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CRISPR-detector:fast and accurate detection,visualization,and annotation of genome-wide mutations induced by genome editing events

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Journal of Genetics and Genomics 2023年第8期50卷 563-572页

作者： Lei Huang Dan Wang Haodong Chen Jinnan Hu Xuechen Dai Chuan Liu Anduo Li Xuechun Shen Chen Qi haixi sun Dengwei Zhang Tong Chen Yuan Jiang College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China BGI-Shenzhen ShenzhenGuangdong 518083China BNU-HKBU United International College ZhuhaiGuangdong 519087China Sentieon Inc San JoseCA 94042USA School of Biology and Biological Engineering South China University of TechnologyGuangzhouGuangdong 510006China National Resource Center for Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China

The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome *** track on/off-target events with emerging new editing techniques,improved bioinformatic tools are *** tools suffer from limitations in speed and scalability,especially with whole-genome sequencing(WGS)data *** address these limitations,we have developed a comprehensive tool called CRISPR-detector,a web-based and locally deployable pipeline for genome editing sequence *** core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline,with additional novel annotation and visualization modules designed to fit CRISPR ***-analysis of the treated and control samples is performed to remove existing background variants prior to genome ***-detector offers optimized scalability,enabling WGS data analysis beyond Browser Extensible Data file-defined regions,with improved accuracy due to haplotype-based variant calling to handle sequencing *** addition,the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by *** advantages facilitate rapid and efficient detection of mutations induced by genome editing events,especially for datasets generated from *** web-based version of CRISPR-detector is available at https://***/crispr-detector,and the locally deployable version is available at https://***/hlcas/CRISPR-detector.

关键词： Genome editing On/off-target Genetic background removal Structural variation

Corrigendum to“CRISPR-detector:fast and accurate detection,visualization,and annotation of genome-wide mutations induced by genome editing events”[Journal of Genetics and Genomics(2023)563-572]

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Journal of Genetics and Genomics 2023年第10期50卷 813-813页

This corrigendum clarifies information in the article“CRISPR-detector:fast and accurate detection,visualization,and annotation of genomewide mutations induced by genome editing events”by Huang et al.(2023).In the figure legend of Fig.S1,the sentence“CRISPR-detector failed to report insertions larger than 72 bp while CRISPResso2 failed to report insertions larger than 53 bp.”should be corrected into“CRISPR-detector failed to report deletions larger than 71 bp while CRISPResso2 failed to report deletions larger than 53 bp.”

关键词： al. Cor insertion

基于原生质体的谷子CRISPR/Cas9基因编辑系统优化

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河南农业科学 2022年第1期51卷 34-42页

作者：刘光宇徐晓静夏科科孙海汐陶月如崔震顾颖深圳华大生命科学研究院广东深圳518083

为了优化和筛选谷子中高效的CRISPR/Cas9(Clustered regularly interspaced short palindromic repeats/CRISRP-associated nuclease 9)基因编辑系统,针对谷子八氢番茄红素脱氢酶基因(SiPDS)设计6种gRNA(gRNA1—gRNA2针对外显子1,gRNA3—gRNA6针对外显子12),构建多种CRISPR/Cas9基因编辑系统,通过聚乙二醇(PEG)介导的方法转入谷子原生质体中,然后利用开发的大规模平行测序技术快速检测它们对SiPDS的突变效率。结果表明,采用7 d谷子黄化苗幼茎建立的原生质体转化系统的转化效率较高,为50.44%~57.36%。将Super启动子(SP)、谷子内源的泛素启动子(Ubi)分别驱动Cas9基因的基因编辑系统转入谷子原生质体中,发现两者对SiPDS基因的突变效率分别为0.5%、5.5%。随后采用Ubi启动子驱动Cas9基因,比较单一gRNA、双gRNA和tRNA结构的基因编辑系统对SiPDS基因的突变效率,发现双gRNA基因编辑系统Ubi-dgRNAE1和Ubi-dgRNAE12的突变效率分别较单一gRNA基因编辑系统提高了1.66倍和1.11倍;tRNA基因编辑系统Ubi-tRNA的突变效率较单一gRNA基因编辑系统提高了5.87倍,为51.24%,且Ubi-tRNA可同时针对多个位点进行编辑,其多位点突变频率为3.23%。比较gRNA3、gRNA4、gRNA5体外转录产物分别与Cas9蛋白混合制成的核糖核蛋白(RNP)复合物的体外切割活性,发现RNP-gRNA5复合物体外切割活性最高,其对SiPDS基因的突变效率是2.0%,并且引起的突变类型主要为小于3 bp的缺失。

关键词：基因编辑 CRISPR/Cas9 tRNA RNP 谷子原生质体

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Long-term survival outcomes and immune checkpoint inhibitor retreatment in patients with advanced cervical cancer treated with camrelizumab plus apatinib in the phase II CLAP study

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Cancer Communications 2024年第6期44卷 654-669页

作者： Chunyan Lan Huaiwu Lu Lin Zhou Kunlun Liao Junxiu Liu Zhiwen Xie haixi Liang Guorong Zou Ting Yang Qin Xu Xin Huang Department of Gynecologic Oncology Sun Yat-sen University Cancer CentreGuangzhouGuangdongP.R.China State Key Laboratory of Oncology in South China Collaborative Innovation Centre for Cancer MedicineGuangzhouGuangdongP.R.China Department of Gynecologic Oncology Sun Yat-sen Memorial HospitalGuangzhouGuangdongP.R.China Clinical Research Daytime Treatment Center Sun Yat-sen University Cancer CentreGuangzhouGuangdongP.R.China Department of Obstetrics and Gynecology The First Affiliated Hospital of Sun Yat-sen UniversityGuangzhouGuangdongP.R.China Cancer Institute of Panyu Panyu Central HospitalGuangzhouGuangdongP.R.China Medical Affairs Jiangsu Hengrui Pharmaceuticals Co.LtdShanghaiP.R.China Department of Gynecology Clinical Oncology School of Fujian Medical UniversityFujian Cancer HospitalFuzhouFujianP.R.China

Background:Camrelizumab plus apatinib have demonstrated robust antitumor activity and safety in patients with advanced cervical cancer(CLAP study;NCT03816553).We herein present the updated long-term results of the CLAP study and explore potential biomarkers for *** outcomes of patients who underwent immune checkpoint inhibitor(ICI)retreatment were also ***:In this phase II trial,eligible patients received camrelizumab 200 mg intravenously every two weeks and apatinib 250 mg orally once daily in 4-week cycles for up to two *** was continued until disease progression,unacceptable toxicity,or withdrawal of ***:Between January 21 and August 1,2019,a total of 45 patients were *** were analyzed as of July 31,2023,representing>48 months since treatment initiation for all ***(20.0%)patients completed the 2-year *** median duration of response(DOR)was 16.6 months,and 45.0%of patients achieved a DOR of≥24 *** 12-month progression-free survival(PFS)rate was 40.7%(95%confidence interval[CI],25.2-55.6),with an 18-month PFS rate of 37.8%(95%CI,22.7-52.8).The median overall survival(OS)was 20.3 months(95%CI,9.3-36.9),and the 24-month OS rate was 47.8%(95%CI,31.7-62.3).Age>50 years,programmed death-ligand 1(PD-L1)combined positive score(CPS)≥1(versus[vs.]<1),CPS≥10(vs.<1),high tumor mutational burden,and PIK3CA mutations were associated with improved PFS(hazard ratio[HR]<1)and longer OS(HR<1).Eight patients who initially responded in the CLAP trial but later experienced disease progression were retreated with *** them,2(25.0%)achieved a partial response,while 5(62.5%)had stable ***,four patients who received retreatment with ICIs survived for more than *** new safety signals were identified in the present ***:Long-term survival follow-up data demonstrated that camrelizumab plus apatinib has robust,sustained,and durable efficacy in patients with advanced cervical ca

关键词： Cemrelizumab apatinib programmed cell death-1(PD-1) programmed death-ligand 1(PD-L1) tumor mutational burden(TMB) PIK3CA advanced cervical cancer

Traffic safety helmet wear detection based on improved YOLOv5 network

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Optoelectronics Letters 2025年第1期 35-42页

作者： GUI Dongdong sun Bo College of Software Southeast University Quanzhou Equipment Research Centre Haixi Institute Chinese Academy of Sciences

Aiming at the problem that the current traffic safety helmet detection model can't balance the accuracy of detection with the size of the model and the poor generalization of the model, a method based on improving you only look once version 5(YOLOv5) is proposed. By incorporating the lightweight Ghost Net module into the YOLOv5 backbone network, we effectively reduce the model size. The addition of the receptive fields block(RFB) module enhances feature extraction and improves the feature acquisition capability of the lightweight model. Subsequently, the high-performance lightweight convolution, GSConv, is integrated into the neck structure for further model size compression. Moreover, the baseline model's loss function is substituted with efficient insertion over union(EIoU), accelerating network convergence and enhancing detection precision. Experimental results corroborate the effectiveness of this improved algorithm in real-world traffic scenarios.

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Fast image reconstruction network in image stitching

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Optoelectronics Letters 2023年第10期19卷 635-640页

作者： XIE Menrui sun Bo Southeast University Suzhou215123China Quanzhou Institute of Equipment Manufacturing Haixi InstitutesChinese Academy of SciencesQuanzhou350108China

Compared with the traditional feature-based image stitching algorithm,the free-view image stitching algorithm based on deep learning has the advantages of fast stitching speed and good ***,these algorithms still cannot achieve real-time splicing *** the image reconstruction stage,we redesign a new fast image reconstruction *** network is designed based on ShuffleNet,and the new network structure and loss function will reduce the time required for image *** addition,this network can also reduce the performance loss after the network is *** is proved by experiments that the fast image reconstruction network can realize real-time high-resolution free-view image reconstruction.

关键词： image network network

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预制铁酸钙技术对钒钛磁铁矿烧结行为的影响

钢铁钒钛 2023年第4期44卷 117-124页

作者：谢皓李刚吕学伟孙小东何海熙中冶赛迪信息技术(重庆)有限公司重庆400041 重庆大学材料科学与工程学院重庆400044

针对钒钛磁铁矿在烧结过程中的成品率低、强度差、能耗高等问题,提出了预制铁酸钙烧结新技术,并通过压块焙烧试验和热分析测试揭示该技术的可行性及理论依据。结果表明,随着预制铁酸钙替代生石灰比例增加,焙烧产物微观形貌由粒状结构向... 详细信息

针对钒钛磁铁矿在烧结过程中的成品率低、强度差、能耗高等问题,提出了预制铁酸钙烧结新技术,并通过压块焙烧试验和热分析测试揭示该技术的可行性及理论依据。结果表明,随着预制铁酸钙替代生石灰比例增加,焙烧产物微观形貌由粒状结构向熔蚀结构转变,四元复合铁酸钙(SFCA)含量增加,钙钛矿含量降低,有利于焙烧过程的液相生成,烧结孔洞熔合程度增大,平均孔隙率从42.9%下降到36.2%,促进基体的致密化。升温过程中铁酸钙液相的生成可分为三个反应,根据生成温度由低到高依次为CF+CF_(2)→L的共熔反应,SFCA-I及SFCA的熔化分解反应;预制铁酸钙的加入可降低初始液相的产生温度,整体提高烧结液相量,提高比例约9%;预制铁酸钙技术可促进铁氧化物向初始液相中熔解,增加铁酸钙含量,促进固-液同化反应。

关键词：烧结钒钛磁铁矿预制铁酸钙热分析(TG-DSC)

显性直接教学的概念演进、核心内涵与实践启示

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远程教育杂志 2023年第5期41卷 28-37页

作者：赵国庆孙兴艳盛海曦樊蓓蓓周歆然北京师范大学教育学部教育技术学院北京100875 北京师范大学未来教育学院广东珠海519087

显性直接教学是在大直接教学(大DI)、小直接教学(小di)、显性教学(EI)等直接类教学法的基础上发展起来的新型教学方法,是“教师中心”教学取向中体现“教学效率”的一面与“学生中心”教学取向中体现“主动建构”一面的双向融合,较好地... 详细信息

显性直接教学是在大直接教学(大DI)、小直接教学(小di)、显性教学(EI)等直接类教学法的基础上发展起来的新型教学方法,是“教师中心”教学取向中体现“教学效率”的一面与“学生中心”教学取向中体现“主动建构”一面的双向融合,较好地体现了“双主”教学结构思想。由于学术界围绕直接类教学的争论较多,对大直接教学、小直接教学、显性教学和显性直接教学这组概念进行深入辨析,并在此基础上提炼出显性直接教学的四大核心要素,有助于研究者准确把握其核心要义。研究表明:认知建模将问题解决中隐藏的思维策略和思维过程显性化从而降低学生的外在认知负荷,支架渐隐通过逐步撤除非必要支架将学生的最近发展区不断向前推进,理解检查通过“提问-讨论-反馈”实现互动建构效果的及时确认,分层干预通过“直接教学-课内指导-课后指导”为大部分学生的学业成功提供保障。显性直接教学通过知识结构可视化帮助学困生达成知识的深度理解,通过还原问题解决中隐含的思维策略与方法促进拔尖生高阶思维发展,为平衡知识传授效率与发展学生高阶思维、兼顾学困生“双基”习得和拔尖生创新能力培养提供解决方案,从而在国家“双减”战略和“核心素养”导向教学改革的双重背景下,在课堂教学层面实现“公平有质量的教育”。显性直接教学还远不是教学法螺旋式优化的终点,未来发展需要积极吸纳学习科学最新研究成果,在现代信息技术的赋能下,加速教师专业发展进程。

关键词：显性直接教学认知建模支架渐隐理解检查分层干预思维可视化思维策略精准教学

X-ray-activated Bi^(3+)/Pr^(3+)co-doped LiYGeO_4 phosphor with UV and NIR dual-emissive persistent luminescence

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Journal of Rare Earths 2024年第5期42卷 955-961,I0005页

作者： Xianggui Yin Hongyun Zhong Lin Liu Junpeng Shi Xia sun Yun Zhang State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou350002China Xiamen Key Laboratory of Rare Earth Photoelectric Functional Materials Xiamen Institute of Rare Earth MaterialsHaixi InstituteChinese Academy of SciencesXiamen361021China Fujian Science and Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou350108China

X-ray-activated luminescence materials have broad application prospects in photodynamic therapy of deep *** them,X-ray-activated persistent luminescence materials(PLMs)exhibiting multiple emission peaks have drawn extensive attention for the ir capacity to achieve a combination of bioimaging and therapeutic ***,we developed a novel PLM,LiYGeO_4:Bi^(3+),Pr^(3+),that simultaneously exhibits UV and NIR dual persistent luminescence(PersL)emissions after irradiation by *** material can be re peatedly excited by X-ray and emits similar lumine scence intensity every time,which shows good PersL *** addition,LiYGeO_4:Bi^(3+),Pr^(3+)exhibits photostimulated PersL properties by stimulation with a red light-emitting diode(LED)or NIR laser after long-term *** work provides a new choice of X-ray-excited PLMs with UV and NIR dual emission and the novel phosphor shows promise as a potential candidate for the integration of treatment and diagnosis of deep tumors.

关键词： Co-doping X-ray-activated Dual emissions Persistent luminescence Rare earths