二代测序技术在原发灶不明肿瘤诊疗中的研究进展

原发灶不明肿瘤(cancer of unknown primary,CUP)是一类罕见且预后不良的恶性肿瘤,分析和寻找原发灶、组织类型或分子免疫特征对改善患者的预后具有重要意义。在精准医疗背景下,二代测序(next-generation sequencing,NGS)可以利用肿瘤组织或外周血标本从基因层面对这类患者进行检测以指导诊断与治疗,延长患者生存期,改善预后。本文针对NGS样本的选择、NGS指导下的CUP患者的组织溯源、分子特征、指导治疗等方面进行综述。

2019新型冠状病毒信息库

2019年12月在中国武汉开始爆发的新型肺炎已造成全球25个国家/地区的31516人感染、638人死亡(截止2020年2月7日16时),引起该肺炎的病毒被世界卫生组织命名为2019新型冠状病毒(2019-nCoV)。为促进2019-nCoV数据共享应用并及时向全球公众提供病毒的相关信息,国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建立了2019新型冠状病毒信息库(2019nCoVR,https://bigd.big.ac.cn/ncov)。该信息库整合了来自德国全球流感病毒数据库、美国国家生物技术信息中心、深圳(国家)基因库、国家微生物科学数据中心及CNCB/NGDC等机构公开发布的2019-nCoV核苷酸和蛋白质序列数据、元信息、学术文献、新闻动态、科普文章等信息,开展了不同冠状病毒株的基因组序列变异分析并提供可视化展示。同时,2019nCoVR无缝对接CNCB/NGDC的相关数据库,提供新测序病毒株系的基因组原始测序数据、组装后序列的在线汇交、管理与共享、国际数据库同步发布等数据服务。本文对2019nCoVR数据汇交、管理、发布及使用等进行全面阐述,以方便用户了解该信息库各项功能及数据状况,为加速开展病毒的分类溯源、变异演化、快速检测、药物研发以及新型肺炎的精准预防与治疗等研究提供重要基础。

A Data-Driven Adaptive Method for Attitude Control of Fixed-Wing Unmanned Aerial Vehicles

In this paper, a real-time online data-driven adaptive method is developed to deal with uncertainties such as high nonlinearity, strong coupling, parameter perturbation and external disturbances in attitude control of fixed-wing unmanned aerial vehicles (UAVs). Firstly, a model-free adaptive control (MFAC) method requiring only input/output (I/O) data and no model information is adopted for control scheme design of angular velocity subsystem which contains all model information and up-mentioned uncertainties. Secondly, the internal model control (IMC) method featured with less tuning parameters and convenient tuning process is adopted for control scheme design of the certain Euler angle subsystem. Simulation results show that, the method developed is obviously superior to the cascade PID (CPID) method and the nonlinear dynamic inversion (NDI) method.

Van der Waals epitaxy of type-Ⅱ band alignment CsPbI_(3)/TMDC heterostructure for optoelectronic applications

Van der Waals epitaxy allows heterostructure formation without considering the lattice match requirement,thus is a promising method to form 2D/2D and 2D/3D heterojunction.Considering the unique optical properties of CsPbI_(3) and transition metal dichalcogenides(TMDCs),their heterostructure present potential applications in both photonics and optoelectronics fields.Here,we demonstrate selective growth of cubic phase CsPbI_(3) nanofilm with thickness as thin as 4.0 nm and Zigzag/armchair orientated nanowires(NWs)on monolayer WSe_(2).Furthermore,we show growth of CsPbI_(3) on both transferred WSe_(2) on copper grid and WSe_(2) based optoelectrical devices,providing a platform for structure analysis and device performance modification.Transmission electron microscopy(TEM)results reveal the epitaxial nature of cubic CsPbI_(3) phase.The revealed growth fundamental of CsPbI_(3) is universal valid for other twodimensional substrates,offering a great advantage to fabricate CsPbI_(3) based van der Waals heterostructures(vdWHs).X-ray photoelectron spectroscopy(XPS)and optical characterization confirm the type-II band alignment,resulting in a fast charger transfer process and the occurrence of a broad emission peak with lower energy.The formation of WSe_(2)/CsPbI_(3) heterostructure largely enhance the photocurrent from 2.38 nA to 38.59 nA.These findings are vital for bottom-up epitaxy of inorganic semiconductor on atomic thin 2D substrates for optoelectronic applications.

Plant genomic resources at National Genomics Data Center:assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among species.Through various efforts in genomic data archiving,integrative analysis and value-added curation,the National Genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database resources.This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts.Here,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application tools.We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

GenBase: A Nucleotide Sequence Database

The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth of sequence data efficiently and on time.To address this issue,we present GenBase(https://ngdc.cncb.ac.cn/genbase),an open-access data repository that follows the International Nucleotide Sequence Database Collaboration(INSDC)data standards and structures,for efficient nucleotide sequence archiving,searching,and sharing.As a core resource within the National Genomics Data Center(NGDC)of the China National Center for Bioinformation(CNCB;https://ngdc.cncb.ac.cn),GenBase offers bilingual submission pipeline and services,as well as local submission assistance in China.GenBase also provides a unique Excel format for metadata description and feature annotation of nucleotide sequences,along with a real-time data validation system to streamline sequence submissions.As of April 23,2024,GenBase received 68,251 nucleotide sequences and 689,574 annotated protein sequences across 414 species from 2319 submissions.Out of these,63,614(93%)nucleotide sequences and 620,640(90%)annotated protein sequences have been released and are publicly accessible through GenBase’s web search system,File Transfer Protocol(FTP),and Application Programming Interface(API).Additionally,in collaboration with INSDC,GenBase has constructed an effective data exchange mechanism with GenBank and started sharing released nucleotide sequences.Furthermore,GenBase integrates all sequences from GenBank with daily updates,demonstrating its commitment to actively contributing to global sequence data management and sharing.

Genome Warehouse: A Public Repository Housing Genome-scale Data

The Genome Warehouse(GWH)is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission,storage,release,and sharing.As one of the core resources in the National Genomics Data Center(NGDC),part of the China National Center for Bioinformation(CNCB;https://ngdc.cncb.ac.cn),GWH accepts both full and partial(chloroplast,mitochondrion,and plasmid)genome sequences with different assembly levels,as well as an update of existing genome assemblies.For each assembly,GWH collects detailed genome-related metadata of biological project,biological sample,and genome assembly,in addition to genome sequence and annotation.To archive high-quality genome sequences and annotations,GWH is equipped with a uniform and standardized procedure for quality control.Besides basic browse and search functionalities,all released genome sequences and annotations can be visualized with JBrowse.By May 21,2021,GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them.Collectively,GWH serves as an important resource for genomescale data management and provides free and publicly accessible data to support research activities throughout the world.GWH is publicly accessible at https://ngdc.cncb.ac.cn/gwh.

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

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/.

MPoxVR: A comprehensive genomic resource for monkeypox virus variant surveillance

Monkeypox is a viral zoonotic disease endemic in Central and West Africa.Since January 1,2022,3413 laboratory-confirmed monkeypox cases and one death have been reported from 50 countries/territories in five WHO regions(as of June 22,2022;https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON396),and 1310 new cases and eight new countries have been reported in the past week.Genomic epidemiology is vital to determine the similarity between viruses and suggest possible links between cases,origins of infection,and transmission dynamics when combined with epidemiological information.However,one of the priority evidence gaps relating to the monkeypox outbreak is genome sequencing and in-host variation analysis.1 So,timely sharing both raw sequence data and consensus genomic data are useful to public health investigators and academic partners undertaking related studies.