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| 1 | Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population显示文摘Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection. | Liangyu Shi Ligang Wang Jiaxin Liu Tianyu Deng Hua Yan Longchao Zhang Xin Liu Hongmei Gao Xinhua Hou Lixian Wang Fuping Zhao | 2020 | Journal of Animal Science and Biotechnology2020，11，4： | 10 |
| 2 | Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses显示文摘Human skeletal stem cells(SSCs)have been discovered in fetal and adult long bones.However,the spatiotemporal ontogeny of human embryonic SSCs during early skeletogenesis remains elusive.Here we map the transcriptional landscape of human limb buds and embryonic long bones at single-cell resolution to address this fundamental question.We found remarkable heterogeneity within human limb bud mesenchyme and epithelium,and aligned them along the proximal-distal and anterior-posterior axes using known marker genes.Osteo-chondrogenic progenitors first appeared in the core limb bud mesenchyme,which give rise to multiple populations of stem/progenitor cells in embryonic long bones undergoing endochondral ossification.Importantly,a perichondrial embryonic skeletal stem/progenitor cell(eSSPC)subset was identified,which could self-renew and generate the osteochondral lineage cells,but not adipocytes or hematopoietic stroma.eSSPCs are marked by the adhesion molecule CADM1 and highly enriched with FOXP1/2 transcriptional network.Interestingly,neural crest-derived cells with similar phenotypic markers and transcriptional networks were also found in the sagittal suture of human embryonic calvaria.Taken together,this study revealed the cellular heterogeneity and lineage hierarchy during human embryonic skeletogenesis,and identified distinct skeletal stem/progenitor cells that orchestrate endochondral and intramembranous ossification. | Jian He Jing Yan Jianfang Wang Liangyu Zhao Qian Xin Yang Zeng Yuxi Sun Han Zhang Zhijie Bai Zongcheng Li Yanli Ni Yandong Gong Yunqiao Li Han He Zhilei Bian Yu Lan Chunyu Ma Lihong Bian Heng Zhu Bing Liu Rui Yue | 2021 | Cell Research2021，31，7： | 5 |
| 3 | Deformation mode-determined misorientation and microstructural characteristics in rolled pure Zr sheet显示文摘In this work, commercially pure Zr sheets were subjected to β air cooling and then rolled to different reductions(10% and 50%)at room temperature. Microstructures of both the β-air-cooled and the rolled specimens were well characterized by electron channelling contrast imaging and electron backscatter diffraction techniques, with special attentions paid to their misorientation characteristics. Results show that the β-air-cooled specimen owns a Widmanst?tten structure featured by lamellar grains with typical phase transformation misorientations. The 10% rolling allows prismatic slip and tensile twinning({11-21}<11-2-6> and{10-12}<10-11>) to be activated profusely, which produce new low-angle(~3°–5°) and high-angle(~35° and ~85°) misorientation peaks, respectively. After increasing the rolling reduction to 50%, twinning is suppressed and dislocation slip becomes the dominant deformation mode, with the lamellar grains highly elongated and aligned towards the rolling direction.Meanwhile, only one strong low-angle misorientation peak related to the prismatic slip is presented in the 50%-rolled specimen,with all other peaks disappeared. Analyses on local misorientations reveal that hardly any residual strains exist in the β-air-cooled specimen, which should be related to their sufficient relaxation during slow cooling. Residual strains introduced by 10% rolling are heterogeneously distributed near grain/twin boundaries while heavier deformation(50% rolling) produces much larger residual strains pervasively existing throughout the specimen microstructure. | CHAI LinJiang XIA JiYing ZHI Yan GOU YinNing CHEN LiangYu YANG ZhiNan GUO Ning | 2018 | Science China(Technological Sciences)2018，61，9： | 3 |
| 4 | Real-Time Pricing of Smart Grid Based on Piece-Wise Linear Functions显示文摘In a power grid system, utility is a measure of the satisfaction of users’ electricity consumption;cost is a monetary value of electricity generated by the supplier. The utility and cost functions represent the satisfaction of different users and the supplier. Quadratic utility, logarithmic utility,and quadratic cost functions are widely used in social welfare maximization models of real-time pricing. These functions are not universal;they have to be discussed in detail for individual models. To overcome this problem, a piece-wise linear utility function and a piece-wise linear cost function with general properties are proposed in this paper. By smoothing the piece-wise linear utility and cost functions, a social welfare maximization model can be transformed into a differentiable convex optimization problem. A dual optimization method is used to solve the smoothed model. Through mathematical deduction and numerical simulations, the rationality of the model and the validity of the algorithm are verified as long as the elastic and cost coefficients take appropriate values. Thus, different user types and the supplier can be determined by selecting different elastic and cost coefficients. | Zhihong XU Liangyu GUO Yan GAO Muhammad HUSSAIN Panhong CHENG | 2019 | Journal of Systems Science and Information2019，10，4： | 3 |
| 5 | HIGH ORDER LOCAL DISCONTINUOUS GALERKIN METHODS FOR THE ALLEN-CAHN EQUATION: ANALYSIS AND SIMULATION显示文摘在这份报纸,我们在场为 Allen-Cahn 方程的一个本地不连续的 Galerkin (LDG ) 方法。我们证明精力稳定性,分析 k + 的最佳的集中率 1 在 L2 标准和现在(2k + 1 )-th 顺序为有光滑的答案的 Allen-Cahn 方程的 semidiscrete LDG 方法的否定标准的估计。为了放松严重时间,走行进方法的明确的时间的限制,我们构造第一基于分离 Allen-Cahn 精力的凸的切开原则订半含蓄的计划并且证明相应无条件的精力稳定性。为了高完成,命令时间的精确性,我们采用半含蓄光谱推迟的修正(SDC ) 方法。与无条件地稳定的凸的切开计划结合, SDC 方法能是在我们的数字测试精确、稳定的高顺序。提高建议方法的效率, multigrid 解答者被改编解决结果非线性的代数学的系统。数字研究被介绍证实我们能在 L2 标准完成 O (hk+1 ) 的最佳的精确性并且与精确性改进 processing 以后技术从 O (hk+1 ) 改进 LDG 答案到 O (h2k+1 ) 。 ' | Ruihan Guo Liangyue Ji Yan Xu | 2016 | Journal of Computational Mathematics2016，34，2： | 3 |
| 6 | The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs显示文摘Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported.To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45,70 and 100 days post coitus(dpc).Results:In total,21,638,35,447 and 60,181 unique regions(or peaks)were found across the embryos at 45 dpc(LW45),70 dpc(LW70)and 100 dpc(LW100),respectively.More than 91%of the peaks were annotated within−1 kb to 100 bp of transcription start sites(TSSs).First,widespread increases in specific accessible chromatin regions(ACRs)from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development.Second,the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes.Moreover,the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle developmentrelated genes,such as MyoG,Mef2c,and Mef2d.Several potential transcriptional repressors,including E2F6,OTX2 and CTCF,were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.Conclusions:This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors.Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development. | Jingwei Yue Xinhua Hou Xin Liu Ligang Wang Hongmei Gao Fuping Zhao Lijun Shi Liangyu Shi Hua Yan Tianyu Deng Jianfei Gong Lixian Wang Longchao Zhang | 2021 | Journal of Animal Science and Biotechnology2021，12，4： | 2 |
| 7 | HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis显示文摘Integration of light signaling and diverse abiotic stress responses contribute to plant survival in a changing environment.Some reports have indicated that light signals contribute a plant’s ability to deal with heat,cold,and stress.However,the molecular link between light signaling and the saltresponse pathways remains unclear.We demonstrate here that increasing light intensity elevates the salt stress tolerance of plants.Depletion of HY5,a key component of light signaling,causes Arabidopsis thaliana to become salinity sensitive.Interestingly,the small heat shock protein(sHsp)family genes are upregulated in hy5-215 mutant plants,and HsfA 2 is commonly involved in the regulation of these sH sps.We found that HY5directly binds to the G-box motifs in the HsfA2promoter,with the cooperation of HISTONE DEACETYLASE 9(HDA9),to repress its expression.Furthermore,the accumulation of HDA9 and the interaction between HY5 and HDA9 are significantly enhanced by salt stress.On the contrary,high temperature triggers HY5 and HDA9 degradation,which leads to dissociation of HY5-HDA9from the HsfA2 promoter,thereby reducing salt tolerance.Under salt and heat stress conditions,fine tuning of protein accumulation and an interaction between HY5 and HDA9 regulate HsfA2 expression.This implies that HY5,HDA9,and HsfA2play important roles in the integration of light signaling with salt stress and heat shock response. | Jiaheng Yang Xiao Qu Tao Li Yixiang Gao Haonan Du Lanjie Zheng Manchun Ji Paifeng Zhang Yan Zhang Jinxin Hu Liangyu Liu Zefu Lu Zijian Yang Huiyong Zhang Jianping Yang Yongqing Jiao Xu Zheng | 2023 | Journal of Integrative Plant Biology2023，65，1： | 1 |
| 8 | Effect of salt and drought stress on antioxidant enzymes activities and SOD isoenzymes of liquoriee(Glycyrrhiza uralensis Fiseh) 显示文摘 | Yan Pan Li Junwu Zeng Liangyu | 2006 | Plant Growth Regulation2006，49，23： | 1 |
| 9 | Characteristics and source apportionment of ambient volatile organic compounds and ozone generation sensitivity in urban Jiaozuo,China显示文摘In recent years,many cities have taken measures to reduce volatile organic compounds(VOCs),an important precursor of ozone(O_(3)),to alleviate O_(3) pollution in China.116 VOC species were measured by online and offline methods in the urban area of Jiaozuo from May to October in 2021 to analyze the compositional characteristics.VOC sources were analyzed by a positive matrix factorization(PMF)model,and the sensitivity of ozone generation was determined by ozone isopleth plotting research(OZIPR)simulation.The results showed that the average volume concentration of total VOCs was 30.54 ppbv and showed a bimodal feature due to the rush-hour traffic in the morning and at nightfall.The most dominant VOC groups were oxygenated VOCs(OVOCs,29.3%)and alkanes(26.7%),and the most abundant VOC species were acetone and acetylene.However,based on the maximum incremental reactivity(MIR)method,the major VOC groups in terms of ozone formation potential(OFP)contribution were OVOCs(68.09μg/m^(3),31.5%),aromatics(62.90μg/m^(3),29.1%)and alkene/alkynes(54.90μg/m^(3),25.4%).This indicates that the control of OVOCs,aromatics and alkene/alkynes should take priority.Five sources of VOCs were quantified by PMF,including fixed sources of fossil fuel combustion(27.8%),industrial processes(25.9%),vehicle exhaust(19.7%),natural and secondary formation(13.9%)and solvent usage(12.7%).The empirical kinetic modeling approach(EKMA)curve obtained by OZIPR on O_(3) exceedance days indicated that the O_(3) sensitivity varied in different months.The results provide theoretical support for O_(3) pollution prevention and control in Jiaozuo. | Pengzhao Li Chun Chen Dan Liu Jie Lian Wei Li Chuanyi Fan Liangyu Yan Yue Gao Miao Wang Hang Liu Xiaole Pan Jing Mao | 2024 | Journal of Environmental Sciences2024，，4： | 0 |
| 10 | A novel 2D graphene oxide modified α-AgVO_(3) nanorods: Design, fabrication, and enhanced visible-light photocatalytic performance显示文摘Silver vanadates are promising visible-light-responded photocatalysts with suitable bandgap for solar absorption.However,the easy recombination of photogenerated carriers limits their performance.To overcome this obstacle,a novel 2D graphene oxide(GO)modifiedα-AgVO_(3) nanorods(GO/α-AgVO_(3) )photocatalyst was designed herein to improve the separation of photocarriers.The GO/α-AgVO_(3) was fabricated through a facile in-situ coprecipitation method at room temperature.It was found that the as-prepared 0.5 wt%GO/α-AgVO_(3) exhibited the most excellent performance for rhodamine B(RhB)decomposition,with an apparent reaction rate constant 18 times higher than that of pureα-AgVO_(3) under visible-light irradiation.In light of the first-principles calculations and the hetero junction analysis,the mechanism underpinned the enhanced photocatalytic performance was proposed.The enhanced photocatalytic performance was ascribed to the appropriate bandgap ofα-AgVO_(3) nanorods for visible-light response and efficient separation of photocarriers through GO nanosheets.This work demonstrates the feasibility of overcoming the easy recombination of photogenerated carriers and provides a valuable GO/α-AgVO_(3) photocatalyst for pollutant degradation. | Jian WU Liangyu LI Xing-ao LI Xin MIN Yan XING | 2022 | Journal of Advanced Ceramics2022，11，2： | 0 |
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