Image Reconstruction with B0 Inhomogeneity using an Interpretable Deep Unrolled Network on an Open-bore MRI-Linac

MRI-Linac systems require fast image reconstruction with high geometric fidelity to localize and track tumours for radiotherapy treatments. However, B0 field inhomogeneity distortions and slow MR acquisition potentially limit the quality of the image guidance and tumour treatments. In this study, we develop an interpretable unrolled network, referred to as RebinNet, to reconstruct distortion-free images from B0 inhomogeneity-corrupted k-space for fast MRI-guided radiotherapy applications. RebinNet includes convolutional neural network (CNN) blocks to perform image regularizations and nonuniform fast Fourier Transform (NUFFT) modules to incorporate B0 inhomogeneity information. The RebinNet was trained on a publicly available MR dataset from eleven healthy volunteers for both fully sampled and subsampled acquisitions. Grid phantom and human brain images acquired from an open-bore 1T MRI-Linac scanner were used to evaluate the performance of the proposed network. The RebinNet was compared with the conventional regularization algorithm and our recently developed UnUNet method in terms of root mean squared error (RMSE), structural similarity (SSIM), residual distortions, and computation time. Imaging results demonstrated that the RebinNet reconstructed images with lowest RMSE (<0.05) and highest SSIM (>0.92) at four-time acceleration for simulated brain images. The RebinNet could better preserve structural details and substantially improve the computational efficiency (ten-fold faster) compared to the conventional regularization methods, and had better generalization ability than the UnUNet method. The proposed RebinNet can achieve rapid image reconstruction and overcome the B0 inhomogeneity distortions simultaneously, which would facilitate accurate and fast image guidance in radiotherapy treatments

2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase

RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2 7 = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism