Xiamen University

About: Xiamen University is a education organization based out in Amoy, Fujian, China. It is known for research contribution in the topics: Catalysis & Population. The organization has 50472 authors who have published 54480 publications receiving 1058239 citations. The organization is also known as: Amoy University & Xiàmén Dàxué.

deepDR: a network-based deep learning approach to in silico drug repositioning.

Abstract: Motivation Traditional drug discovery and development are often time-consuming and high risk. Repurposing/repositioning of approved drugs offers a relatively low-cost and high-efficiency approach toward rapid development of efficacious treatments. The emergence of large-scale, heterogeneous biological networks has offered unprecedented opportunities for developing in silico drug repositioning approaches. However, capturing highly non-linear, heterogeneous network structures by most existing approaches for drug repositioning has been challenging. Results In this study, we developed a network-based deep-learning approach, termed deepDR, for in silico drug repurposing by integrating 10 networks: one drug-disease, one drug-side-effect, one drug-target and seven drug-drug networks. Specifically, deepDR learns high-level features of drugs from the heterogeneous networks by a multi-modal deep autoencoder. Then the learned low-dimensional representation of drugs together with clinically reported drug-disease pairs are encoded and decoded collectively via a variational autoencoder to infer candidates for approved drugs for which they were not originally approved. We found that deepDR revealed high performance [the area under receiver operating characteristic curve (AUROC) = 0.908], outperforming conventional network-based or machine learning-based approaches. Importantly, deepDR-predicted drug-disease associations were validated by the ClinicalTrials.gov database (AUROC = 0.826) and we showcased several novel deepDR-predicted approved drugs for Alzheimer's disease (e.g. risperidone and aripiprazole) and Parkinson's disease (e.g. methylphenidate and pergolide). Availability and implementation Source code and data can be downloaded from https://github.com/ChengF-Lab/deepDR. Supplementary information Supplementary data are available online at Bioinformatics.

Activatable Singlet Oxygen Generation from Lipid Hydroperoxide Nanoparticles for Cancer Therapy

Abstract: Reactive oxygen species (ROS)-induced apoptosis is a widely practiced strategy for cancer therapy. Although photodynamic therapy (PDT) takes advantage of the spatial–temporal control of ROS generation, the meticulous participation of light, photosensitizer, and oxygen greatly hinders the broad application of PDT as a first-line cancer treatment option. An activatable system has been developed that enables tumor-specific singlet oxygen (1O2) generation for cancer therapy, based on a Fenton-like reaction between linoleic acid hydroperoxide (LAHP) tethered on iron oxide nanoparticles (IO NPs) and the released iron(II) ions from IO NPs under acidic-pH condition. The IO-LAHP NPs are able to induce efficient apoptotic cancer cell death both in vitro and in vivo through tumor-specific 1O2 generation and subsequent ROS mediated mechanism. This study demonstrates the effectiveness of modulating biochemical reactions as a ROS source to exert cancer death.

Improved In Vitro and In Vivo Biocompatibility of Graphene Oxide through Surface Modification: Poly(Acrylic Acid)-Functionalization is Superior to PEGylation

Abstract: The unique physicochemical properties of two-dimensional (2D) graphene oxide (GO) could greatly benefit the biomedical field; however, recent research demonstrated that GO could induce in vitro and in vivo toxicity. We determined the mechanism of GO induced toxicity, and our in vitro experiments revealed that pristine GO could impair cell membrane integrity and functions including regulation of membrane- and cytoskeleton-associated genes, membrane permeability, fluidity and ion channels. Furthermore, GO induced platelet depletion, pro-inflammatory response and pathological changes of lung and liver in mice. To improve the biocompatibility of pristine GO, we prepared a series of GO derivatives including aminated GO (GO-NH2), poly(acrylamide)-functionalized GO (GO-PAM), poly(acrylic acid)-functionalized GO (GO-PAA) and poly(ethylene glycol)-functionalized GO (GO-PEG), and compared their toxicity with pristine GO in vitro and in vivo. Among these GO derivatives, GO-PEG and GO-PAA induced less toxicity than pristine GO, and GO-PAA was the most biocompatible one in vitro and in vivo. The differences in biocompatibility were due to the differential compositions of protein corona, especially immunoglobulin G (IgG), formed on their surfaces that determine their cell membrane interaction and cellular uptake, the extent of platelet depletion in blood, thrombus formation under short-term exposure and the pro-inflammatory effects under long-term exposure. Overall, our combined data delineated the key molecular mechanisms underlying the in vivo and in vitro biological behaviors and toxicity of pristine GO, and identified a safer GO derivative that could be used for future applications.

Toward the Controlled Synthesis of Hexagonal Boron Nitride Films

Abstract: Atomically smooth hexagonal boron nitride (h-BN) layers have very useful properties and thus potential applications for protective coatings, deep ultraviolet (DUV) emitters, and as a dielectric for nanoelectronics devices. In this paper, we report on the growth of h-BN by a low-pressure chemical vapor deposition (LPCVD) process using diborane and ammonia as the gas precursors. The use of LPCVD allows synthesis of h-BN with a controlled number of layers defined by the growth conditions, temperature, time, and gas partial pressure. Furthermore, few-layer h-BN was also grown by a sequential growth method, and insights into the growth mechanism are described, thus forming the basis of future growth of h-BN by atomic layer epitaxy.