RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

Optimization of heterogeneous Catalyst-assisted fatty acid methyl esters biodiesel production from Soybean oil with different Machine learning methods

There is a growing attention to the bio and renewable energies due to fast depletion of fossil fuels as well as the global warming problem. Here, we developed a modeling and simulation method by means of artificial intelligence (AI) for prediction of the bioenergy production from vegetable bean oil. AI methods are well known for prediction of complex and nonlinear process. Three distinct Adaptive Boosted models including Huber regression, LASSO, and Support Vector Regression (SVR) as well as artificial neural network (ANN) were applied in this study to predict actual yield of Fatty acid methyl esters (FAME) production. All boosted utilizing the Adaptive boosting algorithm. The important influencing parameters on the biodiesel production such as the catalyst loading (CAO/Ag, wt%) and methanol to oil (Soybean oil) molar ratio were selected as the input variables of models while the yield of FAME production was selected as output. Model hyper-parameters were tuned to maintain generality while improving prediction accuracy. The models were evaluated using three distinct metrics Mean Absolute Error (MAE), Root Mean Square Error (RMSE), and R². Error rates of 8.16780E-01, 4.43895E-01, 2.06692E + 00, and 3.92713 E-01 were obtained with the MAE metric for boosted Huber, SVR, LASSO and ANN models. On the other hand, the RMSE error of these models were about 1.092E-02, 1.015E-02, 2.669E-02, and 1.01174E-02, respectively. Finally, the R-square score were calculated for boosted Huber, boosted SVR, and boosted LASSO as 0.976, 0.990, 0.872, and 0.99702, respectively. Therefore, it can be concluded that although the boosted SVR and ANN models were better models for prediction of process efficiency in terms of error, but all algorithms had high accuracy. The optimum yield of 83.77% and 81.60% for biodiesel production were observed at optimum operating values from boosted SVR and ANN models, respectively.     

Design,synthesis and evaluation of novel dehydroabietic acid-dithiocarbamate hybrids as potential multi-targeted compounds for tumor cytotoxicity

In the present study, novel representatives of the important group of biologically-active, dehydroabietic acid-bearing dithiocarbamate moiety, were synthesized and characterized by ¹H NMR, ¹³C NMR, HR-MS. The in vitro antiproliferative activity evaluation (MTT) indicated that these compounds exhibited potent inhibitory activities in various cancer cell lines (HepG-2, MCF-7, HeLa, T-24, MGC-803). Particularly, compound III-b possessed extraordinary cytotoxicity with low micromolar IC₅₀ values ranging from 4.07 to 38.84 µM against tested cancer cell lines, while displayed weak cytotoxicity on two normal cell lines (LO-2 and HEK 293 T). Subsequently, the potential mechanisms of representative compound III-b were elementarily investigated by Transwell experiment, which showed III-b can inhibit cancer cells migration. Annexin-V/PI dual staining showed that the compound can induce HepG-2 cells apoptosis in a dose-dependent manner. Meanwhile this apoptosis may be related to the upregulated protein expression of cleaved-caspase 3, cleaved-caspase 9, Bax and downregulated of Bcl-2 indicated by Western Blot. Later study further confirmed that ROS levels in HepG-2 cells increased significantly with the rise of concentrations. In addition, through the network pharmacology data analyzing, the core targets and signaling pathways of compound III-b for treatment of liver neoplasms were forecasted. Molecular docking model showed that compound III-b had high affinity with hub targets (CASP3, EGFR, HSP90AA1, MAPK1, ERBB2, MDM2), suggesting that compound III-b might target the hub protein to modulate signaling activity. Taken together, these data indicated that dehydroabietic acid structural modification following the “Molecular hybridization” principle is a feasible way to discover the potential multi-targeted antitumor compounds.     

Theoretical study of (e,2e) triple differential cross sections of pyrimidine and tetrahydrofurfuryl alcohol molecules using multi-center distorted-wave method

We report theoretical studies of electron impact triple differential cross sections of two bio-molecules,pyrimidine and tetrahydrofurfuryl alcohol,in the coplanar asymmetric kinematic conditions with the impact energy of 250 eV and ejected electron energy of 20 eV at three scattering angles of-5°,-10°,and-15°.Present multi-center distorted-wave method well describes the experimental data,which was obtained by performing(e,2e)experiment.The calculations show that the secondary electron produced by the primary impact electron is strongly influenced by the molecular ionic multi-center potential,which must be considered when the low energy electron interacts with DNA analogues.     

Generalized Jacobi spectral Galerkin method for fractional pantograph differential equation

This work is concerned with the extension of the Jacobi spectral Galerkin method to a class of nonlinear fractional pantograph differential equations. First, the fractional differential equation is converted to a nonlinear Volterra integral equation with weakly singular kernel. Second, we analyze the existence and uniqueness of solutions for the obtained integral equation. Then, the Galerkin method is used for solving the equivalent integral equation. The error estimates for the proposed method are also investigated. Finally, illustrative examples are presented to confirm our theoretical analysis.     

基于TOPSIS模型的机场网络节点重要度评估

在机场网络中单个机场节点的失效往往会对其他的节点产生影响,特别是关键节点的失效会波及整个网络.准确客观的识别重要节点机场关乎整个机场网络的安全运营.本文分析了机场网络拓扑特性中的度、集聚系数和接近度指标,考虑了机场旅客吞吐量和所在城市人口等交通经济特性指标,使用熵权法确定权重的基础上,应用TOPSIS法构建综合评价体系模型,最后以华东地区机场网络为例进行节点重要度排序.结果表明与单一指标的评估结果相比,该方法更加全面客观的确定不同属性指标的权重,避免了不同指标取值的差异性,使评价更加全面,更符合机场网络实际运营情况.     

p-Adic函数空间上Hardy型算子的多线性交换子估计

在p-adic域上研究分数次Hardy型算子与CMO(Q_p~n)函数生成的多线性交换子,建立了交换子在Lebesgue空间和Herz空间上的有界性.对Hardy算子的多线性交换子也得到了相应的结果.     

计算代数方程组孤立奇异解的符号数值方法

求解代数方程组是计算代数几何的最基本问题之一,孤立奇异解的计算则是其中最具挑战性的课题之一,在科学与工程计算中有着广泛的应用,如机器人、计算机视觉、机器学习、人工智能、运筹学、密码学和控制论等.本文结合作者的研究成果,综述了符号数值方法在计算代数系统孤立奇异解、特别是近似奇异解精化与验证方面的研究进展,并对未来的研究方向提出了展望.