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Broadening environmental research in the era of accurate protein structure determination and predictions

Frontiers of Environmental Science & Engineering 2024年第7期18卷 169-178页

作者： Mingda Zhou tong Wang Ke Xu han Wang Zibin Li Wei-xian Zhang Yayi Wang State Key Laboratory of Pollution Control and Resources Reuse Shanghai Institute of Pollution Control and Ecological SecurityCollege of Environmental Science and EngineeringTongji UniversityShanghai 200092China Translational Research Institute of Brain and Brain-Like Intelligence Shanghai Fourth People's HospitalSchool of MedicineTongji UniversityShanghai 200434China

The deep-learning protein structure prediction method AlphaFold2 has garnered enormous attention beyond the realm of structural biology,for its groundbreaking contribution to solving the"protein foiding problem"In this perspective,we explore the connection between protein structure studies and environmental research,delving into the potential for addressing specific environmental *** are promising for environmental applications because of the functional diversity endowed by their structural ***,structural studies on proteins with environmental significance remain ***,we present the opportunity to study proteins by advancing experimental determination and deep-learning prediction ***,the latest progress in environmental research via cryogenic electron microscopy is *** allows us to determine the structure of protein complexes in their native state within cells at molecular resolution,revealing environmentally-associated structural *** the remarkable advancements in computational power and experimental resolution,the study of protein structure and dynamics has reached unprecedented depth and *** advancements will undoubtedly accelerate the establishment of comprehensive environmental protein structural and functional *** opportunities for protein engineering exist to enable innovative solutions for environmental applications,such as the degradation of persistent contaminants,and the recovery of valuable metals as well as rare earth elements.

关键词： Environmental proteins Protein structure Cryogenic electron microscopy Protein structure prediction Protein engineering Artificial Intelligence

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Network Pharmacology and Molecular Docking Analysis of the Mechanisms of Combined Radix Bupleuri(Chai-Hu) and Radix Paeoniae Alba(Bai-Shao) Treatment in the Prevention and Treatment of Alzheimer's Disease

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World Journal of Traditional Chinese Medicine 2024年第2期10卷 254-262页

作者： Zhao-han Huang Yuan Fang Qi Yu tong Wang College of Traditional Chinese Medicine Beijing University of Chinese MedicineBeijingChina Shanghai Center for Women and Children's Health ShanghaiChina

Objective: Radix Bupleuri and Radix Paeoniae Alba are referred to as Chai-Hu and Bai-Shao, respectively, in Chinese. We used molecular docking and network pharmacological approaches to explore the active components of this Chinese herb combination which is commonly used for treating Alzheimer's disease(AD), the Chai-Hu and Bai-Shao pair(CBP). Materials and Methods: The active compounds and action targets of Chai-Hu and Bai-Shao were identified in the Traditional Chinese Medicine Systems Pharmacology database, and the Therapeutic Target Database, Drug Bank, Gen Cards, Dis Ge NET, and Online Mendelian Inheritance in Man databases were used to identify therapeutic targets in patients with AD. To identify a common target of CBP in the treatment of AD, we used the Metascape tool to perform Gene Ontology function enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. In addition, CBP-AD protein–protein interaction(PPI) and herb-component-target networks were created using Cytoscape 3.8.2. Molecular docking was verified using Auto Dock tools. Results: We identified 20 active compounds of CBP, 202 active targets, 1,323 disease targets, and 117 active compound disease intersection targets;the PPI network showed that the top eight key targets were AKT1, interleukin(IL) 6, JUN, MAPK1, tumor necrosis factor, TP53, vascular endothelial growth factor, and epidermal growth factor. These act mainly on the fluid shear stress, atherosclerosis, IL-17, hypoxia-inducible factor-1, and nonalcoholic fatty liver disease pathways, among others, which control immune inflammation, cell proliferation, and apoptosis. Based on molecular docking results, the active components of CBP bind well to its key targets. Conclusion: Our results indicated that CBP was effective for treating AD by reducing the expression of inflammatory factors, promoting cell proliferation and differentiation, and preventing nerve cell death and anti-neuronal cell apoptosis.

关键词： Alzheimer's disease Bai-Shao Chai-Hu molecular docking network pharmacology

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Printable,flexible ceramic fiber paper based on electrospinning

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Rare Metals 2024年第6期43卷 2739-2746页

作者： Yong-Shuai Xie Yuan cheng Yang Lyu Rui Li Jie-Cai han National Key Laboratory of Science and Technology on Advanced Composites in Special Environments Harbin Institute of TechnologyHarbin 150001China State Key Laboratory of Intelligent Manufacturing Equipment and Technology Huazhong University of Science and TechnologyWuhan 430074China

Based on the fact that it is challenging for the polymer flexible circuit substrates to meet the requirements of serving in high-temperature environments,this work proposed the idea of using printable ceramic fiber paper as a high-temperature flexible circuit substrate.A ceramic fiber paper with all ceramic components had been developed via electrospinning,solving the problems of low strength and severe strength drop at high temperatures of traditional ceramic fiber *** tensile strength of the prepared ceramic fiber paper is 2.63 MPa,and the reliable service temperature is 1200℃.Its bulk density is about 1.5 times that of traditional ceramic fiber *** can be printed with patterns by commercial inkjet printers like ordinary printing paper and has excellent *** feasibility of ceramic fiber paper as a flexible circuit substrate was verified by constructing a simple *** the fiber paper is significantly bent,the circuit still forms a complete path,which proves that it has a strong application potential for high-temperature flexible circuit substrate and is expected to promote the development of flexible electronic devices serving at extreme high-temperature environments.

关键词： Ceramic fiber paper High temperature Inkjet printing Flexible electronic

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Discriminative explicit instance selection for implicit discourse relation classification

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Frontiers of Computer Science 2024年第4期18卷 129-138页

作者： Wei SONG Hongfei han Xu han Miaomiao cheng Jiefu GONG Shijin WANG Ting LIU Information Engineering College Capital Normal UniversityBeijing 100048China iFLYTEK AI Research Institute Hefei 230088China Research Center for Social Computing and Information Retrieval Harbin Institute of TechnologyHarbin 150006China

Discourse relation classification is a fundamental task for discourse analysis,which is essential for understanding the structure and connection of *** discourse relation classification aims to determine the relationship between adjacent sentences and is very challenging because it lacks explicit discourse connectives as linguistic cues and sufficient annotated training *** this paper,we propose a discriminative instance selection method to construct synthetic implicit discourse relation data from easy-to-collect explicit discourse *** expanded instance consists of an argument pair and its sense *** introduce the argument pair type classification task,which aims to distinguish between implicit and explicit argument pairs and select the explicit argument pairs that are most similar to natural implicit argument pairs for data *** also propose a simple label-smoothing technique to assign robust sense labels for the selected argument *** evaluate our method on PDTB 2.0 and PDTB *** results show that our method can consistently improve the performance of the baseline model,and achieve competitive results with the state-of-the-art models.

关键词： discourse analysis PDTB discourse relation implicit discourse relation classification data expansion

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Recent process developments in beneficiation and metallurgy of rare earths:A review

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Journal of Rare Earths 2024年第4期42卷 629-642页

作者： Shaokai cheng Wenbo Li Yuexin han Yongsheng Sun Peng Gao Xiaolong Zhang School of Resources and Civil Engineering Northeastern UniversityShenyang110819China National-local Joint Engineering Research Center of High-efficient Exploitation Technology for Refractory Iron Ore Resources Shenyang110819China

Rare earth elements(REEs)are irreplaceable materials supporting low-carbon technology and equip-ment,and their commercial demand and strategic position are becoming increasingly *** the continuous depletion of rare earth(RE)resources,developing high-efficiency beneficiation and eco-friendly metallurgical processes has attracted widespread *** paper reviews the major minerals exploited for RE production and their deposits,as well as the beneficiation and metallurgical processes of RE ***,monazite,mixed RE ores,and ion-adsorption clays are the main raw materials in the world to ***-bearing ores(except ion-adsorption minerals)are generally beneficiated by flotation,gravity and magnetic separation *** mainstream metallurgical processes for bastnaesite,monazite and mixed RE concentrates are oxidation roasting-HCl leaching,caustic soda decomposition and high-temperature concentrated sulfuric acid roasting,***-adsorption clays are directly processed by in situ leaching-precipitation/solvent *** achieve the sustainable development of RE resources,it is essential to further explore innovative techniques to achievecomprehensive utilization and cleaner production.

关键词： Rare earths Beneficiation processes Metallurgical processes Cleaner production

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A Comparative Study on the Post-Buckling Behavior of Reinforced Thermoplastic Pipes(RTPs)Under External Pressure Considering Progressive Failure

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China Ocean Engineering 2024年第2期38卷 233-246页

作者： DING Xin-dong WANG Shu-qing LIU Wen-cheng YE Xiao-han College of Engineering Ocean University of ChinaQingdao 266100China Shandong Provincial Key Laboratory of Ocean Engineering Ocean University of ChinaQingdao 266100China Department of Marine Technology Norwegian University of Science and Technology(NTNU)Trondheim NO-7491Norway

The collapse pressure is a key parameter when RTPs are applied in harsh deep-water *** investigate the collapse of RTPs,numerical simulations and hydrostatic pressure tests are *** the numerical simulations,the eigenvalue analysis and Riks analysis are combined,in which the Hashin failure criterion and fracture energy stiffness degradation model are used to simulate the progressive failure of composites,and the“infinite”boundary conditions are applied to eliminate the boundary *** for the hydrostatic pressure tests,RTP specimens were placed in a hydrostatic chamber after filled with *** has been observed that the cross-section of the middle part collapses when it reaches the maximum *** collapse pressure obtained from the numerical simulations agrees well with that in the ***,the applicability of NASA SP-8007 formula on the collapse pressure prediction was also *** has a relatively greater difference because of the ignorance of the progressive failure of *** the parametric study,it is found that RTPs have much higher first-ply-failure pressure when the winding angles are between 50°and 70°.Besides,the effect of debonding and initial ovality,and the contribution of the liner and coating are also discussed.

关键词： reinforced thermoplastic pipes post-buckling behavior progressive failure of composites debonding initial ovality

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Accelerated aging and frailty in cardiovascular diseases

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Journal of Geriatric Cardiology 2024年第8期21卷 828-830页

作者： Xue-Hua cheng Tao WU Li han Department of Traditional Chinese Medicine Geriatrics Huadong Hospital Affiliated to Fudan UniversityShanghaiChina

Aging is the greatest risk factor for cardiovascular disease(CVD),which is the most common cause of death in European countries.[1]It is estimated that during the period from 2020 to 2022,there were 9.0%more excess deaths from CVD than expected.[2]By 2030,approximately 20%of the population will be aged 65 years and older,and CVD will account for 40%of deaths in this age group,[3]imposing a significant burden on the healthcare system and society as a *** is related to frailty,which represents the dynamic progression of physical and physiological decline in older *** limits an individual’s ability to recover from acute stressors and serves as a predictor of clinical adverse *** the uncertainties in screening,assessing,and managing frailty in clinical practice,emphasizing the connections between frailty,aging,and CVD will provide new insights for the prediction,prevention and management of CVD in the aging population.

关键词： aging prevention prediction

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Centrifuge modeling of a large-scale surcharge on adjacent foundation

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第8期16卷 3181-3191页

作者： Jinzhang Zhang Zhenwei Ye Dongming Zhang Hongwei Huang Shijie han tong Zou Le Zhang Key Laboratory of Geotechnical and Underground Engineering of Ministry of Education and Department of Geotechnical Engineering Tongji UniversityShanghai200092China CCCC Third Harbor Consultants Co LtdShanghai200032China Qingdao Conson Jiaozhou Bay Second Subsea Tunnel Co. LtdQingdao266000China

This study investigates the ground and structural response of adjacent raft foundations induced by largescale surcharge by ore in soft soil areas through a 130g centrifuge modeling test with an innovative layered loading *** prototype of the test is a coastal iron ore yard with a natural foundation of deep soft ***,it is necessary to adopt some measures to reduce the influence of the large-scale surcharge on the adjacent raft foundation,such as installing stone columns for foundation *** an acceleration of 130 g,the model conducts similar simulations of iron ore,stone columns,and raft foundation *** tested soil mass has dimensions of 900 mm×700 mm×300 mm(lengthwidthdepth),which is remodeled from the soil extracted from the drilling *** test conditions are consistent with the actual engineering conditions and the effects of four-level loading conditions on the composite foundation of stone columns,unreinforced zone,and raft foundations are *** automatic layer-by-layer loading device was innovatively developed to simulate the loading process of actual engineering more *** composite foundation of stone columns had a large settlement after the loading,forming an obvious settlement trough and causing the surface of the unreinforced zone to *** 12 m surcharge loading causes a horizontal displacement of 13.19 cm and a vertical settlement of 1.37 m in the raft *** stone columns located on both sides of the unreinforced zone suffered significant shear damage at the sand-mud *** to the reinforcement effect of stone columns,the sand layer below the top of the stone columns moves ***,the horizontal earth pressure in the raft foundation zone increases *** stone columns will form new drainage channels and accelerate the dissipation of excess pore pressure.

关键词： Centrifuge modeling Stone column Composite foundation Ground movement Raft foundation

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New insight into the role of exosomes in idiopathic membrane nephropathy

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BIOCELL 2024年第1期48卷 21-32页

作者： JIANHONG LIU KAI HE han WANG XIAOHONG cheng Department of Nephrology Shaanxi Provincial Hospital of Traditional Chinese MedicineXian710000China School of BasicMedical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese MedicineChengdu611137China Department of Pathophysiology West China College of Basic Medical Sciences&Forensic MedicineSichuan UniversityChengdu610041China

Exosomes,nanoscale extracellular vesicles(EVs)derived from the invagination of the endosomal membrane,are secreted by a majority of cell *** carriers of DNA,mRNA,proteins,and microRNAs,exosomes are implicated in regulating biological activities under physiological and pathological ***-derived exosomes,which vary in origin and function,may either contribute to the pathogenesis of disease or represent a potential therapeutic *** nephropathy(MN),an autoimmune kidney disease characterized by glomerular damage,is a predominant cause of nephrotic ***,MN,especially idiopathic membranous nephropathy(IMN),often results in end-stage renal disease(ESRD),affecting approximately 30%of patients and posing a considerable economic challenge to healthcare *** substantial research,therapeutic options remain ineffective at halting IMN progression,underscoring the urgent need for innovative *** evidence has implicated exosomes in IMN’s pathophysiology;Providing a fresh perspective for the discovery of novel biomarkers and therapeutic *** review aims to scrutinize recent developments in exosome-related mechanisms in IMN and evaluate their potential as promising therapeutic targets and diagnostic biomarkers,with the hope of catalyzing further investigations into the utility of exosomes in MN,particularly IMN,ultimately contributing to improved patient outcomes in these challenging disease settings.

关键词： Exosomes Biomarkers Membranous nephropathy Therapeutic targets

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Autocatalytic bifunctional supramolecular hydrogels for osteoporotic bone repair

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National Science Review 2024年第7期11卷 263-278页

作者： Zhihui han Xiang Gao Yuanjie Wang cheng Huang Hao Song Shuning cheng Xiaoyuan Yang Xiaoliang Cui Jie Wu Kailu Wei Liang cheng Institute of Functional Nano&Soft Materials(FUNSOM) Collaborative Innovation Center of Suzhou Nano Science and TechnologySoochow University Department of Orthopedics The Second Affiliated Hospital of Soochow University Macao Institute of Materials Science and Engineering Macau University of Science and Technology

Conventional bone scaffolds, which are mainly ascribed to highly active osteoclasts and an inflammatory microenvironment with high levels of reactive oxygen species and pro-inflammatory factors, barely satisfy osteoporotic defect repair. Herein, multifunctional self-assembled supramolecular fiber hydrogels(Ce–Aln gel) consisting of alendronate(Aln) and cerium(Ce) ions were constructed for osteoporotic bone defect repair. Based on the reversible interaction and polyvalent cerium ions, the Ce–Aln gel, which was mainly composed of ionic coordination and hydrogen bonds, displayed good injectability and autocatalytic amplification of the antioxidant effect. In vitro studies showed that the Ce–Aln gel effectively maintained the biological function of osteoblasts by regulating redox homeostasis and improved the inflammatory microenvironment to enhance the inhibitory effect on osteoclasts. Ribonucleic acid(RNA) sequencing further revealed significant downregulation of various metabolic pathways, including apoptosis signaling,hypoxia metabolism and tumor necrosis factor-alpha(TNF-α) signaling via the nuclear factor kappa-B pathway after treatment with the Ce–Aln gel. In vivo experiments showed that the clinical drug-based Ce–Aln gel effectively promoted the tissue repair of osteoporotic bone defects by improving inflammation and inhibiting osteoclast formation at the defect. Notably, in vivo systemic osteoporosis was significantly ameliorated, highlighting the strong potential of clinical translation for precise therapy of bone defects.

关键词： autocatalysis supramolecular hydrogel anti-inflammation osteoporosis bone defect

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