Prediction of RNA secondary structures is an important problem in computational biology and bioinformatics, since RNA secondary structures are fundamental for functional analysis of RNA molecules. ...However, small RNA secondary structures are scarce and few algorithms have been specifically designed for predicting the secondary structures of small RNAs. Here we propose an algorithm named "PSRna" for predicting small-RNA secondary structures using reverse complementary folding and characteristic hairpin loops of small RNAs. Unlike traditional algorithms that usually generate multi-branch loops and 5Formula: see text end self-folding, PSRna first estimated the maximum number of base pairs of RNA secondary structures based on the dynamic programming algorithm and a path matrix is constructed at the same time. Second, the backtracking paths are extracted from the path matrix based on backtracking algorithm, and each backtracking path represents a secondary structure. To improve accuracy, the predicted RNA secondary structures are filtered based on their free energy, where only the secondary structure with the minimum free energy was identified as the candidate secondary structure. Our experiments on real data show that the proposed algorithm is superior to two popular methods, RNAfold and RNAstructure, in terms of sensitivity, specificity and Matthews correlation coefficient (MCC).
The poisoning effect of PbO and PbCl
on CeO
-TiO
catalyst for selective catalytic reduction of NO with NH
was investigated and compared. Both Pb species could deactivate the CeO
-TiO
catalyst and PbO ...had a stronger poisoning effect than PbCl
. From the characterization results of BET, XRD, XPS, NH
-TPD and H
-TPR, it was concluded that the more serious deactivation by PbO could be ascribed to smaller BET surface area, fewer surface Ce
and chemisorbed oxygen, stronger interaction between PbO and CeO
-TiO
catalyst, lower redox properties and surface acidity. The in situ DRIFT study results revealed that the NH
-SCR reaction over CeO
-TiO
catalyst was governed by both E-R and L-H mechanisms, which wasn't changed over the Pb-poisoned samples. The greater loss of Brønsted acid sites attributed to fewer surface Ce
and more serious inhibition of NO oxidation to NO
due to fewer surface chemisorbed oxygen were two key factors responsible for more serious deactivation by PbO. Furthermore, the presence of Pb species inhibited the NH
adsorption on the Lewis acid sites, aggravating the deactivation of CeO
-TiO
catalyst.
Background. MicroRNAs (miRNAs) are short noncoding RNAs integral for regulating gene expression at the posttranscriptional level. However, experimental methods often fall short in finding miRNAs ...expressed at low levels or in specific tissues. While several computational methods have been developed for predicting the localization of mature miRNAs within the precursor transcript, the prediction accuracy requires significant improvement. Methodology/Principal Findings. Here, we present MatPred, which predicts mature miRNA candidates within novel pre-miRNA transcripts. In addition to the relative locus of the mature miRNA within the pre-miRNA hairpin loop and minimum free energy, we innovatively integrated features that describe the nucleotide-specific RNA secondary structure characteristics. In total, 94 features were extracted from the mature miRNA loci and flanking regions. The model was trained based on a radial basis function kernel/support vector machine (RBF/SVM). Our method can predict precise locations of mature miRNAs, as affirmed by experimentally verified human pre-miRNAs or pre-miRNAs candidates, thus achieving a significant advantage over existing methods. Conclusions. MatPred is a highly effective method for identifying mature miRNAs within novel pre-miRNA transcripts. Our model significantly outperformed three other widely used existing methods. Such processing prediction methods may provide important insight into miRNA biogenesis.
Conventional crystalline β-MnO2 usually exhibits poor electrochemical activities due to the narrow tunnels in its rutile-type structure. In this study, we synthesized a novel 2D β-MnO2 network with ...long-range order assembled by β-MnO2 nanowires and demonstrated that the novel 2D β-MnO2 network exhibits enhanced electrochemical performances. The 2D network is interwoven by crossed uniform β-MnO2 nanowires and the angle between the adjacent nanowires is about 60°. Such a novel structure makes efficient contact of β-MnO2 with electrolyte during the electrochemical process, decreases the polarization of the electrode and thus increases the discharge capacity and high-rate capability. The specific capacitance of the obtained 2D β-MnO2 network is 453.0 F/g at a current density of 0.5 A/g.
Based on the general features of the pre-microRNA secondary structure, this paper specifically predicts the pre-microRNA secondary structure, which focuses on the reverse complementary folding and ...forces them to form hairpin loop structures, this algorithm named 'rcfold'. In the result, a number of pre-microRNA sequencing data structure level as the test data set of the proposed algorithm, and then the predicted results obtained by the proposed 'rcfold' algorithm is compared with the ones acquired by rnafold. The experimental results show that in sensitivity, specificity and MCC value, the proposed algorithm outperforms rnafold.
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