1.Improvements and Recent Advances of Metadynamics Enhanced Sampling Method
Ming-Qiong TONG ; Yue-Wen YIN ; Zhi-Hong SHI ; Zan-Xia CAO
Progress in Biochemistry and Biophysics 2026;53(6):1793-1797
The functional realization of proteins and other biological macromolecules depends on conformational dynamics and allosteric regulation, and elucidating their molecular mechanisms is an important foundation for understanding life processes. Molecular dynamics simulations are a powerful tool for investigating conformational evolution at the atomic level. However, traditional methods are limited by simulation timescales and high free-energy barriers, making it difficult to effectively capture rare conformations and their transition pathways. As a result, the development of enhanced sampling techniques has become key to overcoming this bottleneck. As a classical enhanced sampling technique, metadynamics suffers from several shortcomings, including strong dependence on collective variables and significant errors caused by bias potential accumulation. This article reviews three major improvement strategies. The first combines stochastic resetting with metadynamics, using trajectory-resetting mechanisms to improve sampling efficiency while avoiding the difficulty of optimizing collective variables. The second, SinkMeta, employs a “sinking” bias effect to enable efficient exploration of specific regions and paths. The third, OPES-based hybrid methods, improve the stability of free-energy estimation by optimizing the target distribution or the way the bias is constructed. These methods provide new ideas for characterizing free-energy landscapes and studying conformational transitions in complex biological systems, while also promoting the continued development of enhanced sampling methodologies.
2.Investigations of tick habitats and potential pathogens carried in urban environments of Jiangsu Province
Zhi-ming WU ; Ye TIAN ; Wei-fang YANG ; Hong-na CHEN ; Jian GAO ; Hui LIU ; Yu-fu ZHANG ; Gan CAO ; Hong-liang CHU
Acta Parasitologica et Medica Entomologica Sinica 2026;33(3):192-197
Objective To investigate the species composition, distribution, density, and pathogen-carrying status of host-seeking ticks in urban environments of Jiangsu Province, and to provide a scientific basis for the prevention and control of tick-borne diseases in urban settings. Methods From April to September 2023, a survey on host-seeking ticks was conducted in three types of habitats (city parks, residential areas, and street greenbelts) across 54 counties (cities, districts) of 13 prefecture-level cities in Jiangsu Province by using the flagging method. RStudio 4.4.3 (Windows version) was employed to perform chi-square test analysis on the species composition of ticks across different months, and Friedman test (for multiple paired samples) was applied to analyze monthly changes in the average tick density index among different habitats. Quantitative real-time PCR was performed to detect pathogens in the captured ticks. Results A total of 863 host-seeking ticks were captured from 54 habitats in 24 counties (cities, districts) of 11 prefecture-level cities (Nanjing, Wuxi, Changzhou, Suzhou, Nantong, Huai'an, Yancheng, Yangzhou, Zhenjiang, Taizhou, and Suqian) in Jiangsu Province, whereas no ticks were captured in Xuzhou and Lianyungang. The collected ticks belonged to three species, with Haemaphysalis longicornis being the dominant species (accounting for 82.62%), followed by Haemaphysalis flava and Hae. phasiana. The average density index of ticks in positive habitats was 3.20 ticks/ (flag·100 m). In terms of tick density among prefecture-level cities, Wuxi had the highest density[13.55 ticks/(flag·100 m)], whereas Nanjing and Taizhou had the lowest[both,0.20 ticks/(flag·100 m)]. With respect to the types of positive habitats,46 positive city parks,7 positive residential areas, and 1 positive street greenbelt were found, with the average tick density index being 3.46, 1.86, and 3.60 ticks/flag · 100 m, respectively. No statistically significant differences were observed in the monthly variations in the average tick density index among different habitats (P>0.05). Pathogen detection showed no Bandavirus dabieense, Rickettsia, or Borrelia burgdorferi in the collected ticks. Conclusions Host-seeking ticks have established populations in urban environments across most prefecture-level cities in Jiangsu Province, with Hae. longicornis identified as the dominant species. City parks serve as the primary breeding habitats for these ticks. Strengthening tick surveillance and control measures in densely populated and frequently visited areas, such as city parks and residential neighborhoods, is crucial for the effective prevention and control of urban tick-borne diseases.
3.Correlation between differences in starch gelatinization, water distribution, and terpenoid content during steaming process of Curcuma kwangsiensis root tubers by multivariate statistical analysis.
Yan LIANG ; Meng-Na YANG ; Xiao-Li QIN ; Zhi-Yong ZHANG ; Zhong-Nan SU ; Hou-Kang CAO ; Ke-Feng ZHANG ; Ming-Wei WANG ; Bo LI ; Shuo LI
China Journal of Chinese Materia Medica 2025;50(10):2684-2694
To elucidate the mechanism by which steaming affects the quality of Curcuma kwangsiensis root tubers, methods such as LSCM, RVA, dual-wavelength spectrophotometry, LF-NMR, and LC-MS were employed to qualitatively and quantitatively detect changes in starch gelatinization characteristics, water distribution, and material composition of C. kwangsiensis root tubers under different steaming durations. Based on multivariate statistical analysis, the correlation between differences in gelatinization parameters, water distribution, and terpenoid material composition was investigated. The results indicate that steaming affects both starch gelatinization and water distribution in C. kwangsiensis. During the steaming process, transformations occur between amylose and amylopectin, as well as between semi-bound water and free water. After 60 min of steaming, starch gelatinization and water distribution reached an equilibrium state. The content of amylopectin, the amylose-to-amylopectin ratio, and parameters such as gelatinization temperature, viscosity, breakdown value, and setback value were significantly correlated(P≤0.05). Additionally, the amylose-to-amylopectin ratio was significantly correlated with total free water and total water content(P≤0.05). Steaming induced differences in the material composition of C. kwangsiensis root tubers. Clustering of primary metabolites in the OPLS-DA model was distinct, while secondary metabolites were classified into 9 clusters using the K-means clustering algorithm. Differential terpenoid metabolites such as(-)-α-curcumene were significantly correlated with zerumbone, retinal, and all-trans-retinoic acid(P<0.05). Curcumenol was significantly correlated with isoalantolactone and ursolic acid(P<0.05), while all-trans-retinoic acid was significantly correlated with both zerumbone and retinal(P<0.05). Alpha-tocotrienol exhibited a significant correlation with retinal and all-trans-retinoic acid(P<0.05). Amylose was extremely significantly correlated with(-)-α-curcumene, curcumenol, zerumbone, retinal, all-trans-retinoic acid, and α-tocotrienol(P<0.05). Amylopectin was significantly correlated with zerumbone(P<0.05) and extremely significantly correlated with(-)-α-curcumene, curcumenol, zerumbone, retinal, all-trans-retinoic acid, and 9-cis-retinoic acid(P<0.01). The results provide scientific evidence for elucidating the mechanism of quality formation of steamed C. kwangsiensis root tubers as a medicinal material.
Curcuma/chemistry*
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Starch/chemistry*
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Multivariate Analysis
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Water/chemistry*
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Terpenes/analysis*
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Plant Roots/chemistry*
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Plant Tubers/chemistry*
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Drugs, Chinese Herbal/chemistry*
4.TRACKING EVALUATION ON THE IMPLEMENTATION OF"DIAGNOSIS OF ASCARIASIS"(WS/T 565-2017)IN ANHUI AND SICHUAN PROVINCES
Wei JIN ; Dao-Hua LIU ; Yang LIU ; Xiao-Hong WU ; Cheng-Hang YU ; Bin ZHENG ; Guang-Ming ZHANG ; Zhi-Guo CAO
Acta Parasitologica et Medica Entomologica Sinica 2025;32(2):73-77,111
Objective To understand the implementation status of"Diagnosis of Ascariasis"(WS/T 565-2017)and provide a scientific basis for promoting,revising,and improving the Standard.Methods Using the convenient sampling method,the investigation targeted professional and technical personnel at the provincial,city,county,and township levels engaged in parasitic disease prevention,control,or diagnosis and treatment in Anhui and Sichuan provinces.No less than 150 individuals were included in each province.The implementation survey of Diagnosis of Ascariasis(WS/T 565-2017)was conducted by the subjects completing a questionnaire by themselves.Results The response rate to the questionnaire was 91.90%(386/420).The awareness and utilization rates of the Standard were 81.87%and 49.22%,respectively and both increased with age(χ2 trend=7.977 and 19.016,respectively,P<0.01).Respondents with college degrees(90.72%)had a higher awareness rate(χ2=8.619,P<0.05).In terms of utilization rate,males(58.38%),those with college degrees(67.01%),staff members of provincial-level units(77.78%),and personnel in medical institutions(71.43%)had higher utilization rates(χ2=13.486,17.166,8.426,and 5.956,respectively,all P<0.05).The survey indicated that 57.77%of the work units of respondents have conducted promotional activities,and 53.89%of the work units of respondents have sent personnel to participate in training.Moreover,this proportion tended to increase as the unit level decreased(χ2 trend=9.403 and 14.729,P<0.01).The level of participation in publicity and training by medical institutions(89.29%)was significantly higher than that of disease control institutions(55.31%and 51.12%,respectively,χ2=12.290 and 15.225,P<0.01).Furthermore,training participation is a crucial factor in enhancing awareness rates.A total of 368 respondents(95.34%)reported that their work units have conducted testing for ascariasis.Additionally,378 individuals(97.92%)believe that the Standard is"applicable"or"basically applicable,"while 369(95.60%)felt that no revisions were needed.Conclusions The results indicated that"Diagnosis of Ascariasis"(WS/T 565-2017)remains applicable to the diagnostic needs of ascariasis and it is recommended to strengthen its promotion and implementation.
5.Expert Consensus on the Ethical Requirements for Generative AI-Assisted Academic Writing
You-Quan BU ; Yong-Fu CAO ; Zeng-Yi CHANG ; Hong-Yu CHEN ; Xiao-Wei CHEN ; Yuan-Yuan CHEN ; Zhu-Cheng CHEN ; Rui DENG ; Jie DING ; Zhong-Kai FAN ; Guo-Quan GAO ; Xu GAO ; Lan HU ; Xiao-Qing HU ; Hong-Ti JIA ; Ying KONG ; En-Min LI ; Ling LI ; Yu-Hua LI ; Jun-Rong LIU ; Zhi-Qiang LIU ; Ya-Ping LUO ; Xue-Mei LV ; Yan-Xi PEI ; Xiao-Zhong PENG ; Qi-Qun TANG ; You WAN ; Yong WANG ; Ming-Xu WANG ; Xian WANG ; Guang-Kuan XIE ; Jun XIE ; Xiao-Hua YAN ; Mei YIN ; Zhong-Shan YU ; Chun-Yan ZHOU ; Rui-Fang ZHU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):826-832
With the rapid development of generative artificial intelligence(GAI)technologies,their widespread application in academic research and writing is continuously expanding the boundaries of sci-entific inquiry.However,this trend has also raised a series of ethical and regulatory challenges,inclu-ding issues related to authorship,content authenticity,citation accuracy,and accountability.In light of the growing involvement of AI in generating academic content,establishing an open,controllable,and trustworthy ethical governance framework has become a key task for safeguarding research integrity and maintaining trust within the academic community.This expert consensus outlines ethical requirements across key stages of AI-assisted academic writing-including topic selection,data management,citation practices,and authorship attribution.It aims to clarify the boundaries and ethical obligations surrounding AI use in academic writing,ensuring that technological tools enhance efficiency without compromising in-tegrity.The goal is to provide guidance and institutional support for building a responsible and sustainable research ecosystem.
6.Expert Consensus on the Ethical Requirements for Generative AI-Assisted Academic Writing
You-Quan BU ; Yong-Fu CAO ; Zeng-Yi CHANG ; Hong-Yu CHEN ; Xiao-Wei CHEN ; Yuan-Yuan CHEN ; Zhu-Cheng CHEN ; Rui DENG ; Jie DING ; Zhong-Kai FAN ; Guo-Quan GAO ; Xu GAO ; Lan HU ; Xiao-Qing HU ; Hong-Ti JIA ; Ying KONG ; En-Min LI ; Ling LI ; Yu-Hua LI ; Jun-Rong LIU ; Zhi-Qiang LIU ; Ya-Ping LUO ; Xue-Mei LV ; Yan-Xi PEI ; Xiao-Zhong PENG ; Qi-Qun TANG ; You WAN ; Yong WANG ; Ming-Xu WANG ; Xian WANG ; Guang-Kuan XIE ; Jun XIE ; Xiao-Hua YAN ; Mei YIN ; Zhong-Shan YU ; Chun-Yan ZHOU ; Rui-Fang ZHU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):826-832
With the rapid development of generative artificial intelligence(GAI)technologies,their widespread application in academic research and writing is continuously expanding the boundaries of sci-entific inquiry.However,this trend has also raised a series of ethical and regulatory challenges,inclu-ding issues related to authorship,content authenticity,citation accuracy,and accountability.In light of the growing involvement of AI in generating academic content,establishing an open,controllable,and trustworthy ethical governance framework has become a key task for safeguarding research integrity and maintaining trust within the academic community.This expert consensus outlines ethical requirements across key stages of AI-assisted academic writing-including topic selection,data management,citation practices,and authorship attribution.It aims to clarify the boundaries and ethical obligations surrounding AI use in academic writing,ensuring that technological tools enhance efficiency without compromising in-tegrity.The goal is to provide guidance and institutional support for building a responsible and sustainable research ecosystem.
7.Therapeutic mechanism of Compound Xuanju Capsule on erectile dysfunction
Zi-jie LI ; Hao-xiang XU ; Wei WANG ; Yue YANG ; Cheng-lin YANG ; Zhi CAO ; Xiao-ming ZHANG
National Journal of Andrology 2025;31(8):675-683
Objective:To investigate the pharmacological mechanism of Compound Xuanju Capsule in the treatment of erectile dysfunction(ED)by using network pharmacology and molecular docking technology.Methods:The active ingredients and targets of Compound Xuanju Capsule were screened using Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform(TCMSP).TTD,OMIM,DrugBank and GeneCards databases were used to obtain genes related to ED,and the union of the results was taken as the disease genes of ED.The common target of drug and disease was taken as the potential target of Compound Xuanju Capsule in ED,and the drug-disease interaction network was constructed by using Cytoscape software.The protein-protein interaction(PPI)network was constructed by using String database,which was then imported into Cytoscape to identify the key target.Based on the drug-disease intersection genes,GO and KEGG enrichment analyses were performed to predict the relevant signaling pathways and molecular mechanisms of Compound Xuanju Capsule for the treatment of ED.Autodock software was used to perform molecular docking between the active ingredients and the core targets.Results:Forty chemical components of Compound Xuanju Capsule were screened,and 239 predicted targets were obtained.A total of 1 907 ED-related genes were screened,and 97 common targets were identified between Compound Xuanju Capsule and ED,among which the core targets included EGFR,ESR1,HIF1A,PTGS2,and STAT3.The signaling pathways obtained by KEGG enrichment analysis included calcium signaling pathway,HIF-1 signaling pathway,PI3K-Akt signaling pathway,cGMP-PKG signaling pathway,relaxin signaling pathway,Serotonergic synapse signaling pathway.The molecular docking results showed that there were molecular binding sites between the key active ingredients and the core targets with strong binding activity.Conclusion:Compound Xuanju Capsule may treat ED through multi-target pathways such as anti-inflamnmato-ry and improving cellular oxidative stress.
8.Rapid Screening of 34 Emerging Contaminants in Surface Water by UHPLC-Q-TOF-MS
Chen-Shan LÜ ; Yi-Xuan CAO ; Xiao-Xi MU ; Hai-Yan CUI ; Tao WANG ; Zhi-Wen WEI ; Ke-Ming YUN ; Meng HU
Journal of Forensic Medicine 2024;40(1):30-36
Objective To establish a rapid screening method for 34 emerging contaminants in surface water by ultra-high performance liquid chromatography-quadrupole-time of flight mass spectrometry(UHPLC-Q-TOF-MS).Methods The pretreatment conditions of solid phase extraction(SPE)were op-timized by orthogonal experimental design and the surface water samples were concentrated and ex-tracted by Oasis? HLB and Oasis? MCX SPE columns in series.The extracts were separated by Kine-tex? EVO C18 column,with gradient elution of 0.1%formic acid aqueous solution and 0.1%formic acid methanol solution.Q-TOF-MS'fullscan'and'targeted MS/MS'modes were used to detect 34 emerging contaminants and to establish a database with 34 emerging contaminants precursor ion,prod-uct ion and retention times.Results The 34 emerging contaminants exhibited good linearity in the con-centration range respectively and the correlation coefficients(r)were higher than 0.97.The limit of de-tection was 0.2-10 ng/L and the recoveries were 81.2%-119.2%.The intra-day precision was 0.78%-18.70%.The method was applied to analyze multiple surface water samples and 6 emerging contaminants were detected,with a concentration range of 1.93-157.71 ng/L.Conclusion The method is simple and rapid for screening various emerging contaminants at the trace level in surface water.
9.COMPARISON OF EFFECTIVENESS OF THE BG-TRAP METHOD AND HUMAN-BAITED DOUBLE NET TRAP METHOD FOR MONITORING DENGUE FEVER VECTOR AEDES ALBOPICTUS
Ye TIAN ; Hong-Liang CHU ; Zhi-Ming WU ; Shou-Gang ZHANG ; Gan CAO ; Xiao-Wu GE ; Li-Ye HUANG
Acta Parasitologica et Medica Entomologica Sinica 2024;31(1):28-32
Objective The effectiveness of the BG-Trap and human-baited double net trap(HDN)methods in monitoring Aedes albopictus were compared to assess the potential use of the BG-Trap method for dengue fever vector monitoring program.These findings would also provide a reference basis for formulating more effective dengue fever prevention and control strategies.Methods The study was conducted at six outdoor monitoring sites in three cities in Jiangsu Province in August and September,following a 3-d monitoring plan.Both traps were evaluated simultaneously at three time slots each day(16:00-16:30,17:00-17:30,and 18:00-18:30).Results Both the BG-Trap and HDN methods effectively captured female Ae.albopictus.The proportion of Ae.albopictus captured by the HDN method was higher than that captured by the BG-Trap method(χ2 = 0.162,P= 0.687),with no statistically significant differences in the composition ratio of male/female between the two methods(χ2=0.162,P=0.687).The average density index of Ae.albopictus for the BG-Trap method was 7.85±5.23/h,significantly lower than that of the HDN method at 27.04±13.86/h under the same sampling sites(t = 6.73,P<0.001).Conclusion These results suggest that the BG-Trap method is less effective than the HDN method in Ae.albopictus monitoring.Further research is required to determine the applicability of this method for dengue fever vector monitoring.
10.Research progress on biofilm microecology in chronic suppurative otitis media.
Xin Cheng ZHONG ; Xiao OUYANG ; Yu Bing LIAO ; Ming Zhu TAO ; Jiao PENG ; Zhi Qing LONG ; Xiang Jie GAO ; Ying CAO ; Ming Hua LUO ; Guo Jiang PENG ; Zhi Xiong ZHOU ; Guan Xiong LEI
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2023;58(6):621-625


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