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| 1 | The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals显示文摘Metabolic diseases are the most common and rapidly growing health issues worldwide.The massive population-based human genetics is crucial for the precise prevention and intervention of metabolic disorders.The China Metabolic Analytics Project(ChinaMAP)is based on cohort studies across diverse regions and ethnic groups with metabolic phenotypic data in China.Here,we describe the centralized analysis of the deep whole genome sequencing data and the genetic bases of metabolic traits in 10,588 individuals from the ChinaMAP.The frequency spectrum of variants,population structure,pathogenic variants and novel genomic characteristics were analyzed.The individual genetic evaluations of Mendelian diseases,nutrition and drug metabolism,and traits of blood glucose and BMI were integrated.Our study establishes a large-scale and deep resource for the genetics of East Asians and provides opportunities for novel genetic discoveries of metabolic characteristics and disorders. | Yanan Cao Lin Li Min Xu Zhimin Feng Xiaohui Sun Jieli Lu Yu Xu Peina Du Tiange Wang Ruying Hu Zhen Ye Lixin Shi Xulei Tang Li Yan Zhengnan Gao Gang Chen Yinfei Zhang Lulu Chen Guang Ning Yufang Bi Weiqing Wang The ChinaMAP Consortium | 2020 | Cell Research2020，30，9： | 20 |
| 2 | Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities显示文摘Hydrogenotrophic denitrification is promising for tertiary nitrogen removal from municipal wastewater. To reveal the influence of residual organics in municipal wastewater on hydrogenotrophic denitrifiers, we adopted high-throughput 16 S r RNA gene amplicon sequencing to examine microbial communities in hydrogenotrophic denitrification enrichments. Using effluent from a municipal wastewater treatment plant as water source, COD,nitrate and p H were controlled the same except for a gradient of biodegradable carbon(i.e., primary effluent(PE), secondary effluent(SE), or combined primary and secondary effluent(CE)). Inorganic synthetic water(IW) was used as a control. Hydrogenophaga, a major facultative autotroph, accounted for 17.1%, 5.3%, 32.7% and 12.9% of the sequences in PE, CE,SE and IW, respectively, implicating that Hydrogenophaga grew well with or without organics.Thauera, which contains likely obligate autotrophic denitrifiers, appeared to be the most dominant genera(23.6%) in IW and accounted for 2.5%, 4.6% and 8.9% in PE, CE and SE,respectively. Thermomonas, which is related to heterotrophic denitrification, accounted for 4.2% and 7.9% in PE and CE fed with a higher content of labile organics, respectively.In contrast, Thermomonas was not detected in IW and accounted for only 0.6% in SE. Our results suggest that Thermomonas are more competitive than Thauera in hydrogenotrophic denitrification with biodegradable organics. Moreover, facultative autotrophic denitrifiers,Hydrogenophaga, are accommodating to residual organic in effluent wastewater, thus we propose that hydrogenotrophic denitrification is amenable for tertiary nitrogen removal. | Wei Xing Jinlong Li Peng Li Chong Wang Yanan Cao Desheng Li Yunfeng Yang Jizhong Zhou Jiane Zuo | 2018 | Journal of Environmental Sciences2018，30，3： | 16 |
| 3 | The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication显示文摘Coix is a grass crop domesticated as early as the Neolithic era.It is still widely cultivated for both highly nutritional food and medicinal use.However,the genetic study and breeding of this crop are hindered by the lack of a sequenced genome.Here,we report de novo sequencing and assembly of the 1619-Mb genome of Coix,and annotation of 75.39%repeats and 39629 protein-coding genes.Comparative genomics analysis showed that Coix is more closely related to sorghum than maize,but intriguingly only Coix and maize had a recent genome duplication event,which was not detected in sorghum.We further constructed a genetic map and mapped several important traits,especially the strength of hull.Selection of papery hull(thin:easy dehulling)from the stony hull(thick:difficult dehulling)in wild progenitors was a key step in Coix domestication.The papery hull makes seed easier to process and germinate.Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis.We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci(QTLs),which are associated with hull thickness and color,respectively.The two QTLs were further fine mapped within intervals of 250 kb and 146 kb,respectively.These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop. | Chao Guo Yanan Wang Aiguo Yang Jun He Chaowen Xiao Shanhua Lv Fengming Han Yibing Yuan Yuan Yuan Xiaolong Dong Juan Guo YawenYang-Hailan Liu Ningzhi Zuo Yaxi Hu Kangxu Zhao Zhengbo Jiang Xing Wang Tingting Jiang Yaou Sherf Moju Cao Yuan Wang Zhaobo Long Tingzhao Rong Luqi Huang Shufeng Zhou | 2020 | Molecular Plant2020，13，2： | 11 |
| 4 | De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments显示文摘Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments. | ZHEN Gang ZHANG Lei DU YaNan YU RenBo LIU XinMin CAO FangRui CHANG Qi DENG Xing Wang XIA Mian HE Hang | 2015 | Science China(Life Sciences)2015，58，11： | 6 |
| 5 | Grain nucleation and growth behavior of a Sn-Pb alloy affected by direct current: An in situ investigation显示文摘In situ synchrotron X-ray radiography was used to study the effect of direct current(DC) on the grain nucleation and growth of Sn-50 wt.%Pb alloy. The results showed that applying DC adequately during solidification could effectively enhance the grain nucleation and inhibit its growth. Imaging of comparative experiments with varying DC intensity indicated that the final grain size, determined by the competition between grain nucleation and growth, was sensitively dependent on the DC intensity. It was found that the average grain size was decreased from 1632 to 567 μm with DC density of 1.5 A/mm^2 compared to the case without DC. Beyond this value, raising the current density may cause a significant decrease in the nucleation rate, and thus lead to a coarsening of the grain structure. | Fenfen Yang Zongning Chen Fei Cao Rong Fan Huijun Kang Wanxia Huang Qingxi Yuan Tiqiao Xiao Yanan Fu Tongmin Wang | 2017 | Journal of Materials Science & Technology2017，33，10： | 5 |
| 6 | The temporal dynamics of antimicrobial-resistant Salmonella enterica and predominant serovars in China显示文摘Salmonella enterica is one of the most common bacterial pathogens in humans and animals.Systematic studies on the trends and geographical distribution of antimicrobial-resistant Salmonella and dominant serovars have been well studied in European and American countries while not in China.Here,taking the One-Health strategy,we used>35000 Salmonella enterica isolates to explore the temporal and spatial dynamics of dominant serovars in China.We found that Salmonella Typhimurium was the dominant serovar causing human infection in China,which was consistent with Australia but inconsistent with North American and European countries.The proportion of Salmonella serovars Typhimurium,London,Rissen,Corvallis,Meleagridis,Kentucky,and Goldcoast showed an increasing trend during 2006-2019.We randomly selected 1962 isolates for comparative genomics and antimicrobial resistance studies and found that the number of antibiotic resistance genes(ARGs)per isolate increased 1.84 and 2.69 times of human and non-human origins,respectively,spanning 14 years.The proportion of antimicrobial-resistant Salmonella isolates had an increasing trend during 2006-2019,especially beta-lactam,quinolone,tetracycline,and rifampicin resistance.Moreover,we found that higher diversity of sequence types(STs)in S.Typhimurium than in other serovars,ST34 from pig and ST 19 from chicken origin,were mainly associated with isolates causing child and adult gastro-infection,respectively.Our results fill in the data gap on the trends of dominant serovars and antimicrobial resistance of Salmonella enterica in China.These data provide useful information for public health decision-makers prioritizing interventions for foodborne diseases and food safety. | Yanan Wang Yue Liu Na Lyu Zhiyuan Li Sufang Ma Demin Cao Yuanlong Pan Yongfei Hu Hua Huang George F.Gao Xuebin Xu Baoli Zhu | 2023 | National Science Review2023，10，3： | 4 |
| 7 | Pan-cancer analysis of somatic mutations across 21 neuroendocrine tumor types显示文摘 | Yanan Cao Weiwei Zhou Lin Li Jiaqian Wang Zhibo Gao Yiran Jiang Xiuli Jiang Aijing Shan Matthew H. Bailey Kuan-lin Huang Sam Q. Sun Michael D. McLellan Beifang Niu Weiqing Wang Li Ding Guang Ning | 2018 | Cell Research2018，28，5： | 3 |
| 8 | High-Throughput Rice Density Estimation from Transplantation to Tillering Stages Using Deep Networks显示文摘Rice density is closely related to yield estimation,growth diagnosis,cultivated area statistics,and management and damage evaluation.Currently,rice density estimation heavily relies on manual sampling and counting,which is inefficient and inaccurate.With the prevalence of digital imagery,computer vision(CV)technology emerges as a promising alternative to automate this task.However,challenges of an in-field environment,such as illumination,scale,and appearance variations,render gaps for deploying CV methods.To fill these gaps towards accurate rice density estimation,we propose a deep learningbased approach called the Scale-Fusion Counting Classification Network(SFC^(2)Net)that integrates several state-of-the-art computer vision ideas.In particular,SFC^(2)Net addresses appearance and illumination changes by employing a multicolumn pretrained network and multilayer feature fusion to enhance feature representation.To ameliorate sample imbalance engendered by scale,SFC^(2)Net follows a recent blockwise classification idea.We validate SFC^(2)Net on a new rice plant counting(RPC)dataset collected from two field sites in China from 2010 to 2013.Experimental results show that SFC^(2)Net achieves highly accurate counting performance on the RPC dataset with a mean absolute error(MAE)of 25.51,a root mean square error(MSE)of 38.06,a relative MAE of 3.82%,and a R^(2) of 0.98,which exhibits a relative improvement of 48.2%w.r.t.MAE over the conventional counting approach CSRNet.Further,SFC^(2)Net provides high-throughput processing capability,with 16.7 frames per second on 1024×1024 images.Our results suggest that manual rice counting can be safely replaced by SFC^(2)Net at early growth stages.Code and models are available online at http://gffzzb7e65fbbf9234179s6pnucqcbvn5c60cc.ffgz.tsg.suse.edu.cn/sfc2net. | Liang Liu Hao Lu Yanan Li Zhiguo Cao | 2020 | Plant Phenomics2020，2，1： | 2 |
| 9 | Low-dose intravenous tissue plasminogen activator for acute ischaemic stroke: an alternative or a new standard?显示文摘Background:With the recent publication of a large clinical trial on the use of a lower dose of intravenous(IV)tissue plasminogen activator(tPA)for acute ischaemic stroke(AIS),the concept of using a different dose has been debated.We intend to review the literature on using a lower dose of IV tPA and gain a better understanding of the impact of different IV doses on the treatment of patients with AIS.Methods:A comprehensive literature search of the related topics in PubMed,EMBASE,Web of Science and MEDLINE was carried out.Key words used include low dose IV tPA,thrombolysis,Alteplace and tPA for AIS.Findings were tabulated according to the size of the cohort studied,outcome,adverse event and level of evidence.The results of all studies using lower doses were analysed for efficacy and adverse events.Results:From 1992 to 2016,there were 23 trials that included 10950 patients published on the use of lower doses of IV tPA for AIS.Doses ranged from 0.5,0.6,0.75 to 0.85 mg/kg.Most were observational,retrospective and registry studies.One was a prospective open-label randomised controlled trial.13 trials combined lower doses of IV tPA with a glycoprotein IIb/IIIa inhibitor or thrombectomy.Patients treated with lower doses of IV tPA showed a trend of lower rate of symptomatic intracranial haemorrhage and mortality at 3 months but slightly more disability.Conclusions:Lower doses of IV tPA showed less haemorrhagic events but were not more effective compared with the standard dose.The optimal low dose of IV tPA remains unclear.Patients with AIS with a high risk of developing sypmtomatic intracranial haemorrhage might benefit from lower dose IV tPA,such as 0.6 mg/kg. | Yi Dong Wenjie Cao Xin Cheng Kun Fang Fei Wu Lumeng Yang Yanan Xie Qiang Dong | 2016 | Stroke & Vascular Neurology2016，1，3： | 2 |
| 10 | RPL Based on Triangle Module Operator for AMI Networks显示文摘the routing protocol for low-power and lossy networks(RPL) has been used in advanced metering infrastructure(AMI)which could provide two-way communication between smart meters and city utilities.To improve the network performance of AMI networks, this paper proposed an improved algorithm of RPL based on triangle module operator(IAR-TMO). IAR-TMO proposes membership functions of the following five typical routing metrics: end-to-end delay, number of hops, expected transmission count(ETX),node remaining energy, and child node count.Moreover, IAR-TMO uses triangle module operator to fuse membership functions of these routing metrics. Then, IAR-TMO selects preferred parents(the next hop) based on the triangle module operator. Theoretical analysis and simulation results show that IAR-TMO has a great improvement when compared with two recent representative algorithms: ETXOF(ETX Objective Function) and OF-FL(Objective Function based on Fuzzy Logic), in terms of network lifetime, average end-to-end delay,etc. Consequently, the network performances of AMI networks can be improved effectively. | Yanan Cao Muqing Wu | 2018 | China Communications2018，15，5： | 2 |
| 11 | Three dimensional microstructures and wear resistance of Al-Bi immiscible alloys with different grain refiners显示文摘The three dimensional(3D) microstructures of Al-Bi alloys with different grain refiners(Al-5Ti-B, Al-3B and Al-3Ti) have been studied using synchrotron X-ray microtomography. The relationships between the microstructures and the corresponding wear behavior are verified through the friction and wear tests. The worn surfaces of the samples with grain refiners tested under 15 and 60 N loads are analyzed using Scanning Electron Microscopy(SEM). The results indicate that the addition of grain refiners is beneficial to the size and distribution of the Bi-rich particles in Al-Bi alloys. Compared with Al-5Ti-B and Al-3B grain refiners, the Bi-rich particles are more uniformly distributed and spherical with finer size with the addition of Al-3Ti grain refiner. The refinement renders the Al-20wt%Bi alloy refined by Al-3Ti the superior wear resistance with respect to those refined by Al-5Ti-B and Al-3B grain refiners, corresponding to the microstructures with fine and uniformly distributed Bi-rich particles in the Al matrix. | WANG TongMin CAO Fei CHEN ZongNing KANG HuiJun ZHU Jing FU YaNan XIAO TiQiao LI TingJu | 2015 | Science China(Technological Sciences)2015，58，5： | 2 |
| 12 | The ChinaMAP reference panel for the accurate genotypeimputation in Chinese populations显示文摘Dear Editor,The genotype imputation is an efficient and pivotal approach to estimate the unobserved genotypes in the genomic data from the single nucleotide polymorphism(SNP)genotyping arrays or whole-genome sequencing(WGS).The fine mapping of variants in the genome-wide association study(GWAS)could be critically improved by the imputation with an optimal reference panel based on the population-specific haplotypes. | Lin Li Peide Huang Xiaohui Sun Siyu Wang Min Xu Sha Liu Zhimin Feng Qing Zhang Xiaoji Wang Xiaole Zheng Mengyao Dai Yufang Bi Guang Ning Yanan Cao Weiqing Wang | 2021 | Cell Research2021，31，12： | 2 |
| 13 | New Small Shelly Fossils(Acanthocassis and Xinlispina Gen.Nov.) from the Fortunian Stage(Early Cambrian) in Southern China显示文摘We describe new material of three-dimensionally phosphatized small shelly fossils Acanthocassis and Xinlispina gen.nov.from the Fortunian Stage(early Cambrian) of southern Shaanxi and northern Sichuan Provinces.The new materials allow description of the delicate morphology of these skeletons, and also their skeletogenesis.Acanthocassis and Xinlispina have comparable morphological features: a main branch and radially arranged sub-branches.They differ from each other in many details, e.g., the presence of a single central branch only in Xinlispina, and the presence of small nodes only in Acanthocassis.Acanthocassis cannot be a naked anthopolyp or hydropolyp because of the more-or-less stiffened cuticle and the absence of a mouth.Acanthocassisand Xinlispina differ from coeval sponge spicules and chancelloriid sclerites and rosettes of crossed pedicellariae of echinoderms, and might be cuticular ornaments of animals of unclear affinities.They occur in the first small shelly fossil assemblage zone, and could be adopted as auxiliary fossils for biostratigraphic correlation in southern China. | SHAO Tiequan LIU Yunhuan WANG Qi ZHANG Huaqiao TANG Hanhua CAO Xi HE Huahua ZHANG Yanan LI Yuan ZHENG Panlin ZHU Chengyu HU Jiaxi | 2015 | Acta Geologica Sinica(English Edition)2015，89，5： | 2 |
| 14 | Silk-based hydrogel incorporated with metal-organic framework nanozymes for enhanced osteochondral regeneration显示文摘Osteochondral defects(OCD)cannot be efficiently repaired due to the unique physical architecture and the pathological microenvironment including enhanced oxidative stress and inflammation.Conventional strategies,such as the control of implant microstructure or the introduction of growth factors,have limited functions failing to manage these complex environments.Here we developed a multifunctional silk-based hydrogel incorporated with metal-organic framework nanozymes(CuTA@SF)to provide a suitable microenvironment for enhanced OCD regeneration.The incorporation of CuTA nanozymes endowed the SF hydrogel with a uniform microstructure and elevated hydrophilicity.In vitro cultivation of mesenchymal stem cells(MSCs)and chondrocytes showed that CuTA@SF hydrogel accelerated cell proliferation and enhanced cell viability,as well as had antioxidant and antibacterial properties.Under the inflammatory environment with the stimulation of IL-1β,CuTA@SF hydrogel still possessed the potential to promote MSC osteogenesis and deposition of cartilage-specific extracellular matrix(ECM).The proteomics analysis further confirmed that CuTA@SF hydrogel promoted cell proliferation and ECM synthesis.In the full-thickness OCD model of rabbit,CuTA@SF hydrogel displayed successfully in situ OCD regeneration,as evidenced by micro-CT,histology(HE,S/O,and toluidine blue staining)and immunohistochemistry(Col I and aggrecan immunostaining).Therefore,CuTA@SF hydrogel is a promising biomaterial targeted at the regeneration of OCD. | Zhicheng Cao Hongmei Wang Jialin Chen Yanan Zhang Qingyun Mo Po Zhang Mingyue Wang Haoyang Liu Xueyang Bao Yuzhi Sun Wei Zhang Qingqiang Yao | 2023 | Bioactive Materials2023，，2： | 2 |
| 15 | Purple-bluish tongue is associated with platelet counts, and the recurrence of epithelial ovarian cancer显示文摘ObjectiveTo 评估在紫色带蓝色的舌头和血小板计数之间的关系,并且推进与 82 个上皮的卵巢的癌症病人全部的上皮的卵巢的 cancer.MethodsA 的复发检验他们的协会在这研究被注册。簇分析被用于组织 patients’P 红绿蓝 (Red-R;Green-G;Blue-B;红绿蓝的平均百分比, P 红绿蓝 ) 价值。接收装置操作特征(巨鸟) 曲线为检测紫色带蓝色的舌头的诊断标准被执行。2 测试被用来估计在紫色带蓝色的舌头和血小板之间的关系上皮的卵巢的癌症的计数,和复发。perioperative (外科手术前) 血小板水平是 examinedwith 舌头图象,疾病 recurrence.ResultsTongue 图象被分类进基于 P 由簇分析的图象的红绿蓝 价值。在簇 “1” 的盒子的数字(正常颜色舌头) 是 16 并且聚类 “2”(紫色带蓝色的舌头) 是 66。二组 P 红绿蓝 价值,由簇分析分类,显著地与基于视觉的舌头颜色识别被相关(Kappa = 0.852, P < 0.001 ) 。巨鸟曲线证明 P b 到 P r 有最高诊断的价值。敏感和 P b 到 P r 分别地是 95.3% 和 88.9% ,最佳的截止的点是 0.71。紫色带蓝色的舌头显著地与增加的血小板计数被相关(P < 0.001 ) 。两个都,增加的血小板数( P = 0.01 )并且紫色带蓝色的舌头与上皮的卵巢的癌症的复发被联系( P < 0.001 ) P b 到 P 当为紫色带蓝色的舌头诊断的指示物在症状模式使用了,比 0.71 大的 r 能服务在繁体中文药的鉴定。紫色带蓝色的舌头,与增加的血小板计数联系了,密切也与上皮的卵巢的癌症的复发被相关。 | Hao Jian Zhu Cuihong Cao Rui Yang Xue Ding Xiuli Man Yanan Wu Xiongzhi | 2016 | Journal of Traditional Chinese Medicine2016，36，3： | 2 |
| 16 | A Novel Qo S Model and Computation Framework in Web Service Selection显示文摘 | Hao Yanan Zhang Yanchun Cao Jinli | 2012 | World Wide Web2012，15，56： | 1 |
| 17 | Boosting imbalanced data learning with Wiener process oversampling显示文摘 | Qian LI Gang LI Wenjia NIU Yanan CAO Liang CHANG Jianlong TAN Li GUO | 2017 | Frontiers of Computer Science2017，11，5： | 1 |
| 18 | Estimating the locations of emergency events from Twitter streams 显示文摘 | AO Ji ZHANG Peng CAO Yanan | 2014 | Procedia Comput- er Science2014，31，1： | 1 |
| 19 | Study on diffusion behavior and microstructural evolution of Al/Cu bimetal interface by synchrotron X-ray radiography显示文摘 | Tongmin Wang Fei Cao Peng Zhou Huijun Kang Zongning Chen Yanan Fu Tiqiao Xiao Wanxia Huang Qingxi Yuan | 2014 | Journal of Alloys and Compounds2014，，： | 1 |
| 20 | Tigecycline resistance tet(X3)gene is going wild显示文摘The emergence of mobile Tigecycline-resistant tet(X3)and tet(X4)is believed to be a global threat to public health.Here,we investigated the prevalence of tet(X3)and tet(X4)in our metagenomic data of migratory birds.While tet(X4)was not identified in our samples,tet(X3)was found in two gut microbiomes of bird fecal samples,with 100%amino acid identity of sites 150–387.These results suggest that tet(X3)has been spreading into the environment for a long period of time and that there is an urgent need to control its further transmission. | Cao Jian Wang Jun Wang Yanan Wang Liang Bi Yuhai Zhu Baoli Fu Gao George | 2020 | Biosafety and Health2020，2，1： | 1 |
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