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.     

Linearizability of planar polynomial Hamiltonian systems

Isochronicity and linearizability of two-dimensional polynomial Hamiltonian systems are revisited and new results are presented. We give a new computational procedure to obtain the necessary and sufficient conditions for the linearization of a polynomial system. Using computer algebra systems we provide necessary and sufficient conditions for linearizability of Hamiltonian systems with homogeneous non-linearities of degrees 5, 6 and 7. We also present some sufficient conditions for systems with nonhomogeneous nonlinearities of degrees two, three and five.     

A self-powered and sensitive terahertz photodetection based on PdSe2

With the rapid development of terahertz technology, terahertz detectors are expected to play a key role in diverse areas such as homeland security and imaging, materials diagnostics, biology, medical sciences, and communication. Whereas self-powered, rapid response, and room temperature terahertz photodetectors are confronted with huge challenges. Here, we report a novel rapid response and self-powered terahertz photothermoelectronic (PTE) photodetector based on a low-dimensional material: palladium selenide (PdSe₂). An order of magnitude performance enhancement was observed in photodetection based on PdSe₂/graphene heterojunction that resulted from the integration of graphene and enhanced the Seebeck effect. Under 0.1-THz and 0.3-THz irradiations, the device displays a stable and repeatable photoresponse at room temperature without bias. Furthermore, rapid rise (5.0 μs) and decay (5.4 μs) times are recorded under 0.1-THz irradiation. Our results demonstrate the promising prospect of the detector based on PdSe₂ in terms of air-stable, suitable sensitivity and speed, which may have great application in terahertz detection.     

On the Brauer p-dimension of Henselian discrete valued fields of residual characteristic p > 0

Let $(K,v)$ be a Henselian discrete valued field with residue field $\stackrel{?}{K}$ of characteristic $p>0$, and ${\text{Brd}}_p(K)$ be the Brauer p-dimension of K. This paper shows that ${\text{Brd}}_p(K)\ge n$ if $[\stackrel{?}{K}:{\stackrel{?}{K}}^p]=p^n$, for some $n\in \mathbb{N}$. It proves that ${\text{Brd}}_p(K)=\infty$ if and only if $[\stackrel{?}{K}:{\stackrel{?}{K}}^p]=\infty$.     

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.