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.Effects of TREM2 on synaptic plasticity induced by cocaine addiction
Rui-ke XU ; Zhi-wen WANG ; Jiao-jiao OUYANG ; Qi DU ; Li-hua LI ; Shi-jun HONG ; Yan-xia PENG ; Gen-meng YANG
Chinese Pharmacological Bulletin 2025;41(12):2341-2347
Aim To investigate the role of triggering receptor expressed on myeloidcells 2(TREM2)in syn-aptic plasticity induced by cocaine addiction.Methods C57BL/6J mice and Trem2 knockout mice were uti-lized in this study to evaluate the alterations in postsyn-aptic density protein 95(PSD-95)and synapsin 1(SYN1)within the cortex and hippocampus of co-caine-addicted mice by using immunological tech-niques.Results HE staining and Nissl staining showed increased neuronal damage in the hippocampus and cortex of mice after cocaine addiction.The results of immunohistochemistry and fluorescence of PSD-95 and SYN1 were consistent with the expression trend of Western blot.In the wild type mouse model,the ex-pression level of PSD-95 in the hippocampus and cortex was lower than that in the saline group,and the ex-pression of SYN1 was higher than that in the saline group.In the knockout mouse model,the expression levels of PSD-95 and SYN1 in the hippocampus and cortex were significantly higher than those in the saline group after cocaine addiction.The expression levels of PSD-95 and SYN1 in the hippocampus and cortex of cocaine knockout mice were higher than those of co-caine wild type mice.Conclusion Cocaine addiction can change the synaptic plasticity,and TREM2 plays a regulatory role in the synaptic plasticity of hippocampus and cortex in mice with cocaine injury.TREM2 is ex-pected to be a new target for studying the mechanism of cocaine addiction.
3.Clinical analysis of 55 children with severe pertussis
Liuying LIU ; Zhi XIA ; Wen TANG ; Buyun SHI
Chinese Journal of Infection Control 2025;24(7):932-939
Objective To investigate the clinical characteristics of severe pertussis in children.Methods Clinical data of 55 children with severe pertussis and admitted to the pediatric intensive care unit(PICU)of Maternal and Child Heath Hospital of Hubei Province from January 2022 to May 2024 were retrospectively analyzed.Patients were grouped according to age(≤3-month group and>3-month group),vaccination status,and mixed infection status,differences in clinical characteristics among different groups of pediatric patients were compared.Results 55 children with severe pertussis were aged 1 month and 5 days-9 years,all had severe pneumonia,54 children were improved and discharged from hospital,1 died.26 children(47.3%)were aged<3 months,45 children(81.8%)were unvaccinated,and 47 children(85.5%)had mixed infection.The rates of post-vomiting cough and blood ex-change transfusion in children in ≤3-month group were lower those in>3-month group(30.8%vs 58.6%;11.5%vs 34.5%,respectively);The rate of elevation of cerebrospinal fluid protein in children in ≤3-month group was higher than that in>3-month group(61.5%vs 31.0%);The pre-admission disease course of children in ≤3-month group was shorter than that in>3-month group([10.15±5.64]days vs[14.24±8.90]days),differences were all statistically significant(all P≤0.05).The absolute counts of lymphocyte in the vaccinated group was lower than that in the unvaccinated group([9.92±5.92]× 109/L vs[17.93±11.41]× 109/L,P<0.05).The usage rate of gamma-globulin in children in the mixed infection group was higher than that in the simple infection group(87.2%vs 50.0%).The length of hospital stay([15.11±6.53]days vs[9.50±4.69]days),length of PICU stay([10.53±5.26]days vs[5.88±4.16]days),and macrolides antibiotic use days([8.36±4.21]days vs[5.00±2.73]days)in children in the mixed infection group were all longer than those in the simple infection group,differences were all statistically significant(all P<0.05).No independent influencing factors were found to prolong the length of PICU stay in children with severe pertussis.Conclusion Severe pertussis mostly occurs in unvaccinated children aged ≤3 months,with a high incidence of mixed infection,all presenting as severe pneumonia.Vaccination status,mixed infection,and complications are key factors affecting prognosis.
4.Analysis of risk factors for noncontiguous spinal fractures in the elderly
Shi-lei TANG ; Hong-wen GU ; Yin HU ; Kang-en HAN ; Hai-long YU ; Zhi-hao ZHANG ; Hong-wei WANG
Journal of Regional Anatomy and Operative Surgery 2025;34(2):130-133
Objective To explore the risk factors for noncontiguous spinal fractures(NSFs)in the elderly.Methods The clinical data of 614 elderly patients with spinal fracture from January 2013 to December 2019 were analyzed retrospectively.Patients were divided into the NSFs group and the Non-NSFs group according to whether NSFs occurred or not.Univariate analysis and multivariate Logistic regression analysis were used to screen the risk factors of NSFs.Results Univariate analysis showed that female(P=0.003),high-energy violent injury(P=0.032),osteoporosis(P=0.004),fracture in spring(P=0.020),and previous spinal fracture history(P<0.001)were associated with the occurrence of NSFs.Multivariate Logistic regression analysis showed that fracture in spring(P=0.024),previous spinal fracture history(P<0.001)and high-energy violent injury(P=0.038)were the independent risk factors for the occurrence of NSFs in the elderly.Conclusion High-energy violent injury,fracture in spring and previous spinal fracture history are the independent risk factors for the occurrence of NSFs in the elderly.Therefore,elderly patients with the above risk factors should be examined more carefully and comprehensively to avoid missed diagnosis and delayed diagnosis.In order to reduce the incidence of this disease,corresponding measures should be taken according to the preventable risk factors.
5.Establishment and validation of a predictive model for increased drainage volume after open transforaminal lumbar interbody fusion
Yin HU ; Hai-long YU ; Hong-wen GU ; Kang-en HAN ; Shi-lei TANG ; Yuan-hang ZHAO ; Zhi-hao ZHANG ; Jun-chao LI ; Le XING ; Hong-wei WANG
Journal of Regional Anatomy and Operative Surgery 2025;34(11):981-986
Objective To analyze the risk factors for increased drainage volume after open transforaminal lumbar interbody fusion(TLIF),and to establish a predictive model and then validate it.Methods The clinical data of 680 patients who underwent open TLIF at the General Hospital of Northern Theater Command from January 2016 to December 2019 were collected and the patients were randomly divided into the training group(n=476)and the validation group(n=204).Taking the predictive factors screened out by LASSO regression analysis as independent variables,a multivariate Logistic regression predictive model was constructed.The model was internally validated through the receiver operating characteristic(ROC)curve,Hosmer-Lemeshow goodness-of-fit test,and calibration curve,and its clinical utility was assessed via decision curve analysis(DCA).Results LASSO regression analysis screened out four predictive variables:age,number of surgical segments,operative duration,and intraoperative blood loss.The multivariate Logistic regression predictive model demonstrated that age≥60 years,number of surgical segments≥4,operative duration≥2 hours,and intraoperative blood loss≥200 mL were independent influencing factors for the increased postoperative drainage volume in patients undergoing TLIF(P<0.05).ROC curve analysis revealed an area under the curve(AUC)of 0.816(95%CI:0.798 to 0.867)in the training group and 0.783(95%CI:0.685 to 0.823)in the validation group,indicating that the predictive model had good discriminatory ability.Additionally,the Hosmer-Lemeshow goodness-of-fit test and calibration curve indicated that the predictive model had a good degree of fit,and the predicted probability was basically consistent with the actual probability,demonstrating a good calibration.The DCA results confirmed that this predictive model could be applied in clinical practice.Conclusion The risk factors for increased drainage volume after open TLIF include age,number of surgical segments,operative duration,and intraoperative blood loss.The predictive model established based on these factors demonstrates good performance,and it can be applied in clinical guidance for the selection of drainage tube removal time after TLIF.
6.Effects of TREM2 on synaptic plasticity induced by cocaine addiction
Rui-ke XU ; Zhi-wen WANG ; Jiao-jiao OUYANG ; Qi DU ; Li-hua LI ; Shi-jun HONG ; Yan-xia PENG ; Gen-meng YANG
Chinese Pharmacological Bulletin 2025;41(12):2341-2347
Aim To investigate the role of triggering receptor expressed on myeloidcells 2(TREM2)in syn-aptic plasticity induced by cocaine addiction.Methods C57BL/6J mice and Trem2 knockout mice were uti-lized in this study to evaluate the alterations in postsyn-aptic density protein 95(PSD-95)and synapsin 1(SYN1)within the cortex and hippocampus of co-caine-addicted mice by using immunological tech-niques.Results HE staining and Nissl staining showed increased neuronal damage in the hippocampus and cortex of mice after cocaine addiction.The results of immunohistochemistry and fluorescence of PSD-95 and SYN1 were consistent with the expression trend of Western blot.In the wild type mouse model,the ex-pression level of PSD-95 in the hippocampus and cortex was lower than that in the saline group,and the ex-pression of SYN1 was higher than that in the saline group.In the knockout mouse model,the expression levels of PSD-95 and SYN1 in the hippocampus and cortex were significantly higher than those in the saline group after cocaine addiction.The expression levels of PSD-95 and SYN1 in the hippocampus and cortex of cocaine knockout mice were higher than those of co-caine wild type mice.Conclusion Cocaine addiction can change the synaptic plasticity,and TREM2 plays a regulatory role in the synaptic plasticity of hippocampus and cortex in mice with cocaine injury.TREM2 is ex-pected to be a new target for studying the mechanism of cocaine addiction.
7.Control of massive hemorrhage from the presacral venous plexus during the surgery of pelvic fracture using woven gelatin sponge balls:a case report.
Zhi-Jie XI ; Xiang-Bin LIU ; Wei-Xin LI ; Shu-Zhong HUANG ; Jie LI ; Wen SHU ; Zhan-Ying SHI
China Journal of Orthopaedics and Traumatology 2025;38(7):755-758
8.Recommendations for the clinical use of anti-amyloid-β monoclonal antibody for Alzheimer's disease(2025)
Nan ZHI ; Jinwen XIAO ; Rujing REN ; Binyin LI ; Jintao WANG ; Jieli GENG ; Wenwei CAO ; Yaying SONG ; Hualong WANG ; Shuguang CHU ; Guoping PENG ; Jun LIU ; Xiaoyun LIU ; Fang YUAN ; Wen WANG ; Ronghua DOU ; Xia LI ; Ling YUE ; Wenshi WEI ; Xiaoling PAN ; Xiangyang ZHU ; Dian HE ; Weinü FAN ; Jingping SHI ; Nan ZHANG ; Hui ZHAO ; Qin CHEN ; Cuibai WEI ; Xiaochun CHEN ; Gang WANG
Journal of Chongqing Medical University 2025;50(9):1133-1140
In recent years,significant breakthroughs have been achieved in the immunotherapy for Alzheimer's disease.In line with global advancements,two anti-amyloid-β monoclonal antibodies have been approved and successfully launched in China for clinical use.Lecanemab and Donanemab were officially used in June 2024 and April 2025 in China,respectively.In order to standardize the rational and safe application of anti-amyloid-β monoclonal antibodies for Alzheimer's disease in China,this article integrates recom-mendations from the clinical trials and real-world experience from the author's team and domestic peers to further update the recom-mendations for the clinical use of anti-amyloid-β monoclonal antibody based on the 2024 version.It includes indications for therapy,pre-treatment evaluation and preparation,administration protocols and safety measures during treatment,and post-treatment monitor-ing strategies.
9.Rapid Monitoring of Key Indicators in Growth Process of Chlorella Using Near-Infrared Spectroscopy Technology
Wen-Hui SONG ; Shi-Jie DU ; Yan LIU ; Qiao WANG ; Xin LIU ; Zhi-Yong GONG
Chinese Journal of Analytical Chemistry 2025;53(4):660-668
The traditional detection methods for monitoring the biomass,protein,chlorophyll content and other key indicators in the growth of chlorella have some problems,including complicated operation,slow detection speed and difficult large-scale application.In this study,a fast and efficient monitoring method for the key indicators in the growth of chlorella was established using near infrared spectroscopy and chemometrics.Near-infrared spectroscopy was used to collect near-infrared spectra of chlorella algal fluid at different growth stages,and standard methods were used to detect the biomass,protein and chlorophyll contents of corresponding samples.A quantitative analysis model was established based on partial least squares regression(PLSR).To improve the prediction ability of the model,multiplicative scatter correction(MSC)was used to reduce the interference of scattering on the raw spectrum(RS),standard normal variate(SNV)was used to normalize the original spectral data to eliminate differences between samples,continuous wavelet transform(CWT)was used to obtain the key features of spectral data,the first derivative(1st)was used to enhance the differentiation of the original spectral features,and monte carlo-uninformative variable elimination(MC-UVE)and randomization test(RT)were used to screen the valid variables in the wavelength.By evaluating the prediction ability of different models,the quantitative analysis models of chlorella biomass,protein and chlorophyll content were finally determined.The results showed that the model based on 1st combined with RT spectra had better predictive ability for chlorella nutrient content detection,and the root mean square errors of prediction(RMSEP)and coefficients of determination(R2)were 0.041 and 0.933 for biomass,0.012 and 0.973 for protein,and 0.517 and 0.962 for chlorophyll,respectively.This model showed practical application value,and could realize the rapid and accurate detection of chlorella biomass,protein and chlorophyll content at the same time.
10.Toxicokinetics of Chlorfenapyr and Its Metabolites in Rats
Wen-Yan LI ; Jin-Feng ZHAO ; Wei-Chen LIU ; Shi-Jing LÜ ; Jia-Xin ZHANG ; Xu-Dong ZHANG ; Zhi-Wen WEI ; Ke-Ming YUN ; Chao ZHANG
Journal of Forensic Medicine 2025;41(4):380-386
Objective To establish a chromatography-tandem mass spectrometry method for detecting chlorfenapyr and its metabolite tralopyril in blood,and to investigate the toxicokinetics in rats.Methods Chlorfenapyr(8 mg/kg)was administered orally to rats,and blood samples were collected from rats'canthus vein at 5 min,15 min,30 min,1 h,3 h,6 h,12 h,24 h and 48 h after administration.The blood samples were extracted using 100 μL of 5%formic acid solution and 400 μL of acetonitrile.Chlorfena-pyr was qualitatively and quantitatively detected by triple quadrupole gas chromatography-tandem mass spectrometry(GC-MS/MS)and tralopyril was detected by triple quadrupole liquid chromatography-tandem mass spectrometry(LC-MS/MS).The DAS 3.0 software was used to fit the toxicokinetic equa-tions and calculate the toxicokinetic parameters.Results Chlorfenapyr was detectable from 5 min to 24 h with a peak time of 1 h.Tralopyril was detectable from 15 min to 48 h with a peak time of 3 h.The toxicokinetic process of chlorfenapyr in rat blood conformed to a first-order absorption one-compartment open model,with the toxicokinetic equation described as C=e-0.265t-e-0.175t.Tralopyril con-formed to the first-order absorption three-compartment model,and the toxicokinetic equation was C=47 361.069e-2.209t-35 404.962e-1.486t+11 956.363e-0.512t.In the equations,C stands for the concentration of the target substance in the blood,e is the natural constant(≈2.718 28),and t stands for time.Conclu-sion This study optimized the detection method for chlorfenapyr and its metabolite tralopyril in blood.The toxicokinetic equations and parameters of chlorfenapyr and tralopyril can provide a reference for the estimation of oral intake time of chlorfenapyr.

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