Mixed-Weight Neural Bagging for Detecting m6A Modifications in SARS-CoV-2 RNA Sequencing.

OBJECTIVE: The m6A modification is the most common ribonucleic acid (RNA) modification, playing a role in prompting the virus's gene mutation and protein structure changes in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Nanopore single-molecule direct RNA sequencing (DRS) provides data support for RNA modification detection, which can preserve the potential m6A signature compared to second-generation sequencing. However, due to insufficient DRS data, there is a lack of methods to find m6A RNA modifications in DRS. Our purpose is to identify m6A modifications in DRS precisely. METHODS: We present a methodology for identifying m6A modifications that incorporated mapping and extracted features from DRS data. To detect m6A modifications, we introduce an ensemble method called mixed-weight neural bagging (MWNB), trained with 5-base RNA synthetic DRS containing modified and unmodified m6A. RESULTS: Our MWNB model achieved the highest classification accuracy of 97.85% and AUC of 0.9968. Additionally, we applied the MWNB model to the COVID-19 dataset; the experiment results reveal a strong association with biomedical experiments. CONCLUSION: Our strategy enables the prediction of m6A modifications using DRS data and completes the identification of m6A modifications on the SARS-CoV-2. SIGNIFICANCE: The Corona Virus Disease 2019 (COVID-19) outbreak has significantly influence, caused by the SARS-CoV-2. An RNA modification called m6A is connected with viral infections. The appearance of m6A modifications related to several essential proteins affects proteins' structure and function. Therefore, finding the location and number of m6A RNA modifications is crucial for subsequent analysis of the protein expression profile.

ECSU-Net: An Embedded Clustering Sliced U-Net Coupled With Fusing Strategy for Efficient Intervertebral Disc Segmentation and Classification.

Automatic vertebra segmentation from computed tomography (CT) image is the very first and a decisive stage in vertebra analysis for computer-based spinal diagnosis and therapy support system. However, automatic segmentation of vertebra remains challenging due to several reasons, including anatomic complexity of spine, unclear boundaries of the vertebrae associated with spongy and soft bones. Based on 2D U-Net, we have proposed an Embedded Clustering Sliced U-Net (ECSU-Net). ECSU-Net comprises of three modules named segmentation, intervertebral disc extraction (IDE) and fusion. The segmentation module follows an instance embedding clustering approach, where our three sliced sub-nets use axis of CT images to generate a coarse 2D segmentation along with embedding space with the same size of the input slices. Our IDE module is designed to classify vertebra and find the inter-space between two slices of segmented spine. Our fusion module takes the coarse segmentation (2D) and outputs the refined 3D results of vertebra. A novel adaptive discriminative loss (ADL) function is introduced to train the embedding space for clustering. In the fusion strategy, three modules are integrated via a learnable weight control component, which adaptively sets their contribution. We have evaluated classical and deep learning methods on Spineweb dataset-2. ECSU-Net has provided comparable performance to previous neural network based algorithms achieving the best segmentation dice score of 95.60% and classification accuracy of 96.20%, while taking less time and computation resources.

[Multi-component of Cibotium baronetz decoction pieces via 1H-NMR spectroscopic analysis].

OBJECTIVE: 1H-NMR technology was carried out to investigate the chemical difference between 30 batches of Cibotium baronetz decoction pieces and look for new method for quality control of C. baronetz decoction pieces. METHOD: Six hundreds MHz H-NMR spectroscopy and principle component analysis (PCA) were used to discriminate between 30 batches of commercially available cibotium samples based on multi-component metabolite profiles. RESULT: Saccharide is the principle component of C. baronetz decoction pieces, and steroid and triterpene were the discriminately chemical component. Protocatechuic acid, protocatechuic aldehyde, cibotiumbaroside A, cibotiumbaroside B and 4-O-caffeoyl-D-glucoside could be used as the marker for controlling the quality of commercial C. baronetz decoction pieces. CONCLUSION: Pattern-recognition techniques applied to proton nuclear magnetic resonance (1H-NMR) spectra of 80% methanol extraction of C. baronetz could correctly discriminate not only the quality, but also the chemical component for batches of commercial C. baronetz decoction pieces.