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PlantcircBase 7.0:Full-length transcripts and conservation of plant circRNAs

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Plant Communications 2022年第4期3卷 64-71页

作者： Xiaoxu Xu Tianyu Du Weihua Mao Xiaohan Li chu-Yu ye Qian-Hao Zhu Longjiang Fan Qinjie chu Institute of Crop Science&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China Shandong(Linyi)Institute of Modern Agriculture of Zhejiang University Linyi 310014China Analysis Center of Agrobiology and Environmental Science Zhejiang UniversityHangzhou 310058China CSIRO Agriculture and Food Black Mountain LaboratoriesCanberraACT 2601Australia

Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and *** years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA ***,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant *** 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the *** this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence *** 7.0 is publicly and freely accessible at http://***/plantcircbase/.

关键词： plant circRNA PlantcircBase conservation full-length transcripts long-read sequencing

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants

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Plant Communications 2022年第3期3卷 102-115页

作者： Dongya Wu Bowen Jiang chu-Yu ye Michael P.Timko Longjiang Fan Hainan Institute of Zhejiang University Yonyou Industrial ParkSanya 572025China Institute of Crop Science&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China Department of Biology University of VirginiaCharlottesvilleVA 22904USA

Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster(BGC)in *** mining of 41 high-quality grass genomes identified complete Bx clusters(containing genes Bx1–Bx5 and Bx8)in three genera(Zea,Echinochloa,and Dichanthelium)of Panicoideae and partial clusters in *** Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx *** ancient Bx cluster that included additional Bx genes(e.g.,Bx6)is presumed to have been present in ancestral *** ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer(HT)from the ancestral Panicoideae and later separated into multiple segments on different ***6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae,as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays,moved to other chromosomes in Echinochloa,and even lost in *** investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass *** study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.

关键词： biosynthetic gene cluster horizontal transfer benzoxazinoid grass purifying selection

Strength failure of spatial reticulated structures under multi-support excitation

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Earthquake Engineering and Engineering Vibration 2011年第1期10卷 21-36页

作者： ye Jihong Zhang Zhiqiang chu ye Key Laboratory of C ＆ PC Structure of Ministry of Education Southeast University Nanjing 210096 China

Under strong earthquakes, long-span spatial latticed structures may collapse due to dynamic instability or strength failure. The elasto-plastic dynamic behaviors of three spatial latticed structures, including two double-layer cylindrical shells and one spherical shell constructed for the 2008 Olympic Games in Beijing, were quantitatively examined under multi-support excitation （MSE） and uniform support excitation （USE）. In the numerical analyses, several important parameters were investigated such as the peak acceleration and displacement responses at key joints, the number and distribution of plastic members, and the deformation of the shell at the moment of collapse. Analysis results reveal the features and the failure mechanism of the spatial latticed structures under MSE and USE. In both scenarios, the double-layer reticulated shell collapses in the ＂overflow＂ mode, and the collapse is governed by the number of invalid plastic members rather than the total number of plastic members, beginning with damage to some of the local regions near the supports. By comparing the numbers and distributions of the plastic members under MSE to those under USE, it was observed that the plastic members spread more sufficiently and the internal forces are more uniform under MSE, especially in cases of lower apparent velocities in soils. Due to the effects of pseudo-static displacement, the stresses in the members near the supports under MSE are higher than those under USE.

关键词： multiple support excitation (MSE) uniform support excitation (USE) elastoplastic spatial latticed structure strength failure

Strength behavior and collapse of spatial-reticulated structures under multi-support excitation

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Science China(Technological Sciences) 2011年第6期54卷 1624-1638页

作者： ye JiHong ZHANG ZhiQiang chu ye Key Laboratory of C & PC Structure of Ministry of Education Southeast University Nanjing 210096 China

Under strong shocks,long-span spatial-latticed structures may collapse due to dynamic instability or strength *** elasto-plastic dynamic behaviors of three spatiallatticed structures,including two double-layer cylindrical shells and a spheri-cal shell used for the 2008 Olympic Games in Beijing,were quantitatively examined under multi-support excitation(MSE) and uniform support excitation(USE).Numerical analyses described several important parameters such as the peak acceleration and displacement responses at key joints,the number and distribution of plastic elements,and the deformation of the shell at the moment of *** of the analysis revealed the features and the failure mechanism of the spatial-latticed structures under MSE and *** both scenarios,the double-layer reticulated shell collapsed in the "overflow" mode,collapse was govrned by the number of invalid plastic elements rather than the total number of plastic elements,and the collapse of the structure began with damage to certain local regions near the *** comparing the numbers and distributions of the plastic members under MSE to those under USE,it was observed that the plastic members spread more sufficiently and the internal forces were more uniform under MSE,especially for lower apparent velocities in *** to the effects of pseudo-static displacement,the stresses in members near supports under MSE were higher than those under *** regions are prone to failure during earthquakes and deserve special attention in the seismic design of reticulated structures.

关键词：网状结构多点激励动态行为倒塌强度 2008年北京奥运会和空间峰值加速度

Clinical efficacy of modified Kamikawa anastomosis in patients with laparoscopic proximal gastrectomy

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World Journal of Gastrointestinal Surgery 2024年第1期16卷 113-123页

作者： chu-Ying Wu Jian-An Lin Kai ye Department of Gastrointestinal Surgery The Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000Fujian ProvinceChina

BACKGROUND With the increasing incidence of proximal gastric cancer,laparoscopic proximal gastrectomy has been ***,reflux esophagitis often occurs after traditional esophagogastric *** order to solve this problem,several methods of digestive tract reconstruction have emerged,but the most satisfying method remains to be ***,we modified traditional Kamikawa anastomosis to investigate the appropriate digestive tract reconstruction in laparo-scopic proximal *** the patients were successfully operated on without conversion to *** duration of operation and digestive tract reconstruction were 203.500(150-224)min and 87.500(73-111)min,*** intraoperative amount of bleeding was 20.500 mL±0.696 *** time of postoperative first flatus,the first postoperative fluid intake,and the postoperative length of stay were 2(1-3)d,4(3-5)d,and 9(8-10)d,*** the patients were followed up for 12-23 *** body mass index at 6 and 12 months after surgery were 22.577 kg/m2±3.098 kg/m2 and 22.594 kg/m2±3.207 kg/m2,*** nutrition risk screening 2002 score,the patient-generated subjective global assessment score,and the gastroesophageal reflux disease scale score were good at 6 and 12 months after *** esophagitis and anastomotic stenosis were not observed in any of the patients during their 12-month postoperative gastroscopy or upper gastrointestinal tract *** the patients exhibited no tumor recurrence or *** The modified Kamikawa anastomosis is safe and feasible for laparoscopic proximal gastrectomy and has good antireflux effects and nutritional status.

关键词： Modified Kamikawa anastomosis Laparoscopy Proximal gastrectomy Antireflux

Orphan Crops and their Wild Relatives in the Genomic Era

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Molecular Plant 2021年第1期14卷 27-39页

作者： chu-Yu ye Longjiang Fan Institute of Crop Sciences&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China Hainan Institute of Zhejiang University Sanya 572024China

More than half of the calories consumed by humans are provided by three major cereal crops(rice,maize,and wheat).Orphan crops are usually well adapted to low-input agricultural conditions,and they not only play vital roles in local areas but can also contribute to food and nutritional needs ***,many wild relatives of orphan crops are important weeds of major *** orphan crops and their wild relatives have received little attentions from researchers for many years,genomic studies have recently been performed on these ***,we provide an overview of genomic studies on orphan crops,with a focus on orphan cereals and their wild *** genomes of at least 12 orphan cereals and/or their wild relatives have been *** addition to genomic benefits for orphan crop breeding,we discuss the potential ways for mutual utilization of genomic data from major crops,orphan crops,and their wild relatives(including weeds)and provide perspectives on genetic improvement of both orphan and major crops(including de novo domestication of orphan crops)in the coming genomic era.

关键词： orphan crop wild relative weed genome crop diversity

Risk factors for the prognosis of colon cancer

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World Journal of Gastrointestinal Oncology 2024年第8期16卷 3738-3740页

作者： chu-Ying Wu Kai ye Department of Gastrointestinal Surgery The Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000Fujian ProvinceChina

A study on clinical outcomes and prognostic factors in T4N0M0 colon cancer patients after R0 resection revealed that ileostomy,T stage,right hemicolectomy,irregular follow-up,and CA199 level were independent risk factors affecting overall survival.T4-stage cancer invades the entire thickness of the intestinal tract,increasing the difficulty of treatment and the risk of recurrence,and requires a combination of chemotherapy,immunotherapy,and targeted therapy to control the spread of cancer *** prognosis of right hemicolectomy is significantly worse than that of left hemicolectomy,and right hemicolectomy is an independent risk factor for a poor *** age,histopathological type,and lymph node metastasis are also risk factors for colon cancer.

关键词： Risk factor Prognosis Colon cancer Tumour stage Right hemicolectomy

Epidemiological and Clinical Characteristics of Non-neonatal Tetanus Patients in Guangxi,China:An 11-year Retrospective Study(2011–2021)

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生物医学与环境科学:英文版 2023年第9期36卷 880-885页

作者： KANG Yi Wen MAI Guo Feng ZHU Xiao Ling DENG Shang Qin YANG Shi Xiong TENG Hong Li YUAN Zong Xiang MO chu ye LIN Jian Yan ye Li TANG Hua Min Guangxi Key Laboratory of AIDS Prevention and Treatment School of Public HealthGuangxi Medical UniversityNanning 530021GuangxiChina Department of Emergency the Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007GuangxiChina The Fourth People's Hospital of Nanning Nanning 530023GuangxiChina Department of Emergency Guangxi International Zhuang Medicine HospitalNanning 530000GuangxiChina

Tetanus is the only non-communicable disease among vaccine-preventable infectious *** is caused by an infection with Clostridium tetanus bacterium and is characterized by continuous tonic contraction and paroxysmal sp... 详细信息

关键词： Tetanus vaccine neonatal

A Support Vector Regression Approach for Recursive Simultaneous Data Reconciliation and Gross Error Detection in Nonlinear Dynamical Systems

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自动化学报 2009年第6期35卷 707-716页

作者： MIAO Yu SU Hong-ye chu Jian National Key Laboratory of Industrial Control Teehnology Institute of Cyber-Systems and Control Zhejiang University Hangzhou 310027 P.R. China

The quality of process data in a chemical plant significantly affects the performance and benefits gained from activities like performance monitoring, online optimization, and control. Since many chemical processes often show nonlinear dynamics, techniques like extended Kalman filter (EKF) and nonlinear dynamic data reconciliation (NDDR) have been developed to improve the data quality. Recently, the recursive nonlinear dynamic data reconciliation (RNDDR) technique has been proposed, which combines the merits of EKF and NDDR techniques. However, the RNDDR technique cannot handle measurements with gross errors. In this paper, a support vector (SV) regression approach for recursive simultaneous data reconciliation and gross error detection in nonlinear dynamical systems is proposed. SV regression is a compromise between the empirical risk and the model complexity, and for data reconciliation it is robust to random and gross errors. By minimizing the regularized risk instead of the maximum likelihood in the RNDDR, our approach could achieve not only recursive nonlinear dynamic data reconciliation but also gross error detection simultaneously. The nonlinear dynamic system simulation results in this paper show that the proposed approach is robust, efficient, stable, and accurate for simultaneous data reconciliation and gross error detection in nonlinear dynamic systems within a recursive real-time estimation framework. It can also give better performance of control.

关键词：数据分析自动化系统智能系统质量数据