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| 1 | Soil physical properties and maize root growth under different tillage systems in the North China Plain显示文摘The standard cultivation system in the North China Plain is double cropping of winter wheat and summer maize. The main effects of this cultivation system on root development and yield are decreases in soil nutrient content and depth of the plow layer under either long-term no-tillage or rotary tillage before winter wheat sowing and no tillage before summer maize sowing. In this study, we investigated the combined effects of tillage practices before winter wheat and summer maize sowing on soil properties and root growth and distribution in summer maize. Zhengdan 958(ZD958) was used as experimental material, with three tillage treatments: rotary tillage before winter wheat sowing and no tillage before summer maize sowing(RTW + NTM), moldboard plowing before winter wheat sowing and no tillage before summer maize sowing(MPW + NTM), and moldboard plowing before winter wheat sowing and rotary tillage before summer maize sowing(MPW + RTM).Tillage practice showed a significant(P < 0.05) effect on grain yield of summer maize. Grain yields under MPW + RTM and MPW + NTM were 30.6% and 24.0% higher, respectively, than that under RTW + NTM. Soil bulk density and soil penetration resistance decreased among tillage systems in the order RTW + NTM > MPW + NTM > MPW + RTM. Soil bulk densities were 3.3% and 515% lower in MPW + NTM and MPW + RTM, respectively, than that in RTW + NTM, and soil penetration resistances were respectively 17.8% and 20.4% lower,across growth stages and soil depths. Root dry matter and root length density were highest under MPW + RTM, with the resulting increased root activity leading to a yield increase of summer maize. Thus the marked effects of moldboard plowing before winter-wheat sowing on root length density, soil penetration resistance, and soil bulk density may contribute to higher yield. | Baizhao Ren Xia Li Shuting Dong Peng Liu Bin Zhao Jiwang Zhang | 2018 | The Crop Journal2018，6，6： | 10 |
| 2 | A Virulent PEDV Strain FJzz1 with Genomic Mutations and Deletions at the High Passage Level Was Attenuated in Piglets via Serial Passage In Vitro显示文摘Highly virulent porcine epidemic diarrhea virus(PEDV)strains re-emerged and circulated in China at the end of 2010,causing significant economic losses in the pork industry worldwide.To understand the genetic dynamics of PEDV during its passage in vitro,the PEDV G2 strain FJzzl was serially propagated in Vero cells for up to 200 passages.The susceptibility and adaptability of the FJzzl strain increased gradually as it was serially passaged in vitro.Sequence analysis revealed that amino acid(aa)changes were mainly concentrated in the S glycoprotein,which accounted for 72.22%-85.71%of all aa changes.A continuous aa deletion(^(55)I^(56)G^(57)E→^(55)K^(56)Δ^(57)Δ)occurred in the N-terminal domain of S1(Sl-NTD).To examine how the aa changes affected its virulence,FJzzl-F20 and FJzzl-F200 were selected to simultaneously evaluate their pathogenicity in suckling piglets.All the piglets in the FJzzl-F20-infected group showed typical diarrhea at 24 h postinfection,and the piglets died successively by 48 h postinfection.However,the clinical signs of the piglets in the FJzzl-F200-infected group were significantly weaker,and no deaths occurred.The FJzzl-F200-infected group also showed a lower level of fecal viral shedding and lower viral loads in the intestinal tissues,and no obvious histopathological lesions.TypeⅠandⅢinterferon were induced in the FJzzl-F200 infection group,together with pro-inflammatory cytokines,such as TNF-α,IL-1βand IL-8.These results indicate that the identified genetic changes may contribute to the attenuation of FJzzl strain,and the attenuated FJzzl-F200 may have the potential for developing PEDV live-attenuated vaccines. | Pengfei Chen Xiongwei Zhao Shuting Zhou Tianxing Zhou Xiangmei Tan Xia Wu Wu Tong Fei Gao Lingxue Yu Yifeng Jiang Hai Yu Zhibiao Yang Guangzhi Tong Yanjun Zhou | 2021 | Virologica Sinica2021，36，5： | 4 |
| 3 | Isogeometric topology optimization based on energy penalization for symmetric structure显示文摘We present an energy penalization method for isogeometric topology optimization using moving morphable components(ITO–MMC),propose an ITO–MMC with an additional bilateral or periodic symmetric constraint for symmetric structures,and then extend the proposed energy penalization method to an ITO–MMC with a symmetric constraint.The energy penalization method can solve the problems of numerical instability and convergence for the ITO–MMC and the ITO–MMC subjected to the structural symmetric constraint with asymmetric loads.Topology optimization problems of asymmetric,bilateral symmetric,and periodic symmetric structures are discussed to validate the effectiveness of the proposed energy penalization approach.Compared with the conventional ITO–MMC,the energy penalization method for the ITO–MMC can improve the convergence rate from 18.6%to 44.5%for the optimization of the asymmetric structure.For the ITO–MMC under a bilateral symmetric constraint,the proposed method can reduce the objective value by 5.6%and obtain a final optimized topology that has a clear boundary with decreased iterations.For the ITO–MMC under a periodic symmetric constraint,the proposed energy penalization method can dramatically reduce the number of iterations and obtain a speedup of more than 2. | Xianda XIE Shuting WANG Ming YE Zhaohui XIA Wei ZHAO Ning JIANG Manman XU | 2020 | Frontiers of Mechanical Engineering2020，15，1： | 3 |
| 4 | stAPAminer:Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies显示文摘Alternative polyadenylation(APA)contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases.Singlecell RNA sequencing(scRNA-seq)has enabled the profiling of APA at the single-cell level;however,the spatial information of cells is not preserved in scRNA-seq.Alternatively,spatial transcriptomics(ST)technologies provide opportunities to decipher the spatial context of the transcriptomic landscape.Pioneering studies have revealed potential spatially variable genes and/or splice isoforms;however,the pattern of APA usage in spatial contexts remains unappreciated.In this study,we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data.APA sites were identified and quantified from the ST data.In particular,an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals,and then APA genes with spatial patterns of APA usage variation were identified.By analyzing wellestablished ST data of the mouse olfactory bulb(MOB),we presented a detailed view of spatial APA usage across morphological layers of the MOB.We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers.By extending this analysis to two additional replicates of the MOB ST data,we observed that the spatial APA patterns of several genes were reproducible among replicates.stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution.This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320. | Guoli Ji Qi Tang Sheng Zhu Junyi Zhu Pengchao Ye Shuting Xia Xiaohui Wu | 2023 | Genomics, Proteomics & Bioinformatics2023，21，3： | 1 |
| 5 | A Strategy for Searching Antigenic Regions in the SARS-CoV Spike Protein显示文摘In the face of the worldwide threat of severe acute respiratory syndrome (SARS)to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA), these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469-882 in the S protein, and one epitope site was located at Codons 599-620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis. | Yan Ren, Zhengfeng Zhou, Jinxiu Liu, Liang Lin, Shuting Li, Hao Wang, Ji Xia, Zhe Zhao, Jie Wen, Cuiqi Zhou, Jingqiang Wang, Jianning Yin, Ningzhi Xu, and Siqi LiuBeijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China & Beijing Proteomics Institute, Beijing 101300, China. | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 1 |
| 6 | Evolution of Meteorological Conditions during a Heavy Air Pollution Event under the Influence of Shallow Foehn in Urumqi, China显示文摘The air pollution in Urumqi which is located on the northern slope of the Tianshan Mountains in northwestern China,is very serious in winter.Of particular importance is the influence of terrain-induced shallow foehn,known locally as elevated southeasterly gale(ESEG).It usually modulates atmospheric boundary layer structure and wind field patterns and produces favorable meteorological conditions conducive to hazardous air pollution.During 2013-17,Urumqi had an average of 50 d yr-1 of heavy pollution(daily average PM2.5 concentration>150μg m-3),of which 41 days were in winter.The majority(71.4%)of heavy pollution processes were associated with the shallow foehn.Based on microwave radiometer,wind profiler,and surface observations,the surface meteorological fields and boundary layer evolution during the worst pollution episode in Urumqi during 16-23 February 2013 are investigated.The results illustrate the significant role of shallow foehn in the building,strengthening,and collapsing of temperature inversions.There were four wind field patterns corresponding to four different phases during the whole pollution event.The most serious pollution phase featured shallow foehn activity in the south of Urumqi city and the appearance of an intense inversion layer below 600 m.Intense convergence caused by foehn and mountain-valley winds was sustained during most of the phase,resulting in pollutants sinking downward to the lower boundary layer and accumulating around urban area.The key indicators of such events identified in this study are highly correlated to particulate matter concentrations and could be used to predict heavy pollution episodes in the feature. | Xia LI Keming ZHAO Shiyuan ZHONG Xiaojing YU Zhimin FENG Yuting ZHONG Ayitken MAULEN Shuting LI | 2023 | Advances in Atmospheric Sciences2023，40，1： | 0 |
| 7 | What makes Chinese rural migrants self-employed:a qualitative perspective显示文摘This study scrutinizes the causes,configuration,and consequences of rural migrants’motivations for becoming self-employed.It aims to solve two main problems in the current literature.The first is that previous studies primarily explain migrants’self-employment through economic variables when other factors(e.g.,autonomy,meaningfulness,and work environment)might be more important.Second,no study has been conducted to qualitatively understand migrants’self-employment outcomes.By drawing on in-depth qualitative interviews with rural-to-urban migrant workers conducted in four regions of China,this article provides insights into the pecuniary and nonpecuniary motivations of rural migrants’employment decisions.Notably,it finds that most rural migrant workers in wage employment sectors are not in a position to exercise free choice regarding their working arrangements.In contrast,the prospect of achieving a higher level of income,greater autonomy,and more flexibility and freedom is important and attractive aspects of self-employment,with apparent gender differences.Nevertheless,migrants’self-employment often involves self-sacrifice and economic and social marginalization.Therefore,it is unlikely that migrants select self-employment as an effective means for status acquisition. | Shuting Xia | 2022 | The Journal of Chinese Sociology2022，9，1： | 0 |
| 8 | Cytarabine delivered by CD44 and bone targeting redox-sensitive liposomes for treatment of acute myelogenous leukemia显示文摘Acute myelogenous leukemia(AML)remains a serious fatal disease for the patients and effective treatment strategies are urgently needed.Based on the characteristics of the AML,we developed the CD44 and bone targeting liposomes delivery system decorated with the redox-cleavable polymer.First,ALN-HA was obtained by amination between alendronate(ALN)and hyaluronic acid(HA),and cholesterol(Chol)was coupled by a disulfide linker(-SS-)with biological reducibility to obtain the goal polymer,ALN-HA-SS-Chol,decorated the liposomes loaded with the Cytarabine(AraC).ALN-HA-SS-AraC-Lip exhibited a spherical morphology with the diameter of 117.5nm and expanded at the environment of 10mM dithiothreitol.Besides,compared with other groups,ALN-HA-SS-AraC-Lip showed benign hydroxyapatite affinity in vitro and bone targeting in C57/BL6 mice,also,ALN-HA-SS-AraC-Lip exhibited encouraging antitumor which significantly reduced the white blood cell amount in bone marrow and blood smear caused by AML model,besides,the dual targeting liposomes also prolong the survival time of mice.In conclusion,the bone and CD44 dual targeting liposomes with redox sensitivity could target to the leukemia stem cells regions and then uptake by the tumor cells,which would be a valuable target for the treatment of the AML. | Hao Wu Yuan Gao Jia Ma Maosong Hu Jing Xia Shuting Bao Yuxi Liu Kai Feng | 2022 | Regenerative Biomaterials2022，9，1： | 0 |
| 9 | The Novel PRRSV Strain HBap4-2018 with a Unique Recombinant Pattern Is Highly Pathogenic to Piglets显示文摘Currently, various porcine reproductive and respiratory syndrome virus(PRRSV) variants emerged worldwide with different genetic characteristics and pathogenicity, increasing the difficulty of PRRS control. In this study, a PRRSV strain named HBap4-2018 was isolated from swine herds suffering severe respiratory disease with high morbidity in Hebei Province of China in 2018. The genome of HBap4-2018 is 15,003 nucleotides in length, and compared with NADC30-like PRRSV, nsp2 of HBap4-2018 has an additional continuous deletion of five amino acids. Phylogenetic analysis based on complete genome and ORF5 showed that HBap4-2018 belonged to lineage 8 of PRRSV-2, which was characterized by highly variable genome. However, HBap4-2018 was classified into lineage 1 based on phylogenetic analysis of nsp2,sharing higher amino acid homology(85.3%–85.5%) with NADC30-like PRRSV. Further analysis suggested that HBap4-2018 was a novel natural recombinant PRRSV with three recombinant fragments in the genome, of which highly pathogenic PRRSV(HP-PRRSV) served as the major parental strains, while NADC30-like PRRSV served as the minor parental strains. Five recombination break points were identified in nsp2, nsp3, nsp5, nsp9 and ORF6, respectively,presenting a novel recombinant pattern in the genome. Piglets inoculated with HBap4-2018 presented typical clinical signs with a mortality rate of 60%. High levels of viremia and obvious macroscopic and histopathological lesions in the lungs were observed, revealing the high pathogenicity of HBap4-2018 in piglets. | Pengfei Chen Xiangmei Tan Mengqin Lao Xia Wu Xiongwei Zhao Shuting Zhou Jiarong Yu Junrui Zhu Lingxue Yu Wu Tong Fei Gao Hai Yu Changlong Liu Yifeng Jiang Guangzhi Tong Yanjun Zhou | 2021 | Virologica Sinica2021，36，6： | 0 |
| 10 | Identification of Monocytes Associated with Severe COVID-19 in the PBMCs of Severely Infected Patients Through Single-Cell Transcriptome Sequencing显示文摘Understanding the immunological characteristics of monocytes-including the characteristics associated with fibrosis-in severe coronavirus disease 2019(COVID-19)is crucial for understanding the pathogenic mechanism of the disease and preventing disease severity.In this study,we performed single-cell transcriptomic sequencing of peripheral blood samples collected from six healthy controls and 14 COVID-19samples including severe,moderate,and convalescent samples from three severely/critically ill and four moderately ill patients.We found that the monocytes were strongly remodeled in the severely/critically ill patients with COVID-19,with an increased proportion of monocytes and seriously reduced diversity.In addition,we discovered two novel severe-disease-specific monocyte subsets:Mono 0 and Mono 5.These subsets expressed amphiregulin(AREG),epiregulin(EREG),and cytokine interleukin-18(IL-18)gene,exhibited an enriched erythroblastic leukemia viral oncogene homolog(ErbB)signaling pathway,and appeared to exhibit pro-fibrogenic and pro-inflammation characteristics.We also found metabolic changes in Mono 0 and Mono 5,including increased glycolysis/gluconeogenesis and an increased hypoxia inducible factor-1(HIF-1)signaling pathway.Notably,one pre-severe sample displayed a monocyte atlas similar to that of the severe/critical samples.In conclusion,our study discovered two novel severedisease-specific monocyte subsets as potential predictors and therapeutic targets for severe COVID-19.Overall,this study provides potential predictors for severe disease and therapeutic targets for COVID-19 and thus provides a resource for further studies on COVID-19. | Yan Zhang Shuting Wang He Xia Jing Guo Kangxin He Chenjie Huang Rui Luo Yanfei Chen Kaijin Xu Hainv Gao Jifang Sheng Lanjuan Li | 2022 | Engineering2022，，10： | 0 |
| 11 | A Hybrid Parallel Strategy for Isogeometric Topology Optimization via CPU/GPU Heterogeneous Computing显示文摘This paper aims to solve large-scale and complex isogeometric topology optimization problems that consumesignificant computational resources. A novel isogeometric topology optimization method with a hybrid parallelstrategy of CPU/GPU is proposed, while the hybrid parallel strategies for stiffness matrix assembly, equationsolving, sensitivity analysis, and design variable update are discussed in detail. To ensure the high efficiency ofCPU/GPU computing, a workload balancing strategy is presented for optimally distributing the workload betweenCPU and GPU. To illustrate the advantages of the proposedmethod, three benchmark examples are tested to verifythe hybrid parallel strategy in this paper. The results show that the efficiency of the hybrid method is faster thanserial CPU and parallel GPU, while the speedups can be up to two orders of magnitude. | Zhaohui Xia Baichuan Gao Chen Yu Haotian Han Haobo Zhang Shuting Wang | 2024 | Computer Modeling in Engineering & Sciences2024，138，2： | 0 |
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