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Anisotropic shearing mechanism of Kangding slate:Experimental investigation and numerical analysis

Journal of Rock Mechanics and Geotechnical Engineering 2024年第5期16卷 1487-1504页

作者： Ping Liu Quansheng Liu Penghai Deng Yucong pan yiming Lei Chenglei Du Xianqi Xie The Key Laboratory of Geotechnical and Structural Engineering Safety of Hubei Province School of Civil EngineeringWuhan UniversityWuhan430072China State Key Laboratory of Water Resources and Hydropower Engineering Science Wuhan UniversityWuhan430072China

The shear mechanical behavior is regarded as an essential factor affecting the stability of the surrounding rocks in underground engineering.The shear strength and failure mechanisms of layered rock are significantly affected by the foliation angles.Direct shear tests were conducted on cubic slate samples with foliation angles of 0°,30°,45°,60°,and 90°.The effect of foliation angles on failure patterns,acoustic emission(AE)characteristics,and shear strength parameters was analyzed.Based on AE characteristics,the slate failure process could be divided into four stages:quiet period,step-like increasing period,dramatic increasing period,and remission period.A new empirical expression of cohesion for layered rock was proposed,which was compared with linear and sinusoidal cohesion expressions based on the results made by this paper and previous experiments.The comparative analysis demonstrated that the new expression has better prediction ability than other expressions.The proposed empirical equation was used for direct shear simulations with the combined finite-discrete element method(FDEM),and it was found to align well with the experimental results.Considering both computational efficiency and accuracy,it was recommended to use a shear rate of 0.01 m/s for FDEM to carry out direct shear simulations.To balance the relationship between the number of elements and the simulation results in the direct shear simulations,the recommended element size is 1 mm.

关键词： Anisotropy Empirical expression of cohesion foliation angles Combined finite-discrete element method(FDEM) Shear rate Element size

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Topological reorganization and functional alteration of distinct genomic components in gallbladder cancer

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Frontiers of Medicine 2024年第1期18卷 109-127页

作者： Guoqiang Li Peng Pu Mengqiao pan Xiaoling Weng Shimei Qiu yiming Li Sk Jahir Abbas Lu Zou Ke Liu Zheng Wang Ziyu Shao Lin Jiang Wenguang Wu Yun Liu Rong Shao Fatao Liu Yingbin Liu Department of Biliary-pancreatic Surgery Renji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer InstituteShanghai200127China Shanghai Key Laboratory of Biliary Tract Disease Shanghai200082China Department of Health Science and Engineering University of Shanghai for Science and TechnologyShanghai200082China Shanghai Tenth People’s Hospital of Tongji University Shanghai200072China Department of General Surgery Xinhua HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200082China Department of Pharmacology Shanghai Jiao Tong University School of MedicineShanghai200025China

Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer.However,knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited.Here,by taking advantage of in situ Hi-C,RNA-sequencing,and chromatin immunoprecipitation sequencing(ChIP-seq),we investigated structural reorganization and functional changes in chromosomal compartments,topologically associated domains(TADs),and CCCTC binding factor(CTCF)-mediated loops in gallbladder cancer(GBC)tissues and cell lines.We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes.Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls.Furthermore,the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial–mesenchymal transition activation were enriched in cancer compared with their control counterparts.Cancer-specific enhancer–promoter loops,which contain multiple transcription factor binding motifs,acted as a central element to regulate aberrant gene expression.Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions.Collectively,our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.

关键词： 3D genome cancer TADs loop gene regulation

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Effectiveness and safety of seven oral Chinese patent medicines as adjuvant therapy for cancer-related anemia: A systematic review and network meta-analysis of randomized controlled trials

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Journal of Traditional Chinese Medical Sciences 2023年第2期10卷 150-160页

作者： Jing Xu Kang Wu Xiao Li Chiah Shean Teo Guangda Li yiming pan Li Hou First School of Clinical Medicine Beijing University of Chinese MedicineBeijing100029China Department of Oncology and Hematology Dongzhimen HospitalBeijing University of Chinese MedicineBeijing100700China Institut Kanser Negara Ministry of Health MalaysiaPutrajaya62250Malaysia

Objective:To evaluate the effectiveness and safety of seven oral Chinese patent medicines(CPMs)as adjuvant therapy for cancer-related anemia(CRA)by network meta-analysis(NMA).Methods:A literature search to obtain randomized controlled trials(RCTs)of seven oral CPMs in the adjuvant treatment of CRA was conducted in multiple databases from the inception to April 2022.The RevMan5.3 and R 4.1.1 software were used for NMA.Results:We ultimately included 29 RCTs with 2140 patients.Traditional meta-analysis showed that Fufang E'jiao syrup(FFEJS),Shengxuebao mixture(SXBM),Shengxuening tablets(SXNT),Jianpi Shengxue granules(JPSXG),and Yixuesheng capsule(YXSC)combined with basic Western treatment(BWT)could improve the hemoglobin(HGB)level.JPSXG combined with BWT could improve the red blood cell(RBC).FFEJS combined with BWT improved the Karnofsky performance status(KPS).NMA showed that FFEJS,JPSXG,SXBM,and SXNT plus BWT improved HGB better than Shengxue tablets(SXT)plus BWT,with top three ranking results being JPSXG plus BWT>SXNT plus BWT>FFEJS plus BWT.FFEJS plus BWT,JPSXG plus BWT,SXBM plus BWT,SXNT plus BWT,and SXT plus BWT improved RBC better than BWT,with top three ranking results being SXNT plus BWT>JPSXG plus BWT>FFEJS plus BWT.In terms of the KPS score,compared with SXT plus BWT,FFEJS,JPSXG,SXBM,SXNT,and Yizhong Shengxue capsule(YZSXC)plus BWT had higher KPS,with top three ranking results being SXBM plus BWT>JPSXG plus BWT>FFEJS plus BWT.Conclusions:Our NMA demonstrated that seven oral CPMs used as adjuvant treatment of CRA had a definite clinical effect.JPSXG not only increases the levels of HGB and RBC to enhance the clinical effect but also improves patients'quality of life.More accurate conclusions need to be verified by more high-quality RCTs.

关键词： Cancer-related anemia Chinese patent medicine Network meta-analysis Effectiveness Safety

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Recent advances in chemical protein synthesis:method developments and biological applications

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Science China Chemistry 2024年第4期67卷 1060-1096页

作者： Suwei Dong Ji-Shen Zheng yiming Li Huan Wang Gong Chen Yongxiang Chen Gemin Fang Jun Guo Chunmao He Honggang Hu Xuechen Li Yanmei Li Zigang Li Man pan Shan Tang Changlin Tian Ping Wang Bian Wu Chuanliu Wu Junfeng Zhao Lei Liu State Key Laboratory of Natural and Biomimetic Drugs and School of Pharmaceutical SciencesPeking UniversityBeijing 100191China Division of Life Sciences and Medicine University of Science and Technology of ChinaHefei 230027China School of Food and Biological Engineering Engineering Research Center of Bio-processMinistry of EducationHefei University of TechnologyHefei 230009China School of Chemistry and Chemical Engineering Nanjing UniversityNanjing 210023China State Key Laboratory of Elemento-Organic Chemistry Nankai UniversityTianjin 300071China Department of Chemistry Tsinghua UniversityBeijing 100084China Institute of Health Sciences Anhui UniversityHefei 230601China College of Chemistry Central China Normal UniversityWuhan 430079China School of Chemistry and Chemical Engineering South China University of TechnologyGuangzhou 510640China School of Medicine or Institute of Translational Medicine Shanghai UniversityShanghai 200444China Department of Chemistry The University of Hong KongHong Kong 999077China Shenzhen Graduate School Peking UniversityShenzhen 518055China School of Chemistry and Chemical Engineering Shanghai Jiao Tong UniversityShanghai 200240China School of Life Sciences University of Science and Technology of ChinaHefei 230026China Department of Chemical Biology Shanghai Jiao Tong UniversityShanghai 200240China Institute of Microbiology Chinese Academy of SciencesBeijing 100101China Department of Chemistry Xiamen UniversityXiamen 361005China School of Pharmaceutical Science Guangzhou Medical UniversityGuangzhou 511436China

The central dogma of modern biology underscores the pivotal roles proteins play in diverse biological processes,the study of which necessitates advanced methods to produce proteins with precision and versatility.Chemical protein synthesis,a powerful approach utilizing chemical reactions for the de novo construction of structurally accurate proteins,has emerged as a transformative tool for studying proteins and generating protein derivatives/mimics inaccessible by natural biological machinery,including post-translationally modified proteins,proteins comprised of unnatural amino acids,as well as mirror-image proteins.This review summarizes recent strides in synthetic method developments for chemical protein synthesis,including innovative techniques in solid-phase peptide synthesis,the challenges presented by difficult sequences in either synthesis or folding and the exploration of novel ligation reactions using both chemical and enzymatic methods.Furthermore,the review also delves into newly developed protocols for site-selective protein modifications and the generation of stapled or macrocyclized peptides/miniproteins,highlighting the power of chemical methods to make structurally diverse proteins.Recent applications of synthetic proteins in investigating post-translational modifications(phosphorylation,lipidation,glycosylation,ubiquitination,etc.),mirror-image biological processes and drug development are further discussed.Together,these topics provide a comprehensive overview of the current landscape of chemical protein synthesis.

关键词： chemical protein synthesis solid-phase peptide synthesis ligation reactions post-translational modifications mirror-image proteins peptide drugs

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Progranulin regulation of autophagy contributes to its chondroprotective effect in osteoarthritis

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Genes & Diseases 2023年第4期10卷 1582-1595页

作者： yiming pan Yuyou Yang Mengtian Fan Cheng Chen Rong Jiang Li Liang Menglin Xian Biao Kuang Nana Geng Naibo Feng Lin Deng Wei Zheng Fengmei Zhang Xiaoli Li Fengjin Guo Department of Cell Biology and Genetics Core Facility of Development BiologyChongqing Medical UniversityChongqing 400016China Department of Orthopaedics The 1st Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Laboratory of Stem Cells and Tissue Engineering Chongqing Medical UniversityChongqing 400016China Department of Orthopaedics The 2nd Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Chongqing Medical University Laboratory Animal Center Chongqing Medical UniversityChongqing 400016China

Progranulin(PGRN)is a multifunctional growth factor involved in many physiolog-ical processes and disease states.The apparent protective role of PGRN and the importance of chondrocyte autophagic function in the progression of osteoarthritis(OA)led us to investi-gate the role of PGRN in the regulation of chondrocyte autophagy.PGRN knockout chondro-cytes exhibited a deficient autophagic response with limited induction following rapamycin,serum starvation,and IL-1b-induced autophagy.PGRN-mediated anabolism and suppression of IL-1b-induced catabolism were largely abrogated in the presence of the BafA1 autophagy inhibitor.Mechanistically,during the process of OA,PGRN and the ATG5eATG12 conjugate form a protein complex;PGRN regulates autophagy in chondrocytes and OA through,at least partially,the interactions between PGRN and the ATG5eATG12 conjugate.Furthermore,the ATG5eATG12 conjugate is critical for cell proliferation and apoptosis.Knockdown or knockout of ATG5 reduces the expression of ATG5eATG12 conjugate and inhibits the chondroprotective effect of PGRN on anabolism and catabolism.Overexpression of PGRN partially reversed this effect.In brief,the PGRN-mediated regulation of chondrocyte autophagy plays a key role in the chondroprotective role of PGRN in OA.Such studies provide new insights into the pathogen-esis of OA and PGRN-associated autophagy in chondrocyte homeostasis.

关键词： Anabolism ATG12 ATG5 Autophagy Catabolism Osteoarthritis PGRN

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基于底栖动物生物完整性指数的黄河干流生态健康评价

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湖泊科学 2024年第2期36卷 512-522页

作者：冯治远侯易明阴琨金小伟韩谞潘保柱西安理工大学西北旱区生态水利国家重点实验室西安710048 中国环境监测总站北京100012

黄河为世界上最长的多沙河流,全河段水沙异质性及其生态健康的空间差异明显。本文基于黄河干流全河段44个断面春秋两季(2019年)底栖动物的系统调查数据,构建黄河底栖动物生物完整性评价体系。该体系融入指示水沙过程变化的ASPT指数及EP... 详细信息

黄河为世界上最长的多沙河流,全河段水沙异质性及其生态健康的空间差异明显。本文基于黄河干流全河段44个断面春秋两季(2019年)底栖动物的系统调查数据,构建黄河底栖动物生物完整性评价体系。该体系融入指示水沙过程变化的ASPT指数及EPT分类单元个体相对丰度,且参照点与受损点得分差异显著,适用于多沙河流生态健康评价。评价结果显示:黄河干流亚健康及以上状态的断面占比为秋季(75.0%)高于春季(54.5%);自源区沿河而下,底栖动物生物完整性指数值呈下降趋势;库区断面底栖动物生物完整性指数低于临近自然河段。回归分析表明,黄河干流底栖动物生物完整性指数与盐度、总氮、城镇及农田用地占比呈显著负相关,与林地及草地占比呈显著正相关。本研究结果可为黄河生态保护与管理提供科学依据。

关键词：黄河干流大型底栖无脊椎动物生物完整性生态健康评价

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无定河流域不同水土流失区底栖动物生物完整性指数构建与健康评价

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湖泊科学 2024年第1期36卷 274-285,I0026-I0037页

作者：侯湘然潘保柱侯易明胡恩贺瑶冯治远西安理工大学西北旱区生态水利国家重点实验室西安710048 陕西省环境科学研究院西安710061

无定河流域位于黄土高原与毛乌素沙地过渡带,水土流失严重,生态环境具有脆弱性和波动性。于2021年春季(4月)和秋季(10月)对无定河流域上、中、下游及其6条支流和流域内的3个淤地坝开展水生态系统调查,旨在厘清无定河流域底栖动物群落特... 详细信息

无定河流域位于黄土高原与毛乌素沙地过渡带,水土流失严重,生态环境具有脆弱性和波动性。于2021年春季(4月)和秋季(10月)对无定河流域上、中、下游及其6条支流和流域内的3个淤地坝开展水生态系统调查,旨在厘清无定河流域底栖动物群落特征,构建底栖动物生物完整性指数并开展健康评价。无定河流域春季共采集到底栖动物105种,平均密度为181 ind./m^(2),平均生物量为0.760 g/m^(2),秋季共采集到底栖动物67种,平均密度为94 ind./m^(2),平均生物量为0.454 g/m^(2)。通过对两季度研究区域内底栖动物27个生物参数开展分布范围检验、判别能力分析和相关性分析,构建无定河流域底栖动物生物完整性指数,对全流域40个样点(6个参照点和34个受损点)进行B-IBI健康评价。评价结果表明,总体上无定河流域底栖动物生物完整性较好,40个样点中春季有19个处于健康或亚健康状态,秋季有23个处于健康或亚健康状态,其中无定河上、中游干支流大都以健康和亚健康为主,无定河下游干支流以及3个淤地坝水体健康状况较差。在不同水土流失类型区域,底栖动物群落特征和生物完整性评价具有显著性差异。本研究结果可为无定河流域河流健康评估提供科学依据。

关键词：无定河流域水土流失底栖动物完整性指数大型底栖无脊椎动物健康评价

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Broadband optical frequency comb generation based on single electro‑absorption modulation driven by radio frequency coupled signals

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Frontiers of Optoelectronics 2022年第4期15卷 43-50页

作者： pan Jiang Peili Li yiming Fan College of Electronic and Optical Engineering&College of Microelectronics Nanjing University of Posts and TelecommunicationsNanjing 210023China

Broadband optical frequency comb(OFC)generation based on a single electro-absorption modulator(EAM)is proposed.The EAM is driven by a radio frequency(RF)multi-frequency signal generated by a multiplication coupler composed of an electrical power splitter and an arithmetic circuit.Thus the number of comb-lines of the generated OFC can be increased.A complete theoretical model of OFC generation by an EAM driven by nth power of the RF source is established,and the performance of the OFC is analyzed by using OptiSystem software.The results show that,the number of comb-lines of the OFC is positively correlated with the number of multiplication of the RF source signal.The frequency spacing of the comb-lines is twice the frequency of the RF source signal and is tunable by adjusting the frequency of the RF source signal.Increasing chirp factor and modulation index of EAM could increase the number of comb-lines of the generated OFC.The amplitude of the RF source signal had little impact on the fatness of the OFC and the average OFC power.The scheme developed is not only simple and low-cost,but also can produce a large number of comb-lines.

关键词： Optical frequency comb(OFC) Electro-absorption modulator(EAM) Radio frequency(RF)coupled signal

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Weak measurements and quantum-to-classical transitions in free electron-photon interactions

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Light(Science & Applications) 2023年第11期12卷 2519-2529页

作者： yiming pan Eliahu Cohen Ebrahim Karimi Avraham Gover Norbert Schönenberger TomášChlouba Kangpeng Wang Saar Nehemia Peter Hommelhoff Ido Kaminer Yakir Aharonov School of Physical Science and Technology and Center for Transformative Science ShanghaiTech UniversityShanghai 200031China Department of Electrical Engineering TechnionHaifa 3200003Israel Department of Physics of Complex Systems Weizmann Institute of ScienceRehovot 7610001Israel Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials Bar Ilan UniversityRamat Gan 5290002Israel Department of Physics University of OttawaOttawaOntario K1N 6N5Canada Department of Electrical Engineering Physical Electronics Center for Laser-Matter Interaction(LMI)Tel Aviv UniversityRamat Aviv 6997801Israel Department of Physics Friedrich-Alexander Universität Erlangen-Nürnberg(FAU)Staudtstraße 191058 ErlangenGermany School of Physics and Astronomy Tel Aviv UniversityRamat Aviv 6997801Israel Institute for Quantum Studies Chapman UniversityOrangeCA 92866USA

How does the quantum-to-classical transition of measurement occur?This question is vital for both foundations and applications of quantum mechanics.Here,we develop a new measurement-based framework for characterizing the classical and quantum free electron-photon interactions and then experimentally test it.We first analyze the transition from projective to weak measurement in generic light-matter interactions and show that any classical electron-laserbeam interaction can be represented as an outcome of weak measurement.In particular,the appearance of classical point-particle acceleration is an example of an amplified weak value resulting from weak measurement.A universal factor,exp(-Γ^(2)=2),quantifies the measurement regimes and their transition from quantum to classical,whereΓcorresponds to the ratio between the electron wavepacket size and the optical wavelength.This measurement-based formulation is experimentally verified in both limits of photon-induced near-field electron microscopy and the classical acceleration regime using a DLA.Our results shed new light on the transition from quantum to classical electrodynamics,enabling us to employ the essence of the wave-particle duality of both light and electrons in quantum measurement for exploring and applying many quantum and classical light-matter interactions.

关键词： quantum photon acceleration

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Recent advances in protein conformation sampling by combining machine learning with molecular simulation

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Chinese Physics B 2024年第3期33卷 80-87页

作者：唐一鸣杨中元姚逸飞周运谈圆王子超潘瞳熊瑞孙俊力韦广红 Department of Physics State Key Laboratory of Surface Physicsand Key Laboratory for Computational Physical Sciences (Ministry of Education)Shanghai 200438China

The rapid advancement and broad application of machine learning(ML)have driven a groundbreaking revolution in computational biology.One of the most cutting-edge and important applications of ML is its integration with molecular simulations to improve the sampling efficiency of the vast conformational space of large biomolecules.This review focuses on recent studies that utilize ML-based techniques in the exploration of protein conformational landscape.We first highlight the recent development of ML-aided enhanced sampling methods,including heuristic algorithms and neural networks that are designed to refine the selection of reaction coordinates for the construction of bias potential,or facilitate the exploration of the unsampled region of the energy landscape.Further,we review the development of autoencoder based methods that combine molecular simulations and deep learning to expand the search for protein conformations.Lastly,we discuss the cutting-edge methodologies for the one-shot generation of protein conformations with precise Boltzmann weights.Collectively,this review demonstrates the promising potential of machine learning in revolutionizing our insight into the complex conformational ensembles of proteins.

关键词： machine learning molecular simulation protein conformational space enhanced sampling

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