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| 1 | De novo assembly of a Chinese soybean genome显示文摘Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for 'Zhonghuang 13' by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future. | Yanting Shen Jing Liu Haiying Geng Jixiang Zhang Yucheng Liu Haikuan Zhang Shilai Xing Jianchang Du Shisong Ma Zhixi Tian | 2018 | Science China(Life Sciences)2018，61，8： | 11 |
| 2 | Cloning of Ln Gene Through Combined Approach of Map-based Cloning and Association Study in Soybean显示文摘Increasing yield is one of the most important goals in crop breeding.Soybean(Glycine max L.Merr.),one of the most economically important leguminous seed crops,provides the majority of plant proteins,and more than a quarter of the world's food and animal feed(Graham and Vance,2003). The yield of soybean is finally determined by the number of seeds per unit area,which affected by many characters,such as height,branching number,photosynthesis,seed size,seed number.The number of seeds per pod is taken for one of the critical components that related to yield(You et al.,1995),and it has long been considered in soybean production(Takahashi, | Chao Fang Weiyu Li Guiquan Li Zheng Wang Zhengkui Zhou Yanming Ma Yanting Shen Congcong Li Yunshuai Wu Baoge Zhu Weicai Yang Zhixi Tian | 2013 | Journal of Genetics and Genomics2013，40，2： | 7 |
| 3 | Efficacy and advantages of modified Traditional Chinese Medicine treatments based on'kidney reinforcing'for chronic aplastic ane-mia:a randomized controlled clinical trial显示文摘OBJECTIVE:To compare the efficacy of modified treatments based on 'kidney reinforcing' in the management of chronic aplastic anemia(CAA),and explore their advantages and specialties.METHODS:One hundred and eleven patients with CAA were randomly divided into three groups:kidney reinforcing alone(KA),'kidney reinforcing and Qi tonifying'(KQ),and 'kidney reinforcing and blood circulation invigorating'(KC).Normal and positive control groups were also formed.All patients were treated for 6 months(two courses).Hemograms,Traditional Chinese Medicine(TCM) syndrome scores,and therapeutic effects were assessed,and changes in T-lymphocyte subsets,regulatory T cells and cytokines were detected.RESULTS:The KQ and KC groups had lower TCM syndrome scores than the positive control group after 6 months(P < 0.05).The KQ group had a higher overall efficacy than the positive control group after 3 months(P < 0.05),while platelet counts increased in the KC group after 6 months(P < 0.05).CD3+ T-lymphocyte ratios decreased only in the KQ group,while CD3 + CD4 + CD8-Tlymphocytes increased only in the KC group after 6 months(P <0.05).Levels of interferon-γ,tumor necrosis fac-tor-α,interleukin(IL)-2 and IL-6 decreased and levels of IL-4 and IL-10 increased in all treated groups after 6 months.Levels of IL-6 in the KQ and KC groups were lower than those in the positive control group(P < 0.05).CONCLUSION:Treatments based on kidney reinforcing have a rebalancing effect on cytotoxic and T helper cells,and regulate expression of interferon-γ,IL-2,IL-6 and IL-4.KQ may be more effective in treating CAA,and KC may have an advantage in platelet recovery. | Wu Dijiong Shen Yiping Ye Baodong Fang Bingmu Lin Shengyun Chen Zhilu Jiang Huifang Feng Changwei He Lüyuan Gao Yanting Liu Yonglin Liu Yonghua Zhu Jiajia Wu Liqiang Shao Keding Zhou Yuhong | 2016 | Journal of Traditional Chinese Medicine2016，36，4： | 6 |
| 4 | Update soybean Zhonghuang 13 genome to a golden reference显示文摘Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13 (Shen et al.,2018,Yang and Huang,2018).However,due to technical limitations at the time when we generated Gmax_ZH13,a large number of small contigs were not anchored onto chromosomes.Therefore,we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads.Furthermore,we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes. | Yanting Shen Huilong Du Yucheng Liu Lingbin Ni Zheng Wang Chengzhi Liang Zhixi Tian | 2019 | Science China(Life Sciences)2019，62，9： | 6 |
| 5 | Design and baseline data of a populationbased metabonomics study of eye diseases in eastern China: the Yueqing Ocular Diseases Investigation显示文摘Background:China is undergoing a massive transition toward an urban and industrial economy.These changes will restructure the demographics and economy which will eventually influence the future patterns of disease.The risk factors of vision-impairing eye diseases remain ambiguous and poorly understood.Metabolomics is an ideal tool to understand and shed light on the ocular disease mechanisms for earlier treatment.This article aims to describe the design,methodology and baseline data of the Yueqing Ocular Diseases Investigation(YODI),a developed county population-based study to determine the prevalence and primary causes of visual impairment;also with metabonomics analysis we aimed to identify,predict and suggest some preventive biomarkers that cause blindness.Methods:A population-based,cross-sectional study.Randomized clustering sampling was used to identify adults aged 50 years and older in Xiangyang Town,Yueqing county-level City.The interviews covered demographic,behavioral,ocular risk factors and mental health state.The ocular examination included visual acuity,autorefraction,intraocular pressure,anterior and posterior segment examinations,fundus photography,retinal tomography and angiography,and visual field testing.Anthropometric measurements included height and weight,waist and hip circumference,blood pressure,pulse rate,electrocardiogram,and abdominal ultrasound scan.A venous blood sample was collected for laboratory tests and metabonomics studies.Results:Of the 5319 individuals recruited for the YODI,4769(89.7%)subjects were enrolled for analyses.The median age was 62.0 years,and 45.6%were male.The educational level of illiteracy or semi-illiteracy,primary,middle and high school or above was 29.8%,45.5%,20.1%,and 3.3%,respectively.Majority of the participants were female,younger,and less educated when compared with nonparticipants.The average body mass index and waist-hip ratios were 24.4±3.4 kg/m^(2) and 0.9±0.1 respectively.Blood sample collection reached a sample size of 1909(479 from subjects with selfreported diabetes and 1430 from one-third of the 4290 subjects without self-reported diabetes).Conclusions:The YODI provides population-based data with a high response rate(89.7%)on the prevalence and primary causes of major vision-impairing eye diseases in developed county areas in eastern China.Metabonomics analysis from YODI will provide further association of metabolic characteristics with the visual impairment eye diseases.The risk prediction model could be created and has the potential to be generalized to developed eastern areas in China for prevention. | Yuxuan Deng Yuanbo Liang Sigeng Lin Liang Wen Jin Li Yue Zhou Meixiao Shen Jingwei Zheng Kemi Feng Yanting Sun Kwapong Willaim Robert Jia Qu Fan Lu | 2020 | Eye and Vision2020，7，1： | 4 |
| 6 | MicroRNA-15b regulates cell cycle progression by targeting cyclins in glioma cells显示文摘 | Hongping Xia Yanting Qi Samuel S. Ng Xiaona Chen Shen Chen Marong Fang Dan Li Yu Zhao Ruiguang Ge Guo Li Yangchao Chen Ming-Liang He Hsiang-fu Kung Lihui Lai Marie C. Lin | 2009 | Biochemical and Biophysical Research Communications2009，，2： | 1 |
| 7 | microRNA-146b inhibits glioma cell migration and invasion by targeting MMPs显示文摘 | Hongping Xia Yanting Qi Samuel S. Ng Xiaona Chen Dan Li Shen Chen Ruiguang Ge Songshan Jiang Guo Li Yangchao Chen Ming-Liang He Hsiang-fu Kung Lihui Lai Marie C. Lin | 2008 | Brain Research2008，，： | 1 |
| 8 | Transcriptome Analysis of Pacific White Shrimp (Litopenaeus vannamei) Under Prolonged High-Salinity Stress显示文摘The Pacific white shrimp(Litopenaeus vannamei)is a marine species commonly farmed worldwide.In northern China,it has been increasingly cultured in high-salinity waters(>40),but exhibits poor growth performance.In this study,postlarval shrimps were acclimated to salinity 55,cultivated for 3 months at this salinity,and compared with a control group reared at general salinity 25.Subsequently,high-throughput RNA sequencing was applied to compare the transcriptomic responses in the gills and hepatopancreas of the shrimps in the control group and the treatment group,while the weights of the shrimps in these two groups were significantly different.The results revealed that 11834 and 2115 genes were significantly differentially expressed in the gills and hepatopancreas,respectively.Additionally,enrichment analysis of the differentially expressed genes indicated that osmoregula-tion-associated Gene Ontology terms and KEGG pathways were similar between the two subgroups of the shrimp maintained at high salinity,suggesting that the growth rate of shrimp at high salinity is independent of osmoregulation.Furthermore,examination of the shrimp with different growth rates(i.e.,weights)at high salinity revealed molt-associated processes,namely,increased expression of ecdysone response genes and downstream effector genes in the gills and hepatopancreas of slow-growing shrimp,suggesting a role of the molt-associated processes in the regulation of shrimp growth at high salinity.Thus,we not only report adaptive transcriptomic responses of L.vannamei to prolonged high-salinity stress,but also provide new insights into the shrimp growth regulation at high salinity. | LI Yuquan CHEN Yigeng CUI Yanting SHEN Min WANG Renjie WANG Zhongkai | 2022 | Journal of Ocean University of China2022，21，2： | 0 |
| 9 | Water transport of native and exotic tree species in relation to xylem anatomical characteristics in low subtropical China显示文摘Aims Exotic fast-growing tree species have been commonly planted as pioneer species to facilitate ecological restoration in South China.Their growth and resource utilization behavior related to intrinsic physiology and structural properties have profound influences on forest ecosystem.However,the contrastive research focusing on water utilization features along with xylem anatomical properties between native and exotic species is scarce in South China.The objective of this study is to investigate the sapwood anatomical characteristics and water utilization conditions of native and exotic fast-growing species,and to elucidate the relationship between sap-flux density and conduit features.Methods We measured sap-flux density,conduit length,diameter and density of four native species(Schima superba,Michelia mac-clurei,Castanopsis hystrix and Castanopsis fissa)and four exotic species(Eucalyptus citriodora,Eucalyptus urophylla×grandis,Acacia auriculaeformis and Acacia mangium).Sap flux density was measured based on the Granier’s thermal dissipation probe method.The whole-tree water transport was quantified by mul-tiplying sap-flux density by sapwood area.The measurements of conduit characteristics were conducted by using segregation and slice method.Important Findings Sapwood area increased with the growing diameter at breast height(DBH)as a power function.Native species had a larger water-conducting tissue area than exotic species at the same DBH value when trees grew to a size with a certain value of DBH.The con-duit diameter of exotic species was significantly larger than that of native species.Conversely,native species,such as S.superba and M.macclurei,had longer conduit length and higher conduit den-sity than other tree species.Based on a physiological interpretation of the measured conduit characteristics,native tree species devel-oped a safe water transport system while exotic fast-growing tree species come into being an efficient system instead.Water trans-port increased with the growing DBH as a power function,and the exponent for native species(1.60)was higher than that for exotic species(1.22).Under the combined impact of sap-flux density and sapwood area,native species presented a larger water transport at a larger DBH value,indicating that growth advantage of exotic fast-growing species might weaken as DBH increased. | Yanting Hu Jianguo Gao Ping Zhao Weijun Shen Peiqiang Zhao Liwei Zhu Guangyan Ni Junfeng Niu Lei Ouyang | 2018 | Journal of Plant Ecology2018，11，3： | 0 |
| 10 | The use of an oxidative stress scoring systemin prognostic prediction for kidney renal clear cell carcinoma显示文摘Dear editor,Oxidative stress induced by reactive oxygen species(ROS)production plays a key role in tumor initiation and progression[1,2].Emerging evidence has shown that oxidative stress-related genes could be used as biomarkers for predicting the progression and prognosis of malignant tumors[3].Our previous study showed that the expression and genotypes of oxidative stress-related genes could be used for predicting the chemosensitivity and clinical outcomes of biliary tract cancer patients[4]. | Xianjin Wang Huan Xu Miaomiao Guo Yanting Shen Peizhang Li Zhong Wang Ming Zhan | 2021 | Cancer Communications2021，41，4： | 0 |
| 11 | A temperature-regulated bioorthogonal reaction to target lysine:Hemiacetal pharmacophore in genipin irreversibly binds with UCP2,inhibiting mitochondrial thermogenesis显示文摘Mitochondria are essential for eukaryotic life as powerhouses for energy metabolism. Excessive mitochondrial hyperthermia and reactive oxygen species(ROS) production have been associated with aging, cancer,neurodegenerative diseases, and other disorders. Uncoupling protein 2(UCP2) is the effector responsible for regulating cellular thermogenesis and ROS production via dissipating protons in an electrochemical gradient. A UCP2 inhibitor named genipin(GNP) is being researched for its effect on mitochondrial temperature, but little is known about its mechanisms. This study developed several molecular probes to explore the interactions between GNP and UCP2. The result indicated that the hemiacetal structure in GNP could selectively react with the ?-amine of lysine on the UCP2 proton leakage channel through ringopening condensation at the mitochondrial, cellular, and animal levels. A notable feature of the reaction is its temperature sensitivity and ability to conjugate with UCP2 at high fever as lysine-specific covalent inhibitors that prevent mitochondrial thermogenesis. The result not only clarifies the existence of an antipyretic properties of GNP via its irreversible coupling to UCP2, but also reveals a bioorthogonal reaction of hemiacetal iridoid aglycone for selectively binding with the ?-amine of lysine on proteins. | Fukui Shen Wen Yang Kaixue Zhang Yanting Jiao Jing Cui Yuanyuan Hou Gang Bai | 2023 | Chinese Chemical Letters2023，34，10： | 0 |
| 12 | Workload Allocation Based on User Mobility in Mobile Edge Computing显示文摘Mobile Edge Computing(MEC)has become the most possible network architecture to realize the vision of interconnection of all things.By offloading compute-intensive or latency-sensitive applications to nearby small cell base stations(sBSs),the execution latency and device power consumption can be reduced on resource-constrained mobile devices.However,computation delay of Mobile Edge Network(MEN)tasks are neglected while the unloading decision-making is studied in depth.In this paper,we propose a workload allocation scheme which combines the task allocation optimization of mobile edge network with the actual user behavior activities to predict the task allocation of single user.We obtain the next possible location through the user's past location information,and receive the next access server according to the grid matrix.Furthermore,the next time task sequence is calculated on the base of the historical time task sequence,and the server is chosen to preload the task.In the experiments,the results demonstrate a high accuracy of our proposed model. | Tengfei Yang Xiaojun Shi Yangyang Li Binbin Huang Haiyong Xie Yanting Shen | 2020 | Journal on Big Data2020，2，3： | 0 |
| 13 | SoyOmics:A deeply integrated database on soybean multi-omics显示文摘Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession'Williams82'opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired. | Yucheng Liu Yang Zhang Xiaonan Liu Yanting Shen Dongmei Tian Xiaoyue Yang Shulin Liu Lingbin Ni Zhang Zhang Shuhui Song Zhixi Tian | 2023 | Molecular Plant2023，16，5： | 0 |
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