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| 1 | Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs显示文摘The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted Ch IP-Seq and RNA-Seq in fetal(prenatal days 74–75) and adult(postnatal days 132–150) tissues(brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages(which could indicate safe harbor locus for exogenous gene insertion) and tissue-and developmental stage-specific peaks(which regulate gene pathways matching tissue-and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results(http://segtp.jxau.edu.cn/pencode/?genome=sus Scr11). | Yaling Zhu Zhimin Zhou Tao Huang Zhen Zhang Wanbo Li Ziqi Ling Tao Jiang Jiawen Yang Siyu Yang Yanyuan Xiao Carole Charlier Michel Georges Bin Yang Lusheng Huang | 2022 | Science China(Life Sciences)2022，65，8： | 5 |
| 2 | Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals显示文摘The global Coronavirus disease 2019(COVID-19)pandemic caused by SARS-CoV-2 has affected more than eight million people.There is an urgent need to investigate how the adaptive immunity is established in COVID-19 patients.In this study,we proled adaptive immune cells of PBMCs from recovered COVID-19 patients with varying disease severity using single-cell RNA and TCR/BCR V(D)J sequencing.The sequencing data revealed SARS-CoV-2-specic shufing of adaptive immune repertories and COVID-19-induced remodeling of peripheral lymphocytes.Characterization of variations in the peripheral T and B cells from the COVID-19 patients revealed a positive correlation of humoral immune response and T-cell immune memory with disease severity.Sequencing and functional data revealed SARS-CoV-2-specic T-cell immune memory in the convalescent COVID-19 patients.Furthermore,we also identied novel antigens that are responsive in the convalescent patients.Altogether,our study reveals adaptive immune repertories underlying pathogenesis and recovery in severe versus mild COVID-19 patients,providing valuable information for potential vaccine and therapeutic development against SARS-CoV-2 infection. | Fan Zhang Rui Gan Ziqi Zhen Xiaoli Hu Xiang Li Fengxia Zhou Ying Liu Chuangeng Chen Shuangyu Xie Bailing Zhang Xiaoke Wu Zhiwei Huang | 2020 | Signal Transduction and Targeted Therapy2020，5，1： | 3 |
| 3 | SP1 governs primordial folliculogenesis by regulating pregranulosa cell development in mice显示文摘Establishment of the primordial follicle(PF)pool is pivotal for the female reproductive lifespan;however,the mechanism of primordial folliculogenesis is poorly understood.Here,the transcription factor SP1 was shown to be essential for PF formation in mice.Our results showed that SP1 is present in both oocytes and somatic cells during PF formation in the ovary.Knockdown of Sp1 expression,especially in pregranulosa cells,significantly suppressed nest breakdown,oocyte apoptosis,and PF formation,suggesting that SP1 expressed by somatic cells functions in the process of primordial folliculogenesis.We further demonstrated that SP1 governs the recruitment and maintenance of Forkhead box L2-positive(FOXL2^+)pregranulosa cells using an Lgr5-EGFP-IRES-CreER^T2(Lgr5-KI)reporter mouse model and a FOXL2^+ cell-specific knockdown model.At the molecular level,SP1 functioned mainly through manipulation of NOTCH2 expression by binding directly to the promoter of the Notch2 gene.Finally,consistent with the critical role of granulosa cells in follicle survival in vitro,massive loss of oocytes in SP1 knockdown ovaries was evidenced before puberty after the ovaries were tranSP1anted under the renal capsules.Conclusively,our results reveal that SP1 controls the establishment of the ovarian reserve by regulating pregranulosa cell development in the mammalian ovary. | Han Cai Bingying Liu Huarong Wang Guanghong Sun Lizhao Feng Ziqi Chen Jiaqi Zhou Jiawei Zhang Tuo Zhang Meina He Tingting Yang Qirui Guo Zhen Teng Qiliang Xin Bo Zhou Hua Zhang Guoliang Xia Chao Wang | 2020 | Journal of Molecular Cell Biology2020，12，3： | 3 |
| 4 | Artificial Intelligence in Pharmaceutical Sciences显示文摘Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market.However,investments in a new drug often go unrewarded due to the long and complex process of drug research and development(R&D).With the advancement of experimental technology and computer hardware,artificial intelligence(AI)has recently emerged as a leading tool in analyzing abundant and high-dimensional data.Explosive growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&D.Driven by big data in biomedicine,AI has led to a revolution in drug R&D,due to its ability to discover new drugs more efficiently and at lower cost.This review begins with a brief overview of common AI models in the field of drug discovery;then,it summarizes and discusses in depth their specific applications in various stages of drug R&D,such as target discovery,drug discovery and design,preclinical research,automated drug synthesis,and influences in the pharmaceutical market.Finally,the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed. | Mingkun Lu Jiayi Yin Qi Zhu Gaole Lin Minjie Mou Fuyao Liu Ziqi Pan Nanxin You Xichen Lian Fengcheng Li Hongning Zhang Lingyan Zheng Wei Zhang Hanyu Zhang Zihao Shen Zhen Gu Honglin Li Feng Zhu | 2023 | Engineering2023，，8： | 1 |
| 5 | An Ultra-stable Eu^(3+)Doped Yttrium Coordination Polymer with Dual-function Sensing for Cr(Ⅵ)and Fe(Ⅲ)Ions in Aqueous Solution显示文摘The exploration of a dual-functional sensor is the key to effectively detect the Cr(Ⅵ)and Fe(Ⅲ)cations in water,which is important to human health and environmental sustainability.Because of the phase stability and excellent luminescence,the rare-earth coordination polymers have great potential as dual-functional sensors.Here,we develop a Y_(0.91)Eu_(0.09)(H_(2)O)_(2){C_(6)H_(3)(CO_(2))_(3)}(MIL-92(Y):9%Eu^(3+))-based dual-function luminescent sensor on Cr(Ⅵ)and Fe(Ⅲ),which exhibits excellent phase stability and dispersibility in water.The luminescence of MIL-92(Y):9%Eu^(3+)aqueous suspension quenches on Fe^(3+)with Stern-Volmer constant K_(sv) of 1.79×10^(3)M^(-1)and limit of detection of 17μM.The MIL-92(Y):9%Eu^(3+)aqueous suspension also has turn-off sensing ability towards Cr_(2)O_(7)^(2-)and Cr O_(4)^(2-)with K_(sv) values of 3.5×10^(3)and 6.14×10^(3)M^(-1),respectively.It has detection limitations of 10 and 5μM on Cr_(2)O_(7)^(2-)and Cr_(2)O_(7)^(2-)ions,respectively. | Fazheng Huang Xinhao Li Zhen Zhang Ziqi Jiang Guoqiang Wang Lingyun Li Yan Yu | 2022 | Chinese Journal of Structural Chemistry2022，41，4： | 1 |
| 6 | Label-free quantification of differentially expressed proteins in mouse liver cancer cells with high and low metastasis rates by a SWATH acquisition method显示文摘Label-free quantification is a valuable tool for the analysis of differentially expressed proteins identified by mass spectrometry methods.Herein,we used a new strategy:data-dependent acquisition mode identification combined with label-free quantification by SWATH acquisition mode,to study the differentially expressed proteins in mouse liver cancer metastasis cells.A total of 1528 protein groups were identified,among which 1159 protein groups were quantified and 249 protein groups were observed as differentially expressed proteins(86 proteins up-regulated and 163 down-regulated).This method provides a commendable solution for the identification and quantification of differentially expressed proteins in biological samples. | YAN ZiQi ZHOU Yuan SHAN YiChu WU Qi ZHANG Shen LIANG Zhen ZHANG LiHua ZHANG YuKui | 2014 | Science China Chemistry2014，57，5： | 1 |
| 7 | Insight into the Electrode Mechanism in Lithium‐Sulfur Batteries with Ordered Microporous Carbon Confined Sulfur as the Cathode显示文摘 | Zhen Li Lixia Yuan Ziqi Yi Yongming Sun Yang Liu Yan Jiang Yue Shen Ying Xin Zhaoliang Zhang Yunhui Huang | 2014 | Adv. Energy Mater2014，，7： | 1 |
| 8 | MIL-101(Cr)-decorated Ti/TiO_(2) anode for electrochemical oxidation of aromatic pollutants from water显示文摘Hydroxyl radicals(·OH) generated on anode play a vital role in electrochemical oxidation(EO) of organic pollutants for water treatment. Inspired by the four-electron oxygen evolution reaction(OER), we supposed an anode-selection strategy to stabilize deeply oxidized states(*O and*OOH) which are beneficial to generating·OH. To verify the hypothesis, a candidate anode component(MIL-101(Cr), a well-known metal-organic framework with active variable-valence transition metal centers) was used to coat Ti/TiO_(2)plate to fabricate anodes. Compared to TiO_(2)(101) plane on undecorated anode surface, fast and complete removal of aniline and phenol, and improved energy utilization were achieved on MIL-101(Cr)-coatedTi/TiO_(2)anode. Mechanism investigation, including pollutant degradation pathways, showed the predominate contribution(69.60%–75.13%) of·OH in pollutant mineralization. Density functional theory(DFT)computations indicated Cr site in MIL-101(Cr) was more conducive to stabilizing*O and*OOH, leading to thermodynamical spontaneous generation of·OH. This work opens up an exciting avenue to explore·OH production, and supplies a useful guidance to the development of anode materials for EO process. | Zepeng Zhang Yunyun Li Longzhang Dong Zhonglong Yin Ziqi Tian Weiben Yang Zhen Yang | 2023 | Chinese Chemical Letters2023，34，2： | 0 |
| 9 | Digital Simulation of Projective Non-Abelian Anyons with 68 Superconducting Qubits显示文摘Non-Abelian anyons are exotic quasiparticle excitations hosted by certain topological phases of matter.They break the fermion-boson dichotomy and obey non-Abelian braiding statistics:their interchanges yield unitary operations,rather than merely a phase factor,in a space spanned by topologically degenerate wavefunctions.They are the building blocks of topological quantum computing.However,experimental observation of non-Abelian anyons and their characterizing braiding statistics is notoriously challenging and has remained elusive hitherto,in spite of various theoretical proposals.Here,we report an experimental quantum digital simulation of projective non-Abelian anyons and their braiding statistics with up to 68 programmable superconducting qubits arranged on a two-dimensional lattice.By implementing the ground states of the toric-code model with twists through quantum circuits,we demonstrate that twists exchange electric and magnetic charges and behave as a particular type of non-Abelian anyons,i.e.,the Ising anyons.In particular,we show experimentally that these twists follow the fusion rules and non-Abelian braiding statistics of the Ising type,and can be explored to encode topological logical qubits.Furthermore,we demonstrate how to implement both single-and two-qubit logic gates through applying a sequence of elementary Pauli gates on the underlying physical qubits.Our results demonstrate a versatile quantum digital approach for simulating non-Abelian anyons,offering a new lens into the study of such peculiar quasiparticles. | Shibo Xu Zheng-Zhi Sun Ke Wang Liang Xiang Zehang Bao Zitian Zhu Fanhao Shen Zixuan Song Pengfei Zhang Wenhui Ren Xu Zhang Hang Dong Jinfeng Deng Jiachen Chen Yaozu Wu Ziqi Tan Yu Gao Feitong Jin Xuhao Zhu Chuanyu Zhang Ning Wang Yiren Zou Jiarun Zhong Aosai Zhang Weikang Li Wenjie Jiang Li-Wei Yu Yunyan Yao Zhen Wang Hekang Li Qiujiang Guo Chao Song H.Wang Dong-Ling Deng | 2023 | Chinese Physics Letters2023，40，6： | 0 |
| 10 | Correction to: Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals显示文摘 | Fan Zhang Rui Gan Ziqi Zhen Xiaoli Hu Xiang Li Fengxia Zhou Ying Liu Chuangeng Chen Shuangyu Xie Bailing Zhang Xiaoke Wu Zhiwei Huang | 2021 | Signal Transduction and Targeted Therapy2021，6，5： | 0 |
| 11 | Application of artificial hibernation technology in acute brain injury显示文摘Controlling intracranial pressure,nerve cell regeneration,and microenvironment regulation are the key issues in reducing mortality and disability in acute brain injury.There is currently a lack of effective treatment methods.Hibernation has the characteristics of low temperature,low metabolism,and hibernation rhythm,as well as protective effects on the nervous,cardiovascular,and motor systems.Artificial hibernation technology is a new technology that can effectively treat acute brain injury by altering the body’s metabolism,lowering the body’s core temperature,and allowing the body to enter a state similar to hibernation.This review introduces artificial hibernation technology,including mild hypothermia treatment technology,central nervous system regulation technology,and artificial hibernation-inducer technology.Upon summarizing the relevant research on artificial hibernation technology in acute brain injury,the research results show that artificial hibernation technology has neuroprotective,anti-inflammatory,and oxidative stress-resistance effects,indicating that it has therapeutic significance in acute brain injury.Furthermore,artificial hibernation technology can alleviate the damage of ischemic stroke,traumatic brain injury,cerebral hemorrhage,cerebral infarction,and other diseases,providing new strategies for treating acute brain injury.However,artificial hibernation technology is currently in its infancy and has some complications,such as electrolyte imbalance and coagulation disorders,which limit its use.Further research is needed for its clinical application. | Xiaoni Wang Shulian Chen Xiaoyu Wang Zhen Song Ziqi Wang Xiaofei Niu Xiaochu Chen Xuyi Chen | 2024 | Neural Regeneration Research2024，19，9： | 0 |
| 12 | In-situ TEM study on the evolution of dislocation loops and bubbles in CeO_(2)during Kr^(+)single-beam and Kr^(+)-H_(2)^(+)dual-beam synergetic irradiation显示文摘CeO_(2)is widely used as the nonradioactive surrogate fuel of UO_(2)when studying the irradiation performance of UO_(2).The evolution and characteristics of dislocation loops and bubbles in CeO_(2)foils were studied by in-situ transmission electron microscopy(TEM)observation during 400 ke V Kr^(+)&30 ke V H_(2)^(+)dual-beam synergetic irradiation and 400 ke V Kr^(+)single-beam irradiation at 1073 K.The rotation of the habit plane of dislocation loops induced by above ion irradiation was found in the CeO_(2)for the first time,such as from[211]to[311]and then to[100].The rafted loops were first observed under Kr^(+)&H_(2)^(+)dual-beam synergetic irradiation,which not only had similar[111]direction,but also belonged to perfect dislocation loops(PDLs).The rafted loops were formed not only by the growth of loops that absorbed irradiation defects,but also by the combination of loops.But,this phenomenon of loop rafting was not obvious during Kr single-beam irradiation.It was first found that Kr^(+)irradiation induced the change of Burgers vectors of PDLs.The absorption of large PDLs to small PDLs was also observed.The average size and areal number density of dislocation loops and gas bubbles as a function of irradiation dose were constructed,which showed that the addition of H_(2)^(+)obviously affected the characteristics of dislocation loops and gas bubbles and the swelling of CeO_(2). | Ziqi Cao Guang Ran Zhen Wang Yipeng Li Xiaoyong Wu Lu Wu Xiuyin Huang Huajun Mo | 2022 | Journal of Materials Science & Technology2022，，28： | 0 |
| 13 | Stiffness-tuned and ROS-sensitive hydrogel incorporating complement C5a receptor antagonist modulates antibacterial activity of macrophages for periodontitis treatment显示文摘Periodontitis is admittedly a microbe-driven intractable infectious disease,in which Porphyromonas gingivalis(Pg)plays a keystone role.Pg can selectively impair the antimicrobial responses of periodontal resident macrophages including their phagocytic and bactericidal activity without interfering their proinflammatory activity,which leads to microflora disturbance,destructive periodontal inflammation and alveolar bone loss eventually.Here,an injectable ROS-sensitive hydrogel is developed for releasing active bone marrow-derived macrophages(named ex-situ macrophages hereafter)and a complement C5a receptor antagonist(C5A)to the gingival crevice.Through appropriately tuning the hydrogel stiffness,the phagocytic activity of these macrophages is greatly enhanced,reaching an optimal performance at the elastic modulus of 106 kPa.Meanwhile,C5A avoids undesired C5a receptor activation by Pg to ensure the bacterial killing activity of both the ex-situ and in-situ macrophages.Besides,the ROS-sensitive hydrogels show another distinct feature of decreasing the ROS level in periodontal niche,which contributes to the alleviated periodontal inflammation and attenuated bone loss as well.This study highlights the potential of utilizing hydrogels with tailored biomechanical properties to remodel the functions of therapeutic cells,which is expected to find wide applications even beyond periodontitis treatment. | Ziqi Gan Zecong Xiao Zhen Zhang Yang Li Chao Liu Xin Chen Yuanbo Liu Dongle Wu Chufeng Liu Xintao Shuai Yang Cao | 2023 | Bioactive Materials2023，，7： | 0 |
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