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| 1 | Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield显示文摘Artemisia annua is the major natural source of artemisinin,an anti-malarial medicine commonly used worldwide.Here,we present chromosome-level haploid maps for two A.annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production.High-fidelity sequencing,optical mapping,and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A.annua.Approximately 5o,ooo genes were annotated for each haplotype genome,and a triplication event that occurred approximately 58.12million years ago was examined for the first time in this species.A total of 3,903,467-5,193,414 variants(SNPs,indels,and structural variants)were identified in the 1.5-Gb genome during pairwise comparison between haplotypes,consistent with the high heterozygosity of this species.Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-dienes ynthasegenes.This correlation was further confirmed by resequencing of 36A.annua samples with varied artemisinin contents.Circular consensus sequencing of transcripts facilitated the detection of paralog expression.Collectively,our study provides chromosome-level allele-aware genome assemblies for two A.annua strains and new insights into the biosynthesis of artemisinin and its regulation,which will contribute to conquering malaria worldwide. | Baosheng Liao Xiaofeng Shen Li Xiang Shuai Guo Shiyu Chen Ying Meng Yu Liang Dandan Ding Junqi Bai Dong Zhang Tomasz Czechowski Yi Li Hui Yao Tingyu Mai Caroline Howard Chao Sun Haitao Liu Jiushi Liu Jin Pei Jihai Gao Jigang Wang Xiaohui Qiu Zhihai Huang Hongyi Li Ling Yuan Jianhe Wei lan Graham Jiang Xu Boli Zhang Shilin Chen | 2022 | Molecular Plant2022，15，8： | 9 |
| 2 | Cholesterol homeostasis regulated by ABCA1 is critical for retinal ganglion cell survival显示文摘Genome-wide association studies have suggested a link between primary open-angle glaucoma and the function of ABCA1.ABCA1 is a key regulator of cholesterol efflux and the biogenesis of high-density lipoprotein(HDL) particles. Here, we showed that the POAG risk allele near ABCA1 attenuated ABCA1 expression in cultured cells. Consistently, POAG patients exhibited lower ABCA1 expression, reduced HDL, and higher cholesterol in white blood cells. Ablation of Abca1 in mice failed to form HDL, leading to elevated cholesterol levels in the retina. Counting retinal ganglion cells(RGCs) by using an artificial intelligence(AI) program revealed that Abca1-deficient mice progressively lost RGCs with age. Single-cell RNA sequencing(scRNA-seq) revealed aberrant oxidative phosphorylation in the Abca1-/-retina, as well as activation of the mTORC1 signaling pathway and suppression of autophagy. Treatment of Abca1-/-mice using atorvastatin reduced the cholesterol level in the retina,thereby improving metabolism and protecting RGCs from death. Collectively, we show that lower ABCA1 expression and lower HDL are risk factors for POAG. Accumulated cholesterol in the Abca1-/-retina causes profound aberrant metabolism, leading to a POAG-like phenotype that can be prevented by atorvastatin. Our findings establish statin use as a preventive treatment for POAG associated with lower ABCA1 expression. | Jialiang Yang Yuhong Chen Tongdan Zou Bai Xue Fang Yang Xiangzhou Wang Yibo Huo Boyun Yan Yuxia Xu Shiyu He Yi Yin Jing Wang Xiong Zhu Lin Zhang Yu Zhou Zhengfu Tai Ping Shuai Man Yu Qian Luo Yilian Cheng Bo Gong Xianjun Zhu Jing Zhang Xinghuai Sun Ying Lin Houbin Zhang Zhenglin Yang | 2023 | Science China(Life Sciences)2023，66，2： | 2 |
| 3 | A Generic Plug-and-Play Navigation Fusion Strategy for Land Vehicles in GNSS-Denied Environment显示文摘Achieving accurate navigation information by integrating multiple sensors is key to the safe operation of land vehicles in global navigation satellite system(GNSS)-denied environment.However,current multi-sensor fusion methods are based on stovepipe architecture,which is optimized with custom fusion strategy for specific sensors.Seeking to develop adaptable navigation that allows rapid integration of any combination of sensors to obtain robust and high-precision navigation solutions in GNSS-denied environment,we propose a generic plug-and-play fusion strategy to estimate land vehicle states.The proposed strategy can handle different sensors in a plug-and-play manner as sensors are abstracted and represented by generic models,which allows rapid reconfiguration whenever a sensor signal is additional or lost during operation.Relative estimations are fused with absolute sensors based on improved factor graph,which includes sensors’error parameters in the non-linear optimization process to conduct sensor online calibration.We evaluate the performance of our approach using a land vehicle equipped with a global positioning system(GPS)receiver as well as inertial measurement unit(IMU),camera,wireless sensor and odometer.GPS is not integrated into the system but treated as ground truth.Results are compared with the most common filtering-based fusion algorithm.It shows that our strategy can process low-quality input sources in a plug-and-play and robust manner and its performance outperforms filtering-based method in GNSS-denied environment. | LAI Jizhou BAI Shiyu XU Xiaowei Lü Pin | 2019 | Transactions of Nanjing University of Aeronautics and Astronautics2019，36，2： | 2 |
| 4 | An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte–tumor cell crosstalk,local immunosuppression and tumor progression显示文摘Dissecting and understanding the cancer ecosystem,especially that around the tumor margins,which have strong implications for tumor cell infiltration and invasion,are essential for exploring the mechanisms of tumor metastasis and developing effective new treatments.Using a novel tumor border scanning and digitization model enabled by nanoscale resolution-SpaTial Enhanced REsolution Omics-sequencing(Stereo-seq),we identified a 500µm-wide zone centered around the tumor border in patients with liver cancer,referred to as“the invasive zone”.We detected strong immunosuppression,metabolic reprogramming,and severely damaged hepatocytes in this zone.We also identified a subpopulation of damaged hepatocytes with increased expression of serum amyloid A1 and A2(referred to collectively as SAAs)located close to the border on the paratumor side.Overexpression of CXCL6 in adjacent malignant cells could induce activation of the JAK-STAT3 pathway in nearby hepatocytes,which subsequently caused SAAs’overexpression in these hepatocytes.Furthermore,overexpression and secretion of SAAs by hepatocytes in the invasive zone could lead to the recruitment of macrophages and M2 polarization,further promoting local immunosuppression,potentially resulting in tumor progression.Clinical association analysis in additional five independent cohorts of patients with primary and secondary liver cancer(n=423)showed that patients with overexpression of SAAs in the invasive zone had a worse prognosis.Further in vivo experiments using mouse liver tumor models in situ confirmed that the knockdown of genes encoding SAAs in hepatocytes decreased macrophage accumulation around the tumor border and delayed tumor growth.The identification and characterization of a novel invasive zone in human cancer patients not only add an important layer of understanding regarding the mechanisms of tumor invasion and metastasis,but may also pave the way for developing novel therapeutic strategies for advanced liver cancer and other solid tumors. | Liang Wu Jiayan Yan Yinqi Bai Feiyu Chen Xuanxuan Zou Jiangshan Xu Ao Huang Liangzhen Hou Yu Zhong Zehua Jing Qichao Yu Xiaorui Zhou Zhifeng Jiang Chunqing Wang Mengnan Cheng Yuan Ji Yingyong Hou Rongkui Luo Qinqin Li Liang Wu Jianwen Cheng Pengxiang Wang Dezhen Guo Waidong Huang Junjie Lei Shang Liu Yizhen Yan Yiling Chen Sha Liao Yuxiang Li Haixiang Sun Na Yao Xiangyu Zhang Shiyu Zhang Xi Chen Yang Yu Yao Li Fengming Liu Zheng Wang Shaolai Zhou Huanming Yang Shuang Yang Xun Xu Longqi Liu Qiang Gao Zhaoyou Tang Xiangdong Wang Jian Wang Jia Fan Shiping Liu Xinrong Yang Ao Chen Jian Zhou | 2023 | Cell Research2023，33，8： | 1 |
| 5 | Understanding recurrent pregnancy loss:recent advances on its etiology,clinical diagnosis,and management显示文摘Recurrent pregnancy loss(RPL)has become an important reproductive health issue worldwide.RPL affects about 2%–3%of reproductive-aged women,and makes serious threats to women’s physical and mental health.However,the etiology of approximately 50%of RPL cases remains unknown(unexplained RPL),which poses a big challenge for clinical management of these patients.RPL has been widely regarded as a complex disease where its etiology has been attributed to numerous factors.Heretofore,various risk factors for RPL have been identified,such as maternal ages,genetic factors,anatomical structural abnormalities,endocrine dysfunction,prethrombotic state,immunological factors,and infection.More importantly,development and applications of next generation sequencing technology have significantly expanded opportunities to discover chromosomal aberrations and single gene variants responsible for RPL,which provides new insight into its pathogenic mechanisms.Furthermore,based upon patients’diagnostic evaluation and etiologic diagnosis,specific therapeutic recommendations have been established.This review will highlight current understanding and recent advances on RPL,with a special focus on the immunological and genetic etiologies,clinical diagnosis and therapeutic management. | Chunwei Cao Shiyu Bai Jing Zhang Xiaoyue Sun Anming Meng Hui Chen | 2022 | Medical Review2022，2，6： | 1 |
| 6 | Design and Optimization of Multiple Interconnected Utility Systems in An Integrated Refining and Petrochemical Complex显示文摘In an integrated refining and petrochemical complex,a centralized utility system(CUS)is introduced to integrate the steam demands of production plants.Besides,two sub-utility systems(SUSs)located inside the alkene and refinery plants,respectively,can satisfy the shaft demands.It is difficult to determine the steam production of the CUS because the steam demands of the alkene and refinery plants also depend on the design and operation of the SUSs.To explore the complicated interaction between the CUS and SUSs,we proposed a mixed-integer nonlinear programming(MINLP)model for the design and optimization of multiple interconnected utility systems to minimize the total annualized cost(TAC).An extended superstructure was suggested to contain multiple inter-plant connected steam pipe alternatives between the CUS and SUSs.A more accurate model of the complex steam turbine was proposed.Then the proposed MINLP framework is applied to a new integrated refining and petrochemical complex.Two scenarios are investigated in the case study to explore the effect of steam main temperatures on system configurations and operating parameters.By optimizing the main temperatures,a TAC of$2.7 million can be saved.Judging from the results of the two scenarios,the feasibility and effectiveness of the proposed framework for the design and optimization of multiple interconnected utility systems have been demonstrated. | Bai Haobo Li Shiyu Wang Xupeng Liu Chang | 2020 | China Petroleum Processing & Petrochemical Technology2020，22，4： | 1 |
| 7 | Principal element design of pyrochlore-fluorite dual-phase medium-and high-entropy ceramics显示文摘1.Introduction Rare earth zirconate(REZrO,RE=La-Lu,Y or Sc)is a kind of significantly important structural or functional ceramic[1,2].It possesses extensive application in numerous fields,such as in thermal barrier coatings(TBCs)[3–5],high-level radioactive wastes[6–8],etc.,due to the excellent thermal stability,low thermal conductivity and low oxygen ion diffusivity.The phase structure of conventional rare earth zirconate is strongly linked with the ionic radius ratio of REto Zr[7,9]. | Wei Fan Yu Bai Yanfen Liu Taotao Li Binmao Li Lei Zhang Chenmin Gao Shiyu Shan Haocen Han | 2022 | Journal of Materials Science & Technology2022，，12： | 1 |
| 8 | Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean显示文摘Advances in plant phenotyping technologies are dramatically reducing the marginal costs of collecting multiple phenotypic measurements across several time points.Yet,most current approaches and best statistical practices implemented to link genetic and phenotypic variation in plants have been developed in an era of single-time-point data.Here,we used time-series phenotypic data collected with an unmanned aircraft system for a large panel of soybean(Glycine max(L.)Merr.)varieties to identify previously uncharacterized loci.Specifically,we focused on the dissection of canopy coverage(CC)variation from this rich data set.We also inferred the speed of canopy closure,an additional dimension of CC,from the time-series data,as it may represent an important trait for weed control.Genome-wide association studies(GWASs)identified 35 loci exhibiting dynamic associations with CC across developmental stages.The time-series data enabled the identification of 10 known flowering time and plant height quantitative trait loci(QTLs)detected in previous studies of adult plants and the identification of novel QTLs influencing CC.These novel QTLs were disproportionately likely to act earlier in development,which may explain why they were missed in previous single-time-point studies.Moreover,this time-series data set contributed to the high accuracy of the GWASs,which we evaluated by permutation tests,as evidenced by the repeated identification of loci across multiple time points.Two novel loci showed evidence of adaptive selection during domestication,with different genotypes/haplotypes favored in different geographic regions.In summary,the time-series data,with soybean CC as an example,improved the accuracy and statistical power to dissect the genetic basis of traits and offered a promising opportunity for crop breeding with quantitative growth curves. | Delin Li Dong Bai Yu Tian Ying-Hui Li Chaosen Zhao Qi Wang Shiyu Guo Yongzhe Gu Xiaoyan Luan Ruizhen Wang Jinliang Yang Malcolm J.Hawkesford James C.Schnable Xiuliang Jin Li-Juan Qiu | 2023 | Journal of Integrative Plant Biology2023，65，1： | 0 |
| 9 | The application of molecular simulation in ash chemistry of coal显示文摘One of the crucial issues in modern ash chemistry is the realization of efficient and clean coal conversion.Industrially,large-scale coal gasification technology is well known as the foundation to improve the atom economy.In practice,the coal ash fusibility is a critical factor to determine steady operation standards of the gasifier,which is also the significant criterion to coal species selection for gasification.Since coal behaviors are resultant from various evolutions in different scales,the multi-scale understanding of the ash chemistry is of significance to guide the fusibility adjustment for coal gasification.Considering important roles of molecular simulation in exploring ash chemistry,this paper reviews the recent studies and developments on modeling of molecular systems for fusibility related ash chemistry for the first time.The discussions are emphasized on those performed by quantum mechanics and molecular mechanics,the two major simulation methods for microscopic systems,which may provide various insights into fusibility mechanism.This review article is expected to present comprehensive information for recent molecular simulations of coal chemistry so that new clues to find strategies controlling the ash fusion behavior can be obtained. | Xin Dai Jin Bai Ping Yuan Shiyu Du Dongtao Li XiaodongWen Wen Li | 2020 | Chinese Journal of Chemical Engineering2020，28，11： | 0 |
| 10 | High-lattice-adapted surface modifying Na_(4)MnV(PO_(4))_(3) for better sodium storage显示文摘Sodium-ion batteries(SIBs)are required to possess long cycle life when used for large-scale energy storage.The polyanionic Na_(4)MnV(PO_(4))_(3)(NMVP)reveals good cyclic stability due to its unique three-dimensional(3D)frame structure,but it still faces the challenge of interfacial degradation in practical applications.In this work,NASICON-type Na_(1.3)Al_(0.7)Ti_(1.3)(PO_(4))_(3)(NATP)was deposited on the surface of NMVP to promote interface stability by surface modification and gradient doping.As a result,the optimized NMVP@2%NATP released a capacity retention of 44.8%after 1000 cycles at 5 C,much higher than that of the initial NMVP(28.9%).The enhanced electrochemical performance was mainly attributed to NATP coating acting as a fast ion transport carrier and physical barrier,significantly facilitating the Na^(+)diffusion and isolating side reaction at the electrode/electrolyte interface.On the other hand,Ti_(4)^(+)and Al^(3+)cations from the NATP were partially doped inside the NMVP surface to boost the transport of Na^(+),and the perfect lattice matching of NVMP and NATP improved the interface and structural stability accompanying long cycling.This work demonstrated the effectiveness of surface modification with high lattice match material and provided new perspectives for high energy density solid-state SIBs. | Chongran Song Shiyu Li Ying Bai | 2024 | Nano Research2024，17，4： | 0 |
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