BackgroundMicroRNAs (miRNAs) are a group of short (~22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology.ResultsA set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information.ConclusionThe local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.

Atherogenesis, the formation of atherosclerotic plaques, is a complex process that involves several mechanisms, including endothelial dysfunction, neovascularization, vascular proliferation, apoptosis, matrix degradation, inflammation, and thrombosis. The pathogenesis and progression of atherosclerosis are explained differently by different scholars. One of the most common theories is the destruction of well-balanced homeostatic mechanisms, which incurs the oxidative stress. And oxidative stress is widely regarded as the redox status realized when an imbalance exists between antioxidant capability and activity species including reactive oxygen (ROS), nitrogen (RNS) and halogen species, non-radical as well as free radical species. This occurrence results in cell injury due to direct oxidation of cellular protein, lipid, and DNA or via cell death signaling pathways responsible for accelerating atherogenesis. This paper discusses inflammation, mitochondria, autophagy, apoptosis, and epigenetics as they induce oxidative stress in atherosclerosis, as well as various treatments for antioxidative stress that may prevent atherosclerosis.

Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.

Background A novel coronavirus (SARS-CoV2) outbreak in more than 200 countries recently caused viral pneumonia that was extremely infectious and pathogenic. The Chinese government proposes that both Traditional Chinese medicine (TCM) and Western medicine can be used in combination to treat pneumonia caused by SARS-CoV2, and TCM effectively provides continuous prevention and treatment. Methods The present review analyzes and summarizes the prevention and treatment of the novel coronavirus disease (COVID-19) with TCM. A classified analysis of the efficacy and advantages of TCM for the prevention and treatment of COVID-19 was performed, and the mechanisms of TCM in treating COVID-19 are summarized. Results TCM is effective in preventing COVID-19, and medical staff can prevent an iatrogenic infection by taking a decoction made based on the principles of TCM. As of March 13, 2020, new cases of COVID-19 in China have decreased in number to single digits. TCM's curative effect was outstanding, with a national participation rate of over 90%. More than 70,000 people were cured of COVID-19 and discharged from the hospital. Only approximately 10,000 patients are currently being treated, and the total treatment time is approximately 2 months. Conclusions TCM is currently the best choice for the treatment and prevention of COVID-19, and it is expected that it will be promoted by countries around the world.