Jansenmcintyre7812

MOTIVATION Biological pathway is important curated knowledge of biological processes. Thus, cancer subtype classification based on pathways will be very useful to understand differences in biological mechanisms among cancer subtypes. However, pathways include only a fraction of the entire gene set, only 1/3 of human genes in KEGG, and pathways are fragmented. For this reason, there are few computational methods to use pathways for cancer subtype classification. RESULTS We present an explainable deep learning model with attention mechanism and network propagation for cancer subtype classification. Each pathway is modeled by a graph convolutional network. then, a multi-attention based ensemble model combines several hundreds of pathways in an explainable manner. Lastly, network propagation on pathway-gene network explains why gene expression profiles in subtypes are different. In experiments with five TCGA cancer data sets, our method achieved very good classification accuracies and, additionally, identified subtype-specific pathways and biological functions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. For Permissions, please email journals.permissions@oup.com.Graphene-based membranes have been extensively explored owing to their excellent separation properties. In this paper, multiple factors regarding desalination performance were investigated by molecular dynamics (MD) simulations. These factors include the interlayer spacing distance (H), the gap width (dG), offset (O), and the number of gaps and layers in a multilayer graphene membrane (MGM). It is found that salt rejection is influenced significantly by the interlayer spacing distance owing to the largest free energy between ions and graphene sheets as well as the relatively larger size of the hydration layer around the ions. The optimal desalting parameter (dG = 1 nm, H = 0.8 nm) was selected; MGM systems based on the optimized parameter exhibited excellent salt rejection for NaCl, MgCl2 and CaCl2 solutions. These results can provide some ideas for the future design of graphene-based membranes.Multi-drug resistant bacterial infection has become one of the most serious threats to global public health. The preparation and application of new antibacterial materials are of great significance for solving the infection problem of bacteria, especially multi-drug resistant bacteria. The exceptional antibacterial effects of metal nanoparticles based on their unique physical and chemical properties make such systems ideal for application as antibacterial drug carriers or self-modified therapeutic agents both in vitro and in vivo. Metal nanoparticles also have admirable clinical application prospects due to their broad antibacterial spectrum, various antibacterial mechanisms and excellent biocompatibility. Nevertheless, the in vivo structural stability, long-term safety and cytotoxicity of the surface modification of metal nanoparticles have yet to be further explored and improved in subsequent studies. Herein, we summarized the research progress concerning the mechanism of metal nanomaterials in terms of antibacterial activity together with the preparation of metal nanostructures. Based on these observations, we also give a brief discussion on the current problems and future developments of metal nanoparticles for antibacterial applications.Nanofibrillar foams and aerogels are traditionally either macroporous with low surface area and high mechanical strength, or mesoporous with high surface area and low mechanical strength. In this work, an anionic cellulose nanofibril (CNF)-based dual-porous aerogel with BET specific surface area up to 430 m2 g-1 was prepared via a modular process combining directional freeze-thawing (creating macro-pores, ca. 50-200 μm) and supercritical drying (creating meso-pores, ca. 2-50 nm). Furthermore, by optionally utilizing both physical and chemical cross-linking strategies, aerogels with a Young's modulus of up to 711 kPa and good stability in aqueous conditions were demonstrated. By altering cross-linking strategies, the properties of resulting aerogels, such as hydrophilicity, mechanical strength and stability in water, can be precisely controlled for different applications. As a result, cationic methylene blue (MB) and metal ions (Ag+) were chosen as model species to investigate the absorption properties of the physically cross-linked aerogels in water. The aerogels showed a maximum adsorption of MB up to 234 mg g-1 and of Ag+ up to 116 mg g-1 as a result of the high specific surface area of the aerogels and their strong electrostatic interaction with the model species. Importantly, the hierarchical dual porosity of the aerogels enabled fast adsorption kinetics combined with a considerable adsorption capacity overall. Finally, it was shown that the adsorbed Ag+ could be converted to metallic Ag, demonstrating the additional functionality of these dual porous hybrid aerogels for antibacterial or catalytic applications.Correction for 'Bis(ethylmaltolato)oxidovanadium(iv) inhibited the pathogenesis of Alzheimer's disease in triple transgenic model mice' by Zhijun He et al., Metallomics, 2020, DOI 10.1039/c9mt00271e.Due to its excellent electrical and optical properties, tin selenide (SnSe), a typical candidate of two-dimensional (2D) semiconductors, has attracted great attention in the field of novel optoelectronics. However, the large-area growth of high-quality SnSe films still remains a great challenge, which limits their practical applications. Here, wafer-size SnSe ultrathin films with high uniformity and crystallization were deposited via a scalable magnetron sputtering method. The results showed that the SnSe photodetector was highly sensitive to a broad range of wavelengths in the UV-visible-NIR range, especially showing an extremely high responsivity of 277.3 A W-1 with the corresponding external quantum efficiency of 8.5 × 104% and detectivity of 7.6 × 1011 Jones. click here These figures of merits are among the best performances for the sputter-fabricated 2D photodetector devices. The photodetecting mechanisms based on a photogating effect induced by the trapping effect of localized defects are discussed in detail. The results indicate that the few-layered SnSe films obtained from sputtering growth have great potential in the design of high-performance photodetector arrays.The attachment of a dimethylallyl moiety to C4 of 1,3-dihydroxynaphthalene led to spontaneous oxidative cyclisations, resulting in the formation of two tetrahydrobenzofuran and one bicyclo[3.3.1]nonane derivatives. Incubation under an 18O-rich atmosphere proved that both the incorporated oxygen atoms originated from O2. A radical-involved mechanism is proposed for these cyclisations.Owing to the capacity of efficiently harvesting and converting incident energy, localized surface-plasmon resonance of noble metals was introduced into a metal-semiconductor design for promoting hydrogen evolution. In this study, a plasmonic nanodumbbell structure was employed to strategically modulate the energy transfer in the water reduction reaction. A maximum H2 evolution rate of 80 μmol g-1 h-1 was obtained in the Au-TiO2 nanodumbbells, and further improvement was achieved through surface modification with Pt nanoparticles functioning as active sites, leading to ∼4.3 times enhanced photocatalytic activity. Compared with similar nanostructures reported previously, the present superior photoactivity response is ascribed to the injection process of the energetic hot electrons generated from the excitation and decay of the longitudinal surface-plasmon resonance (LSPR) and transverse surface-plasmon resonance (TSPR) in the Au nanorods, which corresponds to the electric field distribution of the finite-difference-time-domain simulation. These intriguing results, originating from the positive synergistic effect of the plasmon and co-catalyst, demonstrated the mechanism of the plasmon-assisted photochemistry and provided a promising strategy for the rational design of novel plasmonic photocatalysts.Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to carry out vital processes in the cell by tuning the organizational and mechanical properties of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. The challenge is due to the high complexity of combining actin, microtubules, and their hundreds of known associated proteins. Here, we use fluorescence microscopy, fluctuation, and cross-correlation analysis to examine the role of actin and microtubules in the presence of an antiparallel microtubule crosslinker, MAP65, and a generic, strong actin crosslinker, biotin-NeutrAvidin. For a fixed ratio of actin and microtubule filaments, we vary the amount of each crosslinker and measure the organization and fluctuations of the filaments. We find that the microtubule crosslinker plays the principle role in the organization of the system, while, actin crosslinking dictates the mobility of the filaments. We have previously demonstrated that the fluctuations of filaments are related to the mechanics, implying that actin crosslinking controls the mechanical properties of the network, independent of the microtubule-driven re-organization.We propose a computational framework for developing Taft-like linear free energy relationships to characterize steric effects on the catalytic activity of transition metal complexes. This framework uses the activation strain model and energy decomposition analysis to isolate electronic and geometric effects, and identifies structural descriptors to construct linear relationships. We demonstrate proof-of-principle for CH activation with enzyme-inspired [Cu2O2]2+ complexes coordinated to bidentate diamine N-donors. Electronic effects are largely similar across chosen systems and geometric effects - quantified by strain energies - are accurately captured by a linear combination of two structural descriptors. A powerful linear free energy relationship emerges that is transferable to asymmetrically substituted complexes. We outline steps for expanding this approach to create a generalizable Taft framework for inorganic catalyst design.Herein, the adsorption of hydrogen on pristine germanene was studied using ab initio calculations. By performing a converged density functional theory calculation, we have found the nearly degenerate nature of hydrogen at the top sites HT1 and HT2, among which HT1 is the most stable site. The adsorption of a hydrogen atom on germanene led to local structural changes in germanene. To the best of our knowledge, this is the first study on the investigation of the localized surface curvature and zero-point energy of hydrogen for 2D germanene. Moreover, we demonstrated the properties of germanene defects via the four obtained defects the Stone-Wales (55-77), divacancy (77-555-6), divacancy (555-7), and pentagon-heptagon linear (5-7) defect. The lowest formation energy of the pentagon-heptagon linear defect is shown for the first time in this study.