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A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression

Science China(Life Sciences) 2024年第4期67卷 765-777页

作者： Hui Zhao Lin-Lin Liu Jian Sun Lian Jin hai-bing xie Jian-Bo Li Hui Xu Dong-Dong Wu Xiao-Lin Zhuang Min-Sheng Peng Ya-Jun Guo Wei-Zhu Qian Newton OOtecko Wei-Jie Sun Liang-Hu Qu Jie He Zhao-Li Chen Rong Liu Ce-Shi Chen Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-resource School of Life SciencesSchool of Ecology and Environmental ScienceYunnan UniversityKunming 650091China School of Forensic Medicine Kunming Medical UniversityKunming 650500China Academy of Biomedical Engineering Kunming Medical UniversityKunming 650500China The Third Affiliated Hospital Kunming Medical UniversityKunming 650118China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province Kunming Institute of ZoologyChinese Academy of SciencesKunming 650201China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650201China The Key Laboratory of Gene Engineering of the Ministry of Education State Key Laboratory for BiocontrolSun Yat-sen UniversityGuangzhou 510275China National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering and Antibody Shanghai 201203China Department of Thoracic Surgery Cancer Institute and HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China

Human-specific insertions play important roles in human phenotypes and *** we reported a 446-bp insertion(Insert-446)in intron 11 of the TBC1D8B gene,located on chromosome X,and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome ***,Insert-446 was present in the human Neanderthal and Denisovans genomes,and was fixed in humans after human-chimpanzee *** have demonstrated that Insert-446 acts as an enhancer through binding transcript factors that promotes a higher expression of human TBC1D8B gene as compared with orthologs in *** addition,over-expression TBC1D8B promoted cell proliferation and migration through“a dual finger”catalytic mechanism(Arg538 and Gln573)in the TBC domain in vitro and knockdown of TBC1D8B attenuated tumorigenesis in *** of Insert-446 prevented cell proliferation and migration in cancer and normal *** results reveal that the human-specific Insert-446 promotes cell proliferation and migration by upregulating the expression of TBC1D8B *** findings provide a significant insight into the effects of human-specific insertions on evolution.

关键词： human-specific insertion enhancer gene expression cell proliferation and migration

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Genomic and transcriptomic analyses reveal selection of genes for puberty in Bama Xiang pigs

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Zoological Research 2018年第6期39卷 424-430页

作者： Yang Yang Adeniyi C.Adeola hai-bing xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences

The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.

关键词： Puberty Bama Xiang pig Pituitary Differentially expressed genes

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Capture Probe: a java tool for designing probes for capture Hi-C applications

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Zoological Research 2020年第1期41卷 94-96页

作者： Yun-Fei Ma Adeniyi CAdeola Yan-Bo Sun hai-bing xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan ProvinceYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding,making it difficult for scientists to reveal the genetic regulatory *** Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic *** can identify interactions among target loci and all other loci in a genome with low cost and high ***,we developed CaptureProbe,a user-friendly,graphical Java tool for the design of capture probes across a range of target sites or *** parameters helped to achieve and optimize the designed *** testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe ***,this program will help scientists conduct genome spatial interaction research.

关键词： Capture EDIT Probe

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Artificial selection drives differential gene expression during pig domestication

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Journal of Genetics and Genomics 2019年第2期46卷 97-100页

作者： Yang Yang Chaorui Liu Adeniyi C.Adeola xierzhatijiang Sulaiman hai-bing xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences National Pilot School of Software Yunnan University College of Uighur Medicine Xinjiang Medical University

Domestication of livestock involves drastic phenotypic changes driven by strong artificial selection,such as tame behavior and coat *** abundant phenotypic variations established during animal domestication have provi... 详细信息

关键词： ASE FST ADP SLC CWB PPARD AWB cis

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Transfer learning framework for multi-scale crack type classification with sparse microseismic networks

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International Journal of Mining Science and Technology 2024年第2期34卷 167-178页

作者： Arnold Yuxuan xie bing QLi Department of Civil and Environmental Engineering Western UniversityLondon N6A 3K7Canada

Rock fracture mechanisms can be inferred from moment tensors(MT)inverted from microseismic ***,MT can only be inverted for events whose waveforms are acquired across a network of *** is limiting for underground mines where the microseismic stations often lack azimuthal ***,there is a need for a method to invert fracture mechanisms using waveforms acquired by a sparse microseismic ***,we present a novel,multi-scale framework to classify whether a rock crack contracts or dilates based on a single *** framework consists of a deep learning model that is initially trained on 2400000+manually labelled field-scale seismic and microseismic waveforms acquired across 692 *** learning is then applied to fine-tune the model on 300000+MT-labelled labscale acoustic emission waveforms from 39 individual experiments instrumented with different sensor layouts,loading,and rock types in *** optimal model achieves over 86%F-score on unseen waveforms at both the lab-and *** model outperforms existing empirical methods in classification of rock fracture mechanisms monitored by a sparse microseismic *** facilitates rapid assessment of,and early warning against,various rock engineering hazard such as induced earthquakes and rock bursts.

关键词： Multi-scale Fracture processes Microseismic Acoustic emission Source mechanism Deep learning

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A Matrilineal Genetic Legacy from the Last Glacial Maximum Confers Susceptibility to Schizophrenia in Han Chinese

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Journal of Genetics and Genomics 2014年第7期41卷 397-407页

作者： Wen Zhang Jinsong Tang A-Mei Zhang Min-Sheng Peng hai-bing xie Liwen Tan Lin Xu Ya-Ping Zhang Xiaogang Chen Yong-Gang Yao Key Laboratory of Animal Models and Human Disease Mechanisms Kunming Institute of ZoologyChinese Academy of Sciences The Institute of Mental Health the Second Xiangya HospitalCentral South University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences National Technology Institute of Psychiatry Key Laboratory of Psychiatry and Mental Health of Hunan ProvinceCentral South University

Mitochondrial dysfunction has been widely reported in schizophrenia patients. To dissect the matrilineal structure of Han Chinese with or without schizophrenia and to decipher the maternal influence and evolutionary history of schizophrenia, a total of 1212 schizophrenia patients and 1005 matched healthy controls, all of Han Chinese origin, were recruited in Hunan Province, China. We classified haplogroup for each individual based on mitochondrial DNA （mtDNA） sequence variations and compared the haplogroup distribution pattern between cases and controls. Haplogroup B5a presented a higher frequency in cases than in controls （P = 0.02, OR = 1.67, 95% CI = [1.09, 2.56]）, and this result could be confirmed by permutation analysis. Age estimation of haplogroup B5a in cases revealed a much younger age than that of controls, which was coincident with the Northern Hemisphere deglaciation at the end of the Last Glacial Maximum. Analysis of complete mtDNA in five patients belonging to haplogroup B5a showed that this background effect might be caused by haplogroup- defining variants m.8584G〉A and m.10398A〉G. Our results showed that matrilineal risk factor for schizophrenia had an ancient origin and might acquire a predisposing effect on schizophrenia due to the environment change and/or orchestration with other nuclear genetic factors appeared recently in human evolutionary history.

关键词： mtDNA haplogroup Schizophrenia Association Last Glacial Maximum Evolutionary medicine

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Monogamy and polygamy for the generalized W-class states using unified-(q,s)entropy

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Science China(Physics,Mechanics & Astronomy) 2024年第1期67卷 10-22页

作者： Bo Li bing xie Zhanjun Zhang Heng Fan School of Computer and Computing Science Hangzhou City UniversityHangzhou 310015China Department of Mathematics East China University of TechnologyNanchang 330013China School of Information&Electronic Engineering(Sussex Artificial Intelligence Institute) Zhejiang Gongshang UniversityHangzhou 310018China Institute of Physics Chinese Academy of SciencesBeijing 100190China

We describe the entanglement distribution and restricted shareability of the multipartite generalized W-class states and their reduced density matrix under arbitrary partitions by using monogamy and polygamy relation based on the unified-(q,s)***,we provide an analytical formula of unified-(q,s)entanglement(UE)and an analytical lower bound of unified-(q,s)entanglement of assistance(UEo A)for a reduced density matrix of a generalized W-class ***,we use these two analytical formulas to derive the monogamy and polygamy inequalities for a reduced density matrix of a qudit generalized W-class(GW)*** establish two partition-dependent residual entanglements based on the new monogamy relation,which is helpful to obtain a comprehensive analysis of entanglement dynamics of generalized W-class ***,we investigate tighter monogamy and polygamy relations based on the power ofαth(α≥0)for UE andβth(β≥0)for UEo A,*** results show that the entanglement distribution characteristics of generalized W-class states satisfying stronger constraints can be described more accurately.

关键词： monogamy polygamy multiqudit unified entropy

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OrthReg:a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

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Zoological Research 2020年第4期41卷 471-475页

作者： Yun-Fei Ma Cui-Ping Huang Fang-Ru Lu Jin-Xiu Li Xu-Man Han Adeniyi CAdeola Yun Gao Jia-Kun Deng hai-bing xie Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Kunming College of Life Science University of Chinese Academy of SciencesKunmingYunnan 650204China University of Chinese Academy of Sciences Beijing100049China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province School of Life SciencesYunnan UniversityKunmingYunnan 650091China

DEAR EDITOR,Cis-regulatory elements play an important role in the development of traits and disease in organisms(Ma et al.,2020;Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements(ENCODE)(Davis et al., 2018) and Functional Annotation of Animal Genomes(FAANG)(FAANG Consortium et al., 2015)offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms.

关键词： species. traits regulatory

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Data-driven mapping-relationship mining between hardness and mechanical properties of dual-phase titanium alloys via random forest and statistical analysis

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Rare Metals 2024年第2期43卷 829-841页

作者： hai-Chao Gong Qun-Bo Fan Hong-Mei Zhang Xing-Wang Cheng Wen-Qiang xie Kai Chen Lin Yang Jun-Jie Zhang bing-Qiang Wei Shun Xu School of Materials Science and Engineering Beijing Institute of TechnologyBeijing100081China National Key Laboratory of Science and Technology on Materials Under Shock and Impact Beijing100081China Beijing Institute of Technology Chongqing Innovation Center Chongqing401135China Department of Mechanical and Materials Engineering University of Nebraska-LincolnLincolnNE68588USA

In order to accelerate the research on the property optimization of titanium alloy based on high-throughput methods,it is necessary to reveal the relationship between hardness and other mechanical properties which is still *** this work,taking Ti20C alloy as research object,almost all the microstructure of dual-phase titanium alloys were covered by traversing over 100 heat treatment ***,massive experiments including microstructure characterization and performance test were conducted,obtaining 51,590 pieces of microstructure data and 3591 pieces of mechanical property ***,based on large-scale data-driven technology,the quantitative mapping relationship between hardness and other mechanical properties was deeply *** results of random forest models showed that the correlation between hardness(H)and Charpy impact energy(A_(k))(or elongation,A)was hardly dependent on the microstructure types,while the relationship between H and tensile strength(R_(m))(or yield strength,R_(p0.2))was highly dependent on microstructure ***,combined with statistical analysis,it was found that the relationship between H and Ak(or A)were negatively ***,the relationship between H and strength was positively linear for equiaxed microstructure,and strength was linked to d^(−1/2)(d,equivalent circle diameter)ofα-grains in the form of classical Hall–Petch formula;but for other microstructures,the relationships were ***,the above rules were nearly the same in the rolling direction and transverse ***,a"four-quadrant partition map"between H and R_(p0.2)/R_(m) was established as a versatile material-screening tool,which can provide guidance for on-demand selection of titanium alloys.

关键词： Dual-phase titanium alloy Data-driven Hardness Mapping relationship

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Adaptive Trajectory Tracking Control for Nonholonomic Wheeled Mobile Robots:A Barrier Function Sliding Mode Approach

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IEEE/CAA Journal of Automatica Sinica 2024年第4期11卷 1007-1021页

作者： Yunjun Zheng Jinchuan Zheng Ke Shao Han Zhao Hao xie hai Wang the School of Mechanical Engineering Hefei University of TechnologyHefei 230009China the School of Science Computing and Engineering TechnologiesSwinburne University of TechnologyHawthorn VIC 3122Australia the School of Civil Aviation Northwestern Polytechnical UniversityXi’an 710072China the Shanghai Aerospace Control Technology Institute Shanghai 201109 the School of Automation Science and Electrical Engineering Beihang UniversityBeijing 100191China the College of Science HealthEngineering and EducationMurdoch UniversityPerth WA6150Australia

The trajectory tracking control performance of nonholonomic wheeled mobile robots(NWMRs)is subject to nonholonomic constraints,system uncertainties,and external *** paper proposes a barrier function-based adaptive sliding mode control(BFASMC)method to provide high-precision,fast-response performance and robustness for *** with the conventional adaptive sliding mode control,the proposed control strategy can guarantee that the sliding mode variables converge to a predefined neighborhood of origin with a predefined reaching time independent of the prior knowledge of the uncertainties and disturbances *** advantage of the proposed algorithm is that the control gains can be adaptively adjusted to follow the disturbances amplitudes thanks to the barrier *** benefit is that the overestimation of control gain can be eliminated,resulting in chattering ***,a modified barrier function-like control gain is employed to prevent the input saturation problem due to the physical limit of the *** stability analysis and comparative experiments demonstrate that the proposed BFASMC can ensure the prespecified convergence performance of the NWMR system output variables and strong robustness against uncertainties/disturbances.

关键词： Adaptive sliding mode barrier function nonholonomic wheeled mobile robot(NWMR) trajectory tracking control

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