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High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion

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Genomics, Proteomics & Bioinformatics 2023年第6期21卷 1195-1205页

作者： Wing Yin Cheng Wei-Xin Liu Yanqiang Ding guoping wang Yu Shi Eagle S.H.Chu Sunny Wong Joseph J.Y.Sung Jun Yu State Key Laboratory of Digestive Disease Institute of Digestive Disease and The Department of Medicine and TherapeuticsLi Ka Shing Institute of Health SciencesShenzhen Research InstituteThe Chinese University of Hong KongHong Kong Special Administrative Region 999077China Lee Kong Chian School of Medicine Nanyang Technology UniversitySingapore 639798Singapore

The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota.We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis.Human or mouse colon biopsies were divided into two groups,with one group undergoing host DNA depletion and the other serving as the control.Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing.The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses.Removing host DNA enhanced bacterial sequencing depth and improved species discovery,increasing bacterial reads by 2.46±0.20 folds while reducing host reads by 6.80%±1.06%.Moreover,2.40 times more of bacterial species were detected after host DNA depletion.This was confirmed from mouse colon tissues,increasing bacterial reads by 5.46±0.42 folds while decreasing host reads by 10.2%±0.83%.Similarly,significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion(P<0.001).Furthermore,an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues(P<0.001).Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy,which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.

关键词： Gut microbiota Colon tissue Host DNAdepletion Shotgun metagenomic sequencing

Genomic insights into the genetic basis of cotton breeding in China

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Molecular Plant 2023年第4期16卷 662-677页

作者： Yiqian Li Zhanfeng Si guoping wang Zhuolin Shi Jinwen Chen Guoan Qi Shangkun Jin Zegang Han Wenhao Gao Yue Tian Yun Mao Lei Fang Yan Hu Hong Chen Xiefei Zhu Tianzhen Zhang zhejiang Provincial Key Laboratory of Crop Genetic Resources the Advanced Seed InstitutePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina Xinjang Production and Construction Corps Seventh Division Agricultural Research Institute KuintunChina state Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricutural UniversityNanjingChina College of Biotechnology Jiangsu University of Science and TechnologyZhenjiangChina Key Laboratory of China Northwestern Inland Region Ministry of AgricultureCotton Research InstituteXinjiang Academy of Agricultural and Reclamation ScienceShiheziChina

The excellent Upland cotton(Gossypium hirsutum)cultivars developed since 1949 have made a huge contribution to cotton production in China,the world's largest producer and consumer of cotton.However,the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear.In this study,we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent,advanced generation,intercross(MAGiC)population comprising 920 recombinant inbred lines.A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality.Of them,25(46.30%)pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits,revealing complex trade-offs and linkage drags in Upland cotton agronomic traits.Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles.Interestingly,85%oftheseelitealleles were selectedandfixed fromdifferent Americanancestors,consistentwithcotton breeding practices in China.However,seven elite alleles of native origin that are responsible for Fusarium wilt resistance,early maturing,good-quality fiber,and other characteristics were not found in American an-cestors but have greatly contributed to Chinese cotton breeding and wide cultivation.Taken together,these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

关键词： cotton MAGiC population GWAS whole-genome sequencing pleiotropic loci breeding history

Discrete time transfer matrix method for dynamics analysis of complex weapon systems

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Science China(Technological Sciences) 2011年第5期54卷 1061-1071页

作者： RUI XiaoTing RONG Bao wang guoping HE Bin Institute of Launch Dynamics Nanjing University of Science and Technology Nanjing 210094 China

Efficient, precise dynamic modeling and analysis for complex weapon systems have become more and more important in their dynamic design and performance optimizing. As a new method developed in recent years, the discrete time transfer matrix method of multibody system is highly efficient for multibody system dynamics. In this paper, taking a shipboard gun system as an example, by deducing some new transfer equations of elements, the discrete time transfer matrix method of multibody sys- tem is used to solve the dynamics problems of complex rigid-flexible coupling weapon systems successfully. This method does not need the global dynamic equations of system and has the low order of system matrix, high computational efficiency. The proposed method has advantages for dynamic design of complex weapon systems, and can be carried over straightforwardly to other complex mechanical systems.

关键词：复杂武器系统传递矩阵法离散时间动力学分析多体系统动力学动力学方程复杂机械系统动态设计

Dynamic modeling and H_∞ independent modal space vibration control of laminate plates

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Science China(Physics,Mechanics & Astronomy) 2011年第9期54卷 1638-1650页

作者： RONG Bao RUI XiaoTing wang guoping YANG FuFeng Institute of Launch Dynamics Nanjing University of Science and Technology Nanjing 210094 China

In this paper, combining the transfer matrix method and the finite element method, the modified finite element transfer matrix method is presented for high efficient dynamic modeling of laminated plates. Then, by constructing the modal filter and the disturbance force observer, and using the feedback and feedforward approaches, the H ∞ independent modal space control strategy is designed for active vibration control of laminate plates subjected to arbitrary, immeasurable disturbance forces. Compared with ordinary dynamic modeling and control methods of laminated plate structures, the proposed method has the low memory requirement, high computational efficiency and robust control performance. Formulations as well as some numerical examples are given to validate the method and the control performance.

关键词：独立模态空间动态建模振动控制层压板有限元方法夹层板结构振动主动控制控制性能

Enhancement of catalytic activity for hydrogenation of nitroaromatic by anionic metal-organic framework

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Chinese Chemical Letters 2024年第3期35卷 144-148页

作者： Qi Wu Anyang Li Ruibo He Yaxi Wu Lei Hou guoping Yang Wenyan Zhang Yao-Yu wang Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education College of Chemistry&Materials ScienceNorthwest UniversityXi'an 710127China

Nitroaromatic hydrogenation catalysis without precious metals remains a longstanding challenge.The rate of electron transfer is the crucial factor affecting hydrogenation catalysis.Herein,an ionic Cd-based metal-organic framework(I-Cd-MOF)exhibiting a unique structure with one-dimensional(1D)opening nanochannels and good electron transfer ability was synthesized for catalyzing hydrogenation of 4-nitrophenol(4-NP).The catalytic activity of the unique I-Cd-MOF without noble metals is detected,which is higher than most reported noble metal catalysts.Remarkably,the reaction rate of I-Cd-MOF(4.28 min^(-1))is about 47.6 times higher than that of the Cd-based neutral MOF(N-Cd-MOF)with the similar crystalline structure.Liquid chromatograph mass spectrometer(LC-MS)and theoretical results demonstrate that 4-NP and five intermediates are stabilized in the channels of I-Cd-MOF,which increases the possibility of contact with H^*and H_(2)g enerated at the Cd sites.The I-Cd-MOF was extended to other nitroaromatic hydrogenation catalysis,which still displays excellent activity.More importantly,the I-MOF@Filter membrane was successfully constructed for continuous hydrogenation catalytic reactions,which maintains a high catalytic performance after 7 cycles of recycling without washing.This work fills in the application of the I-MOFs in hydrogenation catalytic reactions and provides an effective way for the rapid and green degradation of nitroaromatic compounds.

关键词： Anions Metal-organic frameworks Catalysis Electron transfer Hydrogen production

An Automatic Implementation of Oropharyngeal Swab Sampling for Diagnosing Respiratory Infectious Diseases via Soft Robotic End-Effectors

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Chinese Journal of Mechanical Engineering 2024年第2期37卷 55-67页

作者： Yafeng Cui Wenjie Yu Jingjing Li Qi Shao Ding Weng guoping Yin Xiaohao Zhang Xinjun Liu Jingying Ye Jiadao wang Huichan Zhao Department of Mechanical Engineering Tsinghua UniversityBeijing 100084China Beijing Huakang Tongbang Technology Company Beijing 102609China Department of Otorhinolaryngology Beijing Tsinghua Changgung HospitalSchool of Clinical MedicineTsinghua UniversityBeijing 102218China Tianjin Research Institute for Advanced Equipment Tsinghua UniversityTianjin 300300China

The most widely adopted method for diagnosing respiratory infectious diseases is to conduct polymerase chain reaction(PCR)assays on patients’respiratory specimens,which are collected through either nasal or oropharyngeal swabs.The manual swab sampling process poses a high risk to the examiner and may cause false-negative results owing to improper sampling.In this paper,we propose a pneumatically actuated soft end-effector specifically designed to achieve all of the tasks involved in swab sampling.The soft end-effector utilizes circumferential instability to ensure grasping stability,and exhibits several key properties,including high load-to-weight ratio,error tolerance,and variable swab-tip stiffness,leading to successful automatic robotic oropharyngeal swab sampling,from loosening and tightening the transport medium tube cap,holding the swab,and conducting sampling,to snapping off the swab tail and sterilizing itself.Using an industrial collaborative robotic arm,we integrated the soft end-effector,force sensor,camera,lights,and remote-control stick,and developed a robotic oropharyngeal swab sampling system.Using this swab sampling system,we conducted oropharyngeal swab-sampling tests on 20 volunteers.Our Digital PCR assay results(RNase P RNA gene absolute copy numbers for the samples)revealed that our system successfully collected sufficient numbers of cells from the pharyngeal wall for respiratory disease diagnosis.In summary,we have developed a pharyngeal swab-sampling system based on an“enveloping”soft actuator,studied the sampling process,and imple-mented whole-process robotic oropharyngeal swab-sampling.

关键词： Diagnosis Medical robot Soft end-effector Swab-sampling Digital PCR

Efficacy and safety of anlotinib combined with the STUPP regimen in patients with newly diagnosed glioblastoma:a multicenter,single-arm,phase II trial

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Cancer Biology & Medicine 2024年第5期21卷 433-444页

作者： Shuzhen Lai Peijing Li Xiaohui Liu Guihong Liu Tieming Xie Xing Zhang Xiaoxuan wang Jing Huang Yiqiang Tang Zhigang Liu guoping Shen Chaoming Li Fangxiao Lu Lei wang Fagui Jiang Caixing Sun Yuanyuan Chen Ming Chen Department of Radiation Oncology The Second Affiliated Hospital of Soochow UniversitySuzhou 215000China Department of Radiation Oncology Yuebei People’s Hospital Affiliated to the Medical College of Shantou UniversityShaoguan 512026China Chinese Academy of SciencesHangzhou 310022China Department of Radiation Oncology The Second Clinical Medical College of Zhejiang Chinese Medical UniversityHangzhou 311403China Department of Radiation Oncology The Affiliated Hospital of Xuzhou Medical UniversityXuzhou 221004China Chinese Academy of SciencesHangzhou 310022China State Key Laboratory of Translational Medicine and Innovative Drug Development Jiangsu Simcere Diagnostics Co.LtdNanjing 210000China Department of Radiation Oncology The Affiliated Huai’an First People’s Hospital of Nanjing Medical UniversityHuai’an 223399China Department of Radiation Oncology Jiangxi Cancer Hospital of Nanchang UniversityNanchang 330029China Department of Radiotherapy Dongguan Institute of Clinical Cancer ResearchDongguan Key Laboratory of Precision Diagnosis and Treatment for TumorsAffiliated Dongguan HospitalSouthern Medical UniversityDongguan 523059China The Cancer Center The Fifth Affiliated Hospital of Sun Yat-Sen UniversityZhuhai 519000China Department of Radiation Oncology The First Affiliated Hospital of Sun Yat-Sen UniversityGuangzhou 510080China Department of Oncology Maoming People’s HospitalMaoming 525000China Department of Radiation Oncology Kecheng District People’s HospitalQuzhou 324003China Chinese Academy of SciencesHangzhou 310022China Department of Radiation Oncology State Key Laboratory of Oncology in South ChinaSun Yat-sen University Cancer CenterGuangzhou 510060China United Laboratory of Frontier Radiotherapy Technology of Sun Yat-sen University&Chinese Academy of Sciences Ion Medical Technology Co. LtdGuangzhou 510060China

Objective:Glioblastomas are highly vascularized malignant tumors.We determined the efficacy and safety of the anti-angiogenic multi-kinase inhibitor,anlotinib,for a newly diagnosed glioblastoma.Methods:This multicenter,single-arm trial(NCT04119674)enrolled 33 treatment-naïve patients with histologically proven glioblastomas between March 2019 and November 2020.Patients underwent treatment with the standard STUPP regimen[fractionated focal irradiation in daily fractions of 1.8-2 Gy given 5 d/w×6 w(total=54-60 Gy)]or radiotherapy plus continuous daily temozolomide(TMZ)(75 mg/m^(2)of body surface area/d,7 d/w from the first to the last day of radiotherapy),followed by 6 cycles of adjuvant TMZ(150-200 mg/m^(2)×5 d during each 28-d cycle)plus anlotinib(8 mg/d on d 1-14 of each 3-w cycle for 2 cycles during concomitant chemoradiotherapy,8 maximal cycles as adjuvant therapy,followed by maintenance at 8 mg/d.The primary endpoint was progression-free survival(PFS).Secondary endpoints included overall survival(OS)and adverse events(AEs).Results:Thirty-three patients received the planned treatment.The median PFS was 10.9 months(95%CI,9.9-18.7 months)and the 12-month PFS rate was 48.5%.The median OS was 17.4 months(95%CI,14.5-21.1 months)and the 12-month OS rate was 81.8%.The most common AEs included hypertriglyceridemia[58%(n=19)],hypoalbuminemia[46%(n=15)],and hypercholesterolemia[46%(n=15)]during concurrent chemoradiotherapy and leukopenia[73%(n=24)],hypertriglyceridemia[67%(n=22)],and neutropenia[52%(n=17)]during adjuvant therapy.Five patients discontinued treatment due to AEs.HEG1(HR,5.6;95%CI,1.3-23.7;P=0.021)and RP1L1 alterations(HR,11.1;95%CI,2.2-57.2;P=0.004)were associated with a significantly shorter PFS.Conclusions:Anlotinib plus the STUPP regimen has promising anti-tumor activity against glioblastoma and manageable toxicity.HEG1 and RP1L1 alterations might be novel predictive biomarkers of the response to anlotinib.

关键词： Glioblastoma anti-angiogenesis multi-kinase inhibitor anlotinib temozolomide progression-free survival

The Differential Equation Algorithm for General Deformed Swept Volumes

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Journal of Computer Science & Technology 2000年第6期15卷 604-610页

作者：汪国平华宣积孙家广 DepartmentofComputerScienceandTechnology PekinUniversityBeijing100871P.R.China

The differential equation approach for characterizing swept volume boundaries is extended to include objects experiencing deformation. For deformed swept volume, it is found that the structure and algorithm of sweep-envelope differential equation (SEDE) are similar between the deformed and the rigid swept volumes. The efficiency of SEDE approach for deformed swept volume is proved with an example.

关键词： CAD geometric modeling sweeping motion deformation swept volume

An Approach towards Synthesis of Nanoarchitectured LiNi1/3Co1/3Mn1/3O2 Cathode Material for Lithium Ion Batteries

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中国化学:英文版 2015年第2期33卷 261-267页

作者： Weibo Hua Yanjie wang Yanjun Zhong guoping wang Benhe Zhong Baizeng Fang Xiaodong Guo Shixuan Liao Haijiang wang College of Chemical Engineering Sichuan UniversityChengduSichuan 610065China Department of Chemical and Biological Engineering University of British Columbia2360 East MallVancouverBCCanadaV6T 1Z3 Institute for Fuel Cell Innovation National Research Council of Canada4250 Wesbrook MallVancouverBC V6T 1W5Canada College of Chemical Engineering University of South ChinaHengyangHunan 421001China

To explore advanced cathode materials for lithium ion batteries(LIBs),a nanoarchitectured LiNi_(1/3)Co_(1/3)Mn_(1/3)O_(2)(LNCM)material is developed using a modified carbonate coprecipitation method in combination with a vacuum distillation-crystallisation process.Compared with the LNCM materials produced by a traditional carbonate copre-cipitation method,the prepared LNCM material synthesized through this modified method reveals a better hexago-nal layered structure,smaller particle sizes(ca.110.5 nm),and higher specific surface areas.Because of its unique structural characteristics,the as-prepared LNCM material demonstrates excellent electrochemical properties in-cluding high rate capability and good cycleability when it is utilized as a cathode in the lithium ion battery(LIB).

关键词： cathode materials nanoarchitectured coprecipitation electrochemical properties lithium ion battery