Abstract
Background
The treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse ...effects and even unknown toxicity. DDI detection in the wet lab is expensive and time-consuming. Thus, it is highly desired to develop the computational methods for predicting DDIs. Generally, most of the existing computational methods predict DDIs by extracting the chemical and biological features of drugs from diverse drug-related properties, however some drug properties are costly to obtain and not available in many cases.
Results
In this work, we presented a novel method (namely DPDDI) to predict DDIs by extracting the network structure features of drugs from DDI network with graph convolution network (GCN), and the deep neural network (DNN) model as a predictor. GCN learns the low-dimensional feature representations of drugs by capturing the topological relationship of drugs in DDI network. DNN predictor concatenates the latent feature vectors of any two drugs as the feature vector of the corresponding drug pairs to train a DNN for predicting the potential drug-drug interactions. Experiment results show that, the newly proposed DPDDI method outperforms four other state-of-the-art methods; the GCN-derived latent features include more DDI information than other features derived from chemical, biological or anatomical properties of drugs; and the concatenation feature aggregation operator is better than two other feature aggregation operators (i.e., inner product and summation). The results in case studies confirm that DPDDI achieves reasonable performance in predicting new DDIs.
Conclusion
We proposed an effective and robust method DPDDI to predict the potential DDIs by utilizing the DDI network information without considering the drug properties (i.e., drug chemical and biological properties). The method should also be useful in other DDI-related scenarios, such as the detection of unexpected side effects, and the guidance of drug combination.
Under investigation in this paper is a coherently coupled nonlinear Schrödinger system which describes the propagation of polarized optical waves in an isotropic medium. By virtue of the Darboux ...transformation, some new solutions have been generated on the vanishing and non-vanishing backgrounds, including multi-solitons, bound solitons, one-breathers, bound breathers, two-breathers, first-order and higher-order rogue waves. Dynamic behaviors of those solitons, breathers and rogue waves have been discussed through graphic simulation.
It is of great significance to study the interactions between structures and supporting soils for both structural engineering and geotechnical engineering. In this paper, based on the refined ...two-parameter elastic foundation model, the bending problem for a finite-length beam on Gibson elastic soil is solved. The effects of axial force and soil heterogeneity on the bending behaviours and stress states of beams on elastic foundations are discussed, and the parameters of the physical model are determined reasonably. The beam and elastic foundation are treated as a single system, and the complete potential energy is obtained. Based on the principle of minimum potential energy, the governing differential equations for the beam bearing axial force on the Gibson foundation are derived, and the equations for attenuation parameters are also defined. The problem of the unknown parameters in foundation models being difficult to determine is solved by an iterative method. The results demonstrate that this calculation method is feasible and accurate, and that the applied theory is universal for the analysis of interactions between beams and elastic foundations. Both axial force and soil heterogeneity have a certain effect on the deformation and internal force of beams on elastic foundations, and the vertical elastic coefficient of foundations is mainly determined by the stiffness of the surface soil. Additionally, attenuation parameters can be obtained relatively accurately by an iterative method, and then the vertical elastic coefficient and shear coefficient can be further obtained. This research lays a foundation for the popularisation and application of the two-parameter elastic foundation model.
With the fast development of object recognition and detection in autonomous driving and video monitoring, image with haze or raindrop can affect the result a lot. As deep learning develops, the hazed ...and raindrop image can lower the accuracy of object recognition and detection significantly. While hazed images cannot be managed using other image refining process. Since the noise in hazed image is signal-dependent. The object degradation in hazed image is related to object depth. So, the dehazing process depends on the input image. This paper provides a survey on single image and video dehazing methods, from end-to-end system to distributed system. General methods based on deep learning of state-of-art papers from 2010 to 2018 are summarized and compared, accompanied with their datasets of the current progress in this field. The application of these methods and relationship between these methos are also discussed in this paper.
2D perovskites have been considered as promising candidates for optoelectronic devices due to their good optical and electronic properties compared to 3D perovskites with significantly higher ...stability. Considering the commercial applications involving displays, image sensors, and fluorescent anti‐counterfeiting labels, the patterning technique of 2D perovskites is urgently required. However, existing patterning approaches still have challenges in high‐resolution fabrication. Here, a facile femtosecond laser direct writing method to fabricate arbitrarily patterned 2D perovskite films with well‐defined profiles and uniform fluorescence properties is developed. The flexible, fine, and non‐thermal diffused patterning abilities of femtosecond laser facilitate diverse 2D perovskite patterns exhibiting bright emission without any pinholes and cracks, as well as high resolution of approximate 2 µm line width. Based on this efficient patterning technique, this study demonstrates fluorescent anti‐counterfeiting labels (quick response code embedded with microlines) based on 2D perovskite films with high humidity stability, which can be identified from 43% to 96% relative humidity. This high‐resolution, reliable, efficient, and facile patterning technique for 2D perovskites with high humidity stability provides a promising technical route for 2D perovskite‐based optoelectronic applications.
For practical applications of 2D perovskites, a femtosecond laser direct writing method for patterning of 2D perovskites is proposed. Benefiting from the flexible, fine, and non‐thermal diffused patterning capabilities of a femtosecond laser, diverse 2D perovskite patterns exhibit bright and uniform emission properties without any pinholes and cracks and a high resolution of approximate 2 µm line width.
Transparent conductive electrodes, as transmission windows of photons and electrons, play important roles in high‐performance organic optoelectronic devices. The replacement of widely used indium tin ...oxide (ITO) electrodes has been attempted due to the increasing cost and intrinsically brittle characteristics of ITO. Ultrathin metal films, with excellent optoelectrical features, high flexibility, and sufficient mechanical stability, have been considered a potential candidate for the use as transparent conductive electrodes. However, ultrathin metal films follow the Volmer–Weber mechanism, resulting in a rough and discontinuous morphology with poor optoelectrical properties due to the bad adhesion to substrates. This review summarizes the progress in strategies for preparing ultrathin and ultrasmooth metal films with superior transmittance and conductivity by successfully suppressing the Volmer–Weber mechanism. The electrical and optical performances of the ultrathin metal films based on improved nucleation processes, as well as applications in ITO‐free organic optoelectronic devices, are also described and discussed in detail.
The development of ultrathin metal films with improved metal nucleation processes based on various strategies is summarized in this review. The great progress in the properties of ultrathin metal films as well as their application in indium tin oxide (ITO)‐free organic optoelectronic devices as transparent conductive electrodes are described.
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different ...types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
Endothelial cell death is linked to vascular diseases such as atherosclerosis and tissue ischemia. miRNA-17-92 (miR-17–92) is a multiple functional oncogenic miRNA cluster which plays vital roles in ...tumor angiogenesis and tissue development. However, its role in regulation of endothelial cell ferroptosis remains unclear. In this study, we revealed that miR-17–92 protects endothelial HUVEC cells from erastin-induced ferroptosis. miR-17-92 overexpression significantly reduced erastin-induced growth inhibition and ROS generation of HUVEC cells. Furthermore, Zinc lipoprotein A20, a validated target of miR-17-92, was identified as a novel regulator of endothelial cell ferroptosis. Lentivirus mediated A20 overexpression increased ROS generation and enhanced erastin-induced ferroptosis, whereas A20 knockdown inhibited erastin-induced ferroptosis. Mechanistic studies revealed that erastin-induced ferroptosis is associated with GPX4 downregulation and ACSL4 upregulation. miR-17-92 overexpression or A20 inhibition increased the ACSL4 expression in HUVEC cells. A20 was identified to directly with and regulate ACSL4 expression by immunoprecipitation. It suggests that the A20-ACSL4 axis plays important roles in erastin-induced endothelial ferroptosis. In conclusion, this study revealed a novel mechanism through which miR-17-92 protects endothelial cells from erastin-induced ferroptosis by targeting the A20-ACSL4 axis.
•miR-17-92 protects endothelial cells from erastin-induced ferroptosis.•Zinc lipoprotein A20 is identified as a novel regulator of ferroptosis.•A20 regulates ACSL4 by their directly interaction in endothelial cells.•miR-17-92 targets the A20-ACSL4 axis in endothelial cells.
Conventional lithium‐ion batteries (LIBs) with graphite anodes are approaching their theoretical limitations in energy density. Replacing the conventional graphite anodes with high‐capacity Si‐based ...anodes represents one of the most promising strategies to greatly boost the energy density of LIBs. However, the inherent huge volume expansion of Si‐based materials after lithiation and the resulting series of intractable problems, such as unstable solid electrolyte interphase layer, cracking of electrode, and especially the rapid capacity degradation of cells, severely restrict the practical application of Si‐based anodes. Over the past decade, numerous reports have demonstrated that polymer binders play a critical role in alleviating the volume expansion and maintaining the integrity and stable cycling of Si‐based anodes. In this review, the state‐of‐the‐art designing of polymer binders for Si‐based anodes have been systematically summarized based on their structures, including the linear, branched, crosslinked, and conjugated conductive polymer binders. Especially, the comprehensive designing of multifunctional polymer binders, by a combination of multiple structures, interactions, crosslinking chemistries, ionic or electronic conductivities, soft and hard segments, and so forth, would be promising to promote the practical application of Si‐based anodes. Finally, a perspective on the rational design of practical polymer binders for the large‐scale application of Si‐based anodes is presented.
Polymer binders play a crucial role in alleviating the volume expansion and maintaining the integrity and stable cycling of Si‐based anodes. This review presents the state‐of‐the‐art designing of polymer binders for Si‐based anodes based on the linear, branched, crosslinked, conjugated polymer structures. Besides, the multifunctional design of polymer binders for the practical application of Si‐based anodes has been discussed.
Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link ...distal regulatory elements to their target genes. Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. We demonstrate that HiCPlus can impute interaction matrices highly similar to the original ones, while only using 1/16 of the original sequencing reads. We show that the models learned from one cell type can be applied to make predictions in other cell or tissue types. Our work not only provides a computational framework to enhance Hi-C data resolution but also reveals features underlying the formation of 3D chromatin interactions.
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