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| 1 | The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR显示文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/. | Shuhui Song Lina Ma Dong Zou Dongmei Tian Cuiping Li Junwei Zhu Meili Chen Anke Wang Yingke Ma Mengwei Li Xufei Teng Ying Cui Guangya Duan Mochen Zhang Tong Jin Chengmin Shi Zhenglin Du Yadong Zhang Chuandong Liu Rujiao Li Jingyao Zeng Lili Hao Shuai Jiang Hua Chen Dali Han Jingfa Xiao Zhang Zhang Wenming Zhao Yongbiao Xue Yiming Bao | 2020 | Genomics, Proteomics & Bioinformatics2020，18，6： | 4 |
| 2 | Single-dose AAV-based vaccine induces a high level of neutralizing antibodies against SARS-CoV-2 in rhesus macaques显示文摘Dear Editor,Coronavirus disease 2019(COVID-19)is a highly infectious respiratory disease that continues to pose a serious global public health emergency.The disease shows a high infection rate,long incubation period,and rapidly emerging variants,which have led to its rapid spread worldwide(Krammer 2020).Many vaccines have been developed for the control of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the virus responsible for COVID-19,including vaccines based on messenger RNA(mRNA)(Polack et al.2020),viral vectors(Zhu et al.2020),recombinant proteins(Yang et al.2020),and inactivated SARS-CoV-2(Zhang et al.2021). | Dali Tong Mei Zhang Yunru Yang Han Xia Haiyang Tong Huajun Zhang Weihong Zeng Muziying Liu Yan Wu Huan Ma Xue Hu Weiyong Liu Yuan Cai Yanfeng Yao Yichuan Yao Kunpeng Liu Shifang Shan Yajuan Li Ge Gao Weiwei Guo Yun Peng Shaohong Chen Juhong Rao Jiaxuan Zhao Juan Min Qingjun Zhu Yanmin Zheng Lianxin Liu Chao Shan Kai Zhong Zilong Qiu Tengchuan Jin Sandra Chiu Zhiming Yuan Tian Xue | 2023 | Protein & Cell2023，14，1： | 0 |
| 3 | Single-cell profiling reveals Müller glia coordinate retinal intercellular communication during light/dark adaptation via thyroid hormone signaling显示文摘Light adaptation enables the vertebrate visual system to operate over a wide range of ambient illumination.Regulation of phototransduction in photoreceptors is considered a major mechanism underlying light adaptation.However,various types of neurons and glial cells exist in the retina,and whether and how all retinal cells interact to adapt to light/dark conditions at the cellular and molecular levels requires systematic investigation.Therefore,we utilized single-cell RNA sequencing to dissect retinal cell-type-specific transcriptomes during light/dark adaptation in mice.The results demonstrated that,in addition to photoreceptors,other retinal cell types also showed dynamic molecular changes and specifically enriched signaling pathways under light/dark adaptation.Importantly,Müller glial cells(MGs)were identified as hub cells for intercellular interactions,displaying complex cell‒cell communication with other retinal cells.Furthermore,light increased the transcription of the deiodinase Dio2 in MGs,which converted thyroxine(T4)to active triiodothyronine(T3).Subsequently,light increased T3 levels and regulated mitochondrial respiration in retinal cells in response to light conditions.As cones specifically express the thyroid hormone receptor Thrb,they responded to the increase in T3 by adjusting light responsiveness.Loss of the expression of Dio2 specifically in MGs decreased the light responsive ability of cones.These results suggest that retinal cells display global transcriptional changes under light/dark adaptation and that MGs coordinate intercellular communication during light/dark adaptation via thyroid hormone signaling. | Min Wei Yanping Sun Shouzhen Li Yunuo Chen Longfei Li Minghao Fang Ronghua Shi Dali Tong Jutao Chen Yuqian Ma Kun Qu Mei Zhang Tian Xue | 2023 | Protein & Cell2023，14，8： | 0 |
| 4 | Voxel modeling and association of ubiquitous spatiotemporal information in natural language texts显示文摘The ubiquitous spatiotemporal information extracted from Internet texts limits its application in spatiotemporal association and analysis due to its unstructured nature and uncertainty.This study uses ST-Voxel modeling to solve the problem of structured modeling and the association of ubiquitous spatiotemporal information in natural language texts.It provides a new solution for associating ubiquitous spatiotemporal information on the Internet and discovering public opinion.The main contributions of this paper include:(1)It proposes a convolved method for ST-Voxel,which solves the voxel modeling problem of unstructured and uncertain spatiotemporal objects and spatiotemporal relation in natural language texts.Experiments show that this method can effectively model 5 types of spatiotemporal objects and 16 types of uncertain spatiotemporal relation founded in texts;(2)It realizes the unknown event discovery based on voxelized spatiotemporal information association.Experiments show that this method can effectively solve the aggregation of ubiquitous spatiotemporal information in multi-natural language texts,which is conducive to discovering spatiotemporal events.The selection of convolution parameters in voxel modeling is also discussed.A parameter selection method for balancing the discovery capability and discovery accuracy of spatiotemporal events is given. | Dali Wang Xiaochong Tong Chenguang Dai Congzhou Guo Yi Lei Chunping Qiu He Li Yuekun Sun | 2023 | International Journal of Digital Earth2023，16，1： | 0 |
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