Population and allelic variation of A-to-I RNA editing in human transcriptomes.

BackgroundA-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing.ResultsIn order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure.ConclusionsOur study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases

Study of Word-Level Accent Classification and Gender Factors

Abstract In this work, we conduct word-level accent classification. Different features, words, and learning methods are explored for accent classification, and results show that HMM-MFCC models show promising performance. Besides, we also explore the effect of gender on accent classification. Results show that models trained on male data do not generalized well on female data; Models trained on both male and female data is not always better than models trained on female data only. At last, we propose to use stacked ensemble classifier to classify gender firstly and then classify accent to improve accuracy

The depositional settings of organic-rich shale in the faulted lacustrine basin: A case study of the Y1 Member of the Yingcheng Formation in the Songliao Basin

Volcanic activity is often associated with the development of faulted lacustrine basins. Organic-rich shale in such basins usually contains abundant volcanic material. The influence of volcanic input on organic-rich shale deposition in the basin studied has not been discussed in detail. Based on the ten shale samples from three wells, this study analyzed the depositional environment of the Yingcheng Formation shale in the Lishu Fault Depression area of the Songliao Basin by using interpretation of logging, total organic carbon analysis, gas chromatography mass spectrometry analysis, and trace element analysis. The impact of fault break to basement and volcanic materials on the organic matter enrichment was evaluated. The results show that the organic matter of Ying 1 (Y1), the First Member of the Yingcheng Formation, in the Lishu Fault Depression is characterized mainly by type I kerogen. The shale of the Y1 Member, having high total organic carbon content, is laterally continuous and could be considered as a potential target for shale oil exploration. The shale with high total organic carbon was deposited in a freshwater deep lake under an anoxic environment. There is a significant input of volcanic material, especially around the Su2 well near the Sangshutai Fault. This study has established a sedimentary model of organic-rich shale in the faulted lacustrine basin affected by volcanic activity, which has significance for the exploration of shale oil in faulted lacustrine basins

The Effects of Modified Simiao Decoction in the Treatment of Gouty Arthritis: A Systematic Review and Meta-Analysis

The modified Simiao decoctions (MSD) have been wildly applied in the treatment of gouty arthritis in China. However, the evidence needs to be evaluated by a systematic review and meta-analysis. After filtering, twenty-four randomised, controlled trials (RCTs) comparing the effects of MSD and anti-inflammation medications and/or urate-lowering therapies in patients with gouty arthritis were included. In comparison with anti-inflammation medications, urate-lowering therapies, or coadministration of anti-inflammation medications and urate-lowering therapies, MSD monotherapy significantly lowered serum uric acid (p<0.00001, mean difference = −90.62, and 95% CI [−128.38, −52.86]; p<0.00001, mean difference = −91.43, and 95% CI [−122.38, −60.49]; p=0.02, mean difference = −40.30, and 95% CI [−74.24, −6.36], resp.). Compared with anti-inflammation medications and/or urate-lowering therapies, MSD monotherapy significantly decreased ESR (p<0.00001; mean difference = −8.11; 95% CI [−12.53, −3.69]) and CRP (p=0.03; mean difference = −3.21; 95% CI [−6.07, −0.36]). Additionally, the adverse effects (AEs) of MSD were fewer (p<0.00001; OR = 0.08; 95% CI [0.05, 0.16]). MSD are effective in the treatment of gouty arthritis through anti-inflammation and lowering urate. However, the efficacy of MSD should be estimated with more RCTs

Online Prototype Alignment for Few-shot Policy Transfer

Domain adaptation in reinforcement learning (RL) mainly deals with the changes of observation when transferring the policy to a new environment. Many traditional approaches of domain adaptation in RL manage to learn a mapping function between the source and target domain in explicit or implicit ways. However, they typically require access to abundant data from the target domain. Besides, they often rely on visual clues to learn the mapping function and may fail when the source domain looks quite different from the target domain. To address these problems, we propose a novel framework Online Prototype Alignment (OPA) to learn the mapping function based on the functional similarity of elements and is able to achieve the few-shot policy transfer within only several episodes. The key insight of OPA is to introduce an exploration mechanism that can interact with the unseen elements of the target domain in an efficient and purposeful manner, and then connect them with the seen elements in the source domain according to their functionalities (instead of visual clues). Experimental results show that when the target domain looks visually different from the source domain, OPA can achieve better transfer performance even with much fewer samples from the target domain, outperforming prior methods.Comment: This paper has been accepted at ICML202

Simultaneous Structural Identification of Natural Products in Fractions of Crude Extract of the Rare Endangered Plant Anoectochilus roxburghii Using 1H NMR/RRLC-MS Parallel Dynamic Spectroscopy

Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to 1H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in 1H NMR/RRLC–MS PDS spectrum, 1H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. 1H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds

Anti-Vibrio Indole-Diterpenoids and C-25 Epimeric Steroids From the Marine-Derived Fungus Penicillium janthinellum

A systematic chemical exploration of the marine-derived fungus Penicillium janthinellum led to the isolation of four indole-diterpenoid derivatives (1–4), including new penijanthines C and D (1 and 2), and a pair of new steroidal epimers, penijanthoids A and B (5 and 6). The calculated ECD spectra and Snatzke's method for the new compound 1 were carried out to determine its absolute configuration. The absolute configuration of 3 was established by X-ray diffraction and calculated ECD methods for the first time. DP4plus approach was used to elucidate the absolute configurations of the C-25 epimeric steroids 5 and 6. 25-Epimeric 5 and 6 represent the first examples of steroids forming a five-membered lactone between C-23 and C-27 from marine fungi. Compounds 1, 2, 5, and 6 displayed significant anti-Vibrio activity (Minimum inhibitory concentration, MIC values ranging from 3.1 to 50.0 μM) against three pathogenic Vibrio spp