neural stem cells, and then fades away in most of the differentiated cell types. There is a limited knowledge concerning how Pax6 is regulated in ES cell differentiation. We report that Pax6 expression in mouse ES cells was controlled by CCCTC binding factor (CTCF) through a promoter repression mechanism. Pax6 expression was significantly enhanced while CTCF activity was kept in the constant during ES cell differentiation to radial glial cells. Instead, the interaction of CTCF with Pax6 gene was regulated by decreased CTCF occupancy in its binding motifs upstream from Pax6 P0 promoter following the course of ES cell differentiation. Reduced occupancy of CTCF in the binding motif region upstream from the P0 promoter was due to increased DNA methylations in the CpG sites identified in the region. Furthermore, changes in DNA methylation levels in vitro and in vivo effectively altered methylation status of these identified CpG sites, which affected ability of CTCF to interact with the P0 promoter, resulting in increases in Pax6 expression. We conclude that there is an epigenetic mechanism involving regulations of Pax6 gene during ES cell differentiation to neural stem cells, which is through increases or decreases in methylation levels of Pax6 gene to effectively alter the ability of CTCF in control of Pax6 expression, respectively

Parametric Study on Dimensional Control of ZnO Nanowalls and Nanowires by Electrochemical Deposition

A simple electrochemical deposition technique is used to synthesize both two-dimensional (nanowall) and one-dimensional (nanowire) ZnO nanostructures on indium-tin-oxide-coated glass substrates at 70°C. By fine-tuning the deposition conditions, particularly the initial Zn(NO3)2·6H2O electrolyte concentration, the mean ledge thickness of the nanowalls (50–100 nm) and the average diameter of the nanowires (50–120 nm) can be easily varied. The KCl supporting electrolyte used in the electrodeposition also has a pronounced effect on the formation of the nanowalls, due to the adsorption of Cl− ions on the preferred (0001) growth plane of ZnO and thereby redirecting growth on the (100) and (20) planes. Furthermore, evolution from the formation of ZnO nanowalls to formation of nanowires is observed as the KCl concentration is reduced in the electrolyte. The crystalline properties and growth directions of the as-synthesized ZnO nanostructures are studied in details by glancing-incidence X-ray diffraction and transmission electron microscopy

Flexible and Transparent All-Graphene Circuits for Quaternary Digital Modulations

In modern communication system, modulation is a key function that embeds the baseband signal (information) into a carrier wave so that it can be successfully broadcasted through a medium such as air or cables. A flexible signal modulation scheme is hence essential to wide range of applications based on flexible electronics. Here we report a fully bendable all-graphene modulator circuit with the capability to encode a carrier signal with quaternary digital information for the first time. By exploiting the ambipolarity and the nonlinearity in a graphene transistor, we demonstrated two types of quaternary modulation schemes: 4-ary amplitude-shift keying (4-ASK) and quadrature phase-shift keying (QPSK). Remarkably, 4-ASK and QPSK can be realized with just 1 and 2 all-graphene transistors, respectively, representing a drastic reduction in circuit complexity when compared with conventional digital modulators. In addition, the circuit is not only flexible but also highly transparent (~95% transmittance) owing to their all-graphene design with every component (channel, interconnects, load resistor, and source/drain/gate electrodes) fabricated from graphene films. Taken together, these results represent a significant step toward achieving a high speed communication system that can be monolithically integrated on a flexible and transparent platform.Comment: 29 pages, 8 figures, 1 tabl

Glassy State Lead Tellurite Nanobelts: Synthesis and Properties

The lead tellurite nanobelts have been first synthesized in the composite molten salts (KNO3/LiNO3) method, which is cost-effective, one-step, easy to control, and performed at low-temperature and in ambient atmosphere. Scanning electron microscopy, X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectrum, energy dispersive X-ray spectroscopy and FT-IR spectrum are used to characterize the structure, morphology, and composition of the samples. The results show that the as-synthesized products are amorphous and glassy nanobelts with widths of 200–300 nm and lengths up to tens of microns and the atomic ratio of Pb:Te:O is close to 1:1.5:4. Thermo-gravimetric analysis (TGA) and differential scanning calorimetry (DSC) and investigations of the corresponding structure and morphology change confirm that the nanobelts have low glass transition temperature and thermal stability. Optical diffuse reflectance spectrum indicates that the lead tellurite nanobelts have two optical gaps at ca. 3.72 eV and 4.12 eV. Photoluminescence (PL) spectrum and fluorescence imaging of the products exhibit a blue emission (round 480 nm)

Analysis of differential gene expression in human melanocytic tumour lesions by custom made oligonucleotide arrays

Melanoma is one of the most aggressive types of cancer and resection of the tumour prior to dissemination of tumour cells is still the most effective treatment. Therefore, early diagnosis of melanocytic lesions is important and identification of novel (molecular) markers would be helpful to improve diagnosis. Moreover, better understanding of molecular targets involved in melanocytic tumorigenesis could possibly lead to development of novel interventions. In this study, we used a custom made oligonucleotide array containing 298 genes that were previously found to be differentially expressed in human melanoma cell lines 1F6 (rarely metastasising) and Mel57 (frequently metastasising). We determined differential gene expression in human common nevocellular nevus and melanoma metastasis lesions. By performing nine dye-swap array experiments, using individual as well as pooled melanocytic lesions, a constant differential expression could be detected for 25 genes in eight out of nine or nine out of nine array analyses. For at least nine of these genes, namely THBD, FABP7, H2AFJ, RRAGD, MYADM, HR, CKS2, NCK2 and GDF15, the differential expression found by array analyses could be verified by semiquantitative and/or real-time quantitative RT–PCR. The genes that we identified to be differentially expressed during melanoma progression could be potent targets for diagnostic, prognostic and/or therapeutic interventions