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Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

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Chinese Physics B 2022年第5期31卷 756-765页

作者： Jian-Gang wang Xiao-Xuan Shi Yu-Ru Liu peng-ye wang Hong Chen Ping Xie School of Material Science and Engineering Central South University of Forestry and TechnologyChangsha 410004China Key Laboratory of Soft Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP *** important factor characterizing the processivity of the kinesin motor is its dissociation from the ***,using all-atom molecular dynamics simulations,we studied the dissociation process of the kinesin head in weak-microtubulebinding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and *** analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation *** found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic ***,the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were *** studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.

关键词： kinesin dissociation energy landscape molecular dynamics simulation

On the superconvergence of a WG method for the elliptic problem with variable coefficients

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Science China Mathematics 2024年第8期67卷 1899-1910页

作者： Junping wang Xiaoshen wang Xiu ye Shangyou Zhang peng Zhu Division of Mathematical Sciences National Science FoundationAlexandriaVA 22314USA Department of Mathematics University of Arkansas at Little RockLittle RockAR 72204USA Department of Mathematical Sciences University of DelawareNewarkDE 19716USA College of Data Science Jiaxing UniversityJiaxing 314001China

This article extends a recently developed superconvergence result for weak Galerkin(WG)approximations for modeling partial differential equations from constant coefficients to variable *** superconvergence features a rate that is two orders higher than the optimal-order error estimates in the usual energy and L^(2)*** extension from constant to variable coefficients for the modeling equations is highly *** underlying technical analysis is based on a sequence of projections and *** results confirm the superconvergence theory for second-order elliptic problems with variable coefficients.

关键词： weak Galerkin finite element methods superconvergence second-order elliptic problems stabilizerfree

Pindel-TD:A Tandem Duplication Detector Based on A Pattern Growth Approach

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 99-104页

作者： Xiaofei Yang Gaoyang Zheng peng Jia Songbo wang Kai ye School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Center for Mathematical Medical the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Faculty of Science Leiden UniversityLeiden 2311 EZNetherland

Tandem duplication(TD)is a major type of structural variations(SVs)that plays an important role in novel gene formation and human ***,TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational ***,we developed a TD detection module for the Pindel tool,referred to as Pindel-TD,based on a TD-specific pattern growth ***-TD is capable of detecting TDs with a wide size range at single nucleotide *** simulated and real read data from HG002,we demonstrated that Pindel-TD outperforms other leading methods in terms of precision,recall,F1-score,and ***,by applying Pindel-TD to data generated from the K562 cancer cell line,we identified a TD located at the seventh exon of SAGE1,providing an explanation for its high ***-TD is available for non-commercial use at https://***/xjtu-omics/pindel.

关键词： Tandem duplication Pattern growth Short-read sequencing Structural variation SAGE1

Decreased Nrf2 protein level and low sperm quality in intractable spermatocystitis

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Asian Journal of Andrology 2024年第2期26卷 189-194页

作者： Shi-Ze wang Jian-Nan Liu Fen-Fang Zhou ye-Jin-peng wang peng Zhang Song-Tao Cheng Department of Urology Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610072China Department of Urology Zhongnan Hospital of Wuhan UniversityWuhan 430071China Department of Health Management and Clinical Medicine School of Medicine and HealthWuhan PolytechnicUniversityWuhan 430071China

To investigate the molecular etiology of low sperm quality in patients with intractable spermatocystitis,spermatozoa samples from patients with persistent hematospermia undergoing transurethral seminal vesiculoscopy and healthy volunteers were *** samples were collected from the seminal vesicles through transurethral seminal vesiculoscopy or by masturbation *** quality was analyzed by a WLJY-9000 color semen analysis *** of tumor necrosis factor alpha(TNFa)and interleukin-6(IL-6)in the seminal plasma was performed using enzyme-linked immunosorbent assay(ELISA).Measurement of H_(2)O_(2)in the seminal plasma was performed with a hydrogen peroxide *** protein levels of nuclear factor erythroid 2-related factor 2(Nrf2)and phosphorylated-Nrf2(p-Nrf2)were measured by western blot analysis and immunofluorescence *** sperm quality parameters and increased levels of inflammatory cytokines(TNFa,IL-6,and H_(2)O_(2))in the seminal plasma were detected among the semen samples from the patients with persistent ***2 and p-Nrf2 were strongly expressed in the nucleus and periphery of human sperm cells,according to the results of the immunofluorescence *** protein levels of Nrf2 and p-Nrf2 were significantly lower in the spermatozoa samples from patients with persistent hematospermia than in those from healthy volunteers with normal sperm *** results suggested that Nrf2 signaling might play a role in the low sperm quality of patients with intractable spermatocystitis.

关键词： H_(2)O_(2) Nrf2 sperm quality spermatocystitis

Achieving exceptionally high strength and rapid degradation rate of Mg-Er-Ni alloy by strengthening with lamellar γ' and bulk LPSO phases

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Journal of Materials Science & Technology 2024年第1期168卷 88-102页

作者： Chaoneng Dai Jingfeng wang Yuanlang Pan Kai Ma Yinhong peng ye wang Danqian wang Chunhua Ran Jinxing wang Yanlong Ma College of Chemistry and Chemical Engineering Chongqing UniversityChongqing 401331China College of Materials Science and Engineering Chongqing UniversityChongqing 400044China National Engineering Research Center for Magnesium Alloys Chongqing 400044China College of Materials Science and Engineering Chongqing University of TechnologyChongqing 400054China

As-extruded Mg-Er-Ni alloys with different volume fractions of long-period stacking ordered(LPSO)phase and density of lamellar γ' phase were prepared,and the microstructure,mechanical,and degradation properties were *** the bulk LPSO phase and the lamellar γ' phase,and controlling the dynamic recrystallization processes during deformation by adjusting the volume fraction of LPSO and the density of the γ' phase,a synergistic increase in strength and degradation rate can be *** the one hand,the increase in corrosion rate was related to the increased volume fraction of the bulk LPSO phase and the densities of the lamellar γ' phase,which provide more galvanic ***,high densities of the lamellar γ' phase can provide more corrosion interface by inhibiting the recrystallization process to refine dynamic recrystallized(DRXed)grains during the hot *** the other hand,the ultimate tensile strength(UTS)and tensile yield strength(TYS)of the Mg-Er-Ni alloy increased from 345 and 265 MPa to 514 MPa and 358 MPa,respectively,which was mainly attributed to grain boundary and texture strengthening,bulk LPSO phase and lamellar γ' phase ***,Mg^(-1)4Er-4Ni alloy,which contains the highest volume fraction bulk LPSO phase and the densities of lamellar γ' phase,re-alized a synergistic enhancement of strength and degradation *** UTS,TYS,and degradation rate of Mg^(-1)4Er-4Ni were 514 MPa,358 MPa,and 142.5 mg cm^(-2)h^(-1)(3 wt%KCl solution at 93◦C),*** research provides new insight into developing Mg alloys with high strength and degradation rates for fracturing tool materials in the application of oil and gas exploitation in harsh environments.

关键词： Mg-Er-Ni alloy Lamellarγ'and bulk LPSO phases Rapid degradation rate High strength Mechanical and corrosion mechanism

OSDA-free synthesis of FeZSM-22 zeolite from natural minerals for n-octane hydroisomerization

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Chinese Journal of Chemical Engineering 2024年第2期66卷 51-59页

作者： Tiesen Li Ting Chen Yinghui ye peng Dong Tinghaiwang Qingyan Cui Chan wang Yuanyuan Yue National Engineering Research Center of Chemical Fertilizer Catalyst College of Chemical EngineeringFuzhou UniversityFuzhou 350002China Qingyuan Innovation Laboratory Quanzhou 362801China

A seed-directed approach to synthesizing Fe ZSM-22 zeolite without organic structure directing agent(OSDA)was developed by using Fe-rich diatomite as all aluminum and iron *** Fe ZSM-22zeolite with optimal crystallinity and purity can be obtained by systematically adjusting feed composition and synthesis *** show that Fe ZSM-22 zeolite synthesized with OSDA-free owns high crystallinity,obvious thin needle-shaped morphology and high Bronsted/Lewis acid ***,when used for n-octane hydroisomerization reaction,its derived catalyst exhibits the best catalytic performance reflected by the highest selectivity to C_(8)isomers compared to the two reference catalysts prepared based on a Fe-containing and a Fe-free ZSM-22 synthesized through an OSDA-directed route from natural diatomite and conventional chemicals,*** work provides an alternative route to sustainably synthesizing heteroatomic zeolites with high performance.

关键词： FeZSM-22 zeolite OSDA-free synthesis Natural minerals n-octane hydroisomerization

Supercoiled DNA Minicircles under Double-strand Breaks

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Chinese Journal of Polymer Science 2024年第9期42卷 1353-1359,I0007页

作者： ye-peng Qiao Chun-Lai Ren National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210093China

Understanding how supercoiled DNA releases intramolecular stress is essential for its functional ***,the molecular mechanism underlying the relaxation process remains insufficiently *** we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed *** simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage *** relaxation process is influenced not only by the separation distance between the fixed ends but also their ***,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled *** findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.

关键词： Supercoiled DNA DNA minicircle DNA relaxation oxDNA model MD simulation

NextPolish2:A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 105-109页

作者： Jiang Hu Zhuo wang Fan Liang Shan-Lin Liu Kai ye De-peng wang School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China GrandOmics Biosciences Beijing 102206China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China

The high-fidelity(HiFi)long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome ***,these assemblies still contain base-level errors,particularly within the error-prone regions of HiFi long *** genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long ***,we describe an upgraded genome polishing tool-NextPolish2,which can fix base errors remaining in those“highly accurate”genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch *** believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere(T2T)***2 is freely available at https://***/Nextomics/NextPolish2.

关键词： Telomere-to-telomere Genome assembly Genome polishing Error correction HiFi long read

Run-and-Tumble Dynamics and Mechanotaxis Discovered in Microglial Migration

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Research 2024年第2期2023卷 95-103页

作者： Yiyu Zhang Da Wei Xiaochen wang Boyi wang Ming Li Haiping Fang Yi peng Qihui Fan Fangfu ye Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejang 325000China Songshan Lake Materials Laboratory DongguanGuangdong 523808China School of Science East China University of Science and TechnologyShanghai 200237China Oujang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)WenzhouZhejiang 325000China

Microglia are resident macrophage cells in the central nervous system that search for pathogens or abnormal neural activities and migrate to resolve the *** effective search and targeted motion of macrophages mean dearly to maintaining a healthy brain,yet little is known about their migration *** this work,we study microglial motion with and without the presence of external *** discover that the cells are promptly attracted by the applied forces(i.e.,mechanotaxis),which is a tactic behavior as yet unconfirmed in ***,in both the explorative and the targeted migration,microglia display dynamics that is strikingly analogous to bacterial run-and-tumble motion.A closer examination reveals that microglial run-and-tumble is more sophisticated,e.g.,they display a short-term memory when tumbling and rely on active steering during runs to achieve mechanotaxis,probably via the responses of mechanosensitive ion *** differences reflect the sharp contrast between microglia and bacteria cells(eukaryotes ***)and their environments(compact tissue ***).Further analyses suggest that the reported migration dynamics has an optimal search efficiency and is shared among a subset of immune cells(human monocyte and macrophage).This work reveals a fruitful analogy between the locomotion of 2 remote systems and provides a framework for studying immune cells exploring complex environments.

关键词： analogy closer prompt