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.Clinical Efficacy and Mechanism of Anmei Dan in Treating Insomnia with Amnesia Based on Principle of Treating Different Diseases with Same Method: A Review
Qiqi FENG ; Bo XU ; Kang SUN ; Miao ZHU ; Zhi ZHANG ; Jing XIA ; Guangjing XIE ; Yuan LIU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(17):107-116
In modern society, the comorbidity of insomnia with amnesia has shown a significantly increasing incidence and become increasingly severe, emerging as a public health issue that endangers people's physical and mental health and quality of life. Anmei Dan (AMD), originally recorded in the Shishi Milu by CHEN Shiduo in the Qing Dynasty, possesses profound theoretical foundations and distinct clinical advantages in ameliorating insomnia with amnesia. Basic research has unequivocally confirmed its definite therapeutic effects on insomnia with amnesia and revealed partial mechanisms. AMD is therefore a veritable classic prescription embodying the principle of treating different diseases with the same method for insomnia and amnesia. However, few researchers have reviewed the related research progress. This article systematically summarized the theoretical connotations of traditional Chinese medicine in treating insomnia with amnesia, delineated the multi-component material basis of AMD in ameliorating insomnia with amnesia (including various chemical components such as ginsenosides, jujubosides, and salvianolic acids), and evaluate its multi-dimensional clinical efficacy (e.g., prolonging total sleep time, improving sleep efficiency, and enhancing memory). Moreover, it systematically summarizes the multi-pathway mechanisms of action. The results indicate that AMD has a clear material basis, definite clinical efficacy, and a favorable safety profile in ameliorating insomnia and amnesia. AMD may exert the therapeutic effect by regulating sleep-wake rhythms, enhancing synaptic plasticity, inhibiting neuroimmune inflammation, and modulating autophagy, oxidative stress, and energy metabolism. In conclusion, AMD exerts synergistic effects through multi-component, multi-dimensional, and multi-pathway approaches, serving as an important prescription for enriching and developing the theory of treating different diseases with the same method for insomnia with amnesia.
3.Research status of traditional Chinese medicine regulating oxidative stress to prevent and treat diabetic kidney disease
Xiao-long MEI ; Kun ZHANG ; LI-hui FAN ; Lu-mei ZHANG ; Xia YANG ; Zhi-gang WANG
The Chinese Journal of Clinical Pharmacology 2025;41(1):127-131
Diabetic kidney disease(DKD)is one of the common microvascular complications of diabetes mellitus,and it has become the main cause of chronic kidney disease and end stage renal disease.Traditional Chinese medicine can delay the progress of DKD by inhibiting oxidative stress,improving renal tissue damage,restoring renal function.This paper will summarize the relationship between oxidative stress and DKD and the prevention and treatment of DKD by traditional Chinese medicine,so as to provide reference for clinical drug application,basic research and new drug research and development of DKD.
4.A retrospective study of BRAF inhibitors and EGFR inhibitors combined with immune checkpoint inhibitors in patients with microsatellite stable, BRAF V600E mutated metastatic colorectal cancer
Zhi JI ; Jinguo MA ; Xia WANG ; Jiaqi XIN ; Lijun MA ; Yixuan WANG ; Nan ZHANG ; Chunyan ZENG ; Rui LIU
Chinese Journal of Oncology 2025;47(9):922-928
Objective:To explore the efficacy and safety of B-Raf proto-oncogene, serine/threonine kinase (BRAF) inhibitor and epidermal growth factor receptor (EGFR) inhibitor combined with immune checkpoint inhibitor in microsatellite stable (MSS) BRAF V600E metastatic colorectal cancer (mCRC) patients.Methods:The data and outcomes of mCRC patients with MSS BRAF V600E who received BRAF inhibitor, EGFR inhibitor combined with immune checkpoint inhibitor in Tianjin Medical University Cancer Hospital from May 2022 to April 2024 were retrospectively collected.Results:A total of 12 mCRC patients were included in this study, the objective response rate was 50.0%, the disease control rate was 66.7%, and the median disease control time of patients who achieved objective response was 8.0 months. The median progression-free survival was 6.8 months and the median overall survival was 8.4 months. Overall adverse reactions were controllable, the most common treatment-related adverse events were fatigue (8 cases), fever (5 cases), and rash (4 cases). There were no grade 4 adverse event, serious adverse event, and treatment-related death.Conclusion:BRAF inhibitor and EGFR inhibitor combined with immune checkpoint inhibitor show good efficacy and controllable safety in BRAF V600E mCRC patients.
5.Comparison of clinical manifestations,laboratory characteristics,and treatment outcomes of 258 patients with acute and chronic brucellosis
Xu ZHAO ; Ke-mei NIU ; Xia GAO ; Chun-xu SONG ; Yu FAN ; Qing-qing XU ; Zhong-rong LU ; Kun LI ; Feng GAO ; Mei-chun HAO ; Bing-zhi LIU ; Hai JIANG
Chinese Journal of Zoonoses 2025;41(6):660-667
To compare and analyze the clinical manifestations,laboratory characteristics,imaging findings,and treatment outcomes of patients with acute and chronic brucellosis,a retrospective analysis was conducted on 258 patients with brucellosis(202 in the acute group and 56 in the chronic group)hospitalized in Xinkang Hospital in Dalad Banner,Ordos City,Inner Mongolia Autonomous Region,from November 2023 to November 2024.General data,epidemiological characteristics,clinical presentations,laboratory test results,imaging findings,treatment outcomes,and prognosis were collected.The incidences of fever(51.5%vs 7.1%),fatigue(30.2%vs 12.5%),joint pain(42.9%vs 16.1%),and muscle pain(9.9%vs.1.8%)were significantly higher in the acute phase group(all P<0.05).The incidence of osteoarthritis complications was higher in the chronic brucellosis group(51.8%vs 8.9%,χ2=75.697,P<0.01).Univariate ANOVA analysisshowed that the Serum Agglutination Tests(SAT),alanine aminotransferase(ALT),aspartate aminotransferase(AST),total bilirubin(TBIL),creatinine(CRE),C-reactive protein(CRP),erythrocyte sedimentation rate(ESR),and bone destructionexhibited statistically significant differences between the acute and chronic phases of brucellosis(all P<0.05).Multivariate logistic regression analysis indicated that abnormal ALT(OR=14.18,95%CI:1.11-181.72;P=0.041)and bone destruction(OR=0.16,95%CI:0.04-0.63;P=0.009)were associated with chronic brucellosis.After treatment,all patients experienced have symptom relief in varying degrees,with 157 patients(60.9%)cured and 101 patients(39.1%)symptomatic improved(P<0.01).In conclusion,the incidences of fever,fatigue,and joint pain in patients during the acute phase is significantly higher than that those in patients during the chronic phase,while the incidence of osteoarthritis complications is higher in chronic phase patients.The incidences of abnormal SAT,ALT,AST,TBIL,CRE,CRP,and ESR,and bone destruction varies at different stages of brucellosis.Of those,abnormal ALT and bone destruction show a stronger association with,which can assist the clinical staging of brucellosis.
6.The role and mechanism of ERK-mediated Drp1 signaling in exercise-induced skeletal muscle damage
Mengyu LI ; Hao DENG ; Shiqiao ZHENG ; Duo ZHANG ; Tianai YANG ; Ranggui MA ; Zhi XIA ; Huayu SHANG
Chinese Journal of Sports Medicine 2025;44(9):717-728
Objective To observe the effect of a heavy load exercise on the ultrastructure,function and fission of skeletal muscle mitochondria in rats,and to analyze the changes of the phosphorylation expression of mitochondrial fission protein and upstream kinase at different times postexercise,and to explore the effect of acute heavy load exercise on mitochondrial fission in skeletal muscle of rats and its possible mechanism.Methods Forty-eight adult male Sprague-Dawley rats were randomly divided in-to a quiet control group(C,n=8)and an exercise group(E,n=40).Rats in the E group exercised on a treadmill down a 16° decline at 16 m/min for 90 min and were further divided into 0 h,12 h,24 h,48 h,and 72 h postexercise subgroups.Soleus muscle was isolated and mitochondria were ex-tracted at the corresponding time points after exercise.The ultrastructure of mitochondria in the soleus muscle was observed using transmission electron microscopy,and mitochondrial quantity and morphomet-ric analysis were conducted.Moreover,the colocalization and quantity of dynamin-related protein 1(Drp1)and cytochrome C oxidease subunit Ⅳ(COXⅣ)in the soleus muscle were detected using im-munofluorescence double-labeling techniques.Meanwhile,protein levels of soleus musclep-Drp1Ser616,p-Drp1Ser637,p-extracellular regulatory protein kinaseThr202/Tyr204(p-ERKThr202/Tyr204),p-protein kinaseAThr197(p-PKAThr197),and mitochondrial NADH of ubiquinone oxidoreductase subunit B8(NDUFB8)and ubiqui-nol-cytochrome C reductase core protein 2(UQCRC2)were determined by using Western blotting.An-other twenty-four rats were randomly divided into a DMSO group(CD),a U0126 group(CU),an Ex-ercise+DMSO group(ED),and an Exercise+U0126 group(EU).Six mice in each group were giv-en a single intra-bitoneal injection of DMSO or ERK inhibitor U0126 20 min before acute downhill running.Then,their phosphorylated expressions of ERKThr202/Tyr204 and Drp1Ser616 in soleus muscle were de-tected by Western blotting.Results(1)From 0 h to 48 h after exercise,the soleus muscle mitochon-dria showed swelling,rounding,and uneven distribution of mitochondria,among which the degree of mitochondrial damage was the most serious at 12 h and 24 h after exercise.Moreover,the protein ex-pression of NDUFB8 and UQCRC2 in the mitochondria fractions from soleus muscle was significantly lower at 12 h post-exercise(P<0.05).(2)The co-localization of Drp1 and COXⅣ in the skeletal muscle increased significantly at 12 h to 24 h after a heavy load exercise compared with group C and group E0(P<0.01).Moreover,the mitochondrial area,circumference,aspect ratio and Ferret diameter in the skeletal muscle were significantly lower at 12 h to 24 h postexercise(P<0.05).Meanwhile,the number of mitochondria was significantly higher at 24 h after exercise(P<0.01).(3)The phosphoryla-tion of ERKThr202/Tyr204,PKAThr197 and Drp1Ser616 was significantly higher at 24 h after exercise(P<0.01),while that of Drp1Ser637 was significantly lower at 48 h and 72 h post-exercise(P<0.01).However,the phosphorylated expressions of ERKThr202/Tyr204 and Drp1Ser616 were significantly down-regulated by U0126 treatment before exercise.Conclusion A session of heavy load exercise caused mitochondrial structure and function damage and induced mitochondrial fission in the skeletal muscle,and then to maintain the homeostasis of skeletal muscle cells by cleaving damaged mitochondria.The mechanism of promot-ing skeletal muscle repair may be related to the positive and negative regulation of Drp1 activity by the phosphorylation of Drp1Ser616 and Drp1Ser637,respectively.Among them,the activation of ERKThr202/Tyr204 mediates the phosphorylation activation of Drp1Ser616,but PKAThr197 is not an upstream kinase that medi-ates the inactivation of Drp1Ser637 phosphorylation.
7.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.
8.The Mechanism of Gongfa Static Training Regulating Mitophagy in Skeletal Muscle of Type 2 Diabetes Mellitus(T2DM)Mice via the PINK1/Parkin Pathway
Lizhen GAN ; Xia WU ; Pei CHEN ; Zhi ZHANG ; Zhewei CHEN ; Qingbo WEI ; Yunchuan WU
Journal of Nanjing University of Traditional Chinese Medicine 2025;41(2):151-159
OBJECTIVE To explore the mechanism by which Gongfa Static Training regulates mitophagy through the PTEN-in-duced kinase 1(PINK1)/Parkin pathway in skeletal muscle insulin resistance in type 2 diabetes mellitus(T2DM).METHODS T2DM mouse model was established using a high-fat diet combined with streptozotocin(STZ)intraperitoneal injection.Mice were ran-domly divided into a model group,a metformin group,an aerobic exercise group,and a Gongfa Static Training group.The intervention effects of Gongfa Static Training were evaluated by measuring fasting blood glucose,Homeostatic Model Assessment of Insulin Resist-ance(HOMA-IR),glycated hemoglobin(HbA1c),lipid metabolism indicators,mitochondrial function in the gastrocnemius muscle,and the expression of PINK1 and Parkin-related genes and proteins.RESULTS Gongfa Static Training significantly reduced fasting blood glucose,HbA1c,and insulin resistance index in T2DM mice,improved lipid metabolism,and enhanced insulin sensitivity.It improved the structure and function of mitochondria in the gastrocnemius muscle by upregulating the mRNA and protein expression of PINK1 and Parkin.CONCLUSION Gongfa Static Training improves mitochondrial function and insulin resistance in the skeletal muscle of T2DM mice by regulating the PINK1/Parkin pathway.
9.Heart-sparing strategy for breast cancer radiotherapy based on nnU-Net: regional optimization and automatic segmentation
Jinghan HUANG ; Maidina BATUER ; Chuanghui ZHOU ; Zhi ZHANG ; Limei DENG ; Yuan XU ; Junyuan ZHONG ; Linghong ZHOU ; Xia LI ; Genggeng QIN
Chinese Journal of Radiation Oncology 2025;34(4):355-362
Objective:To investigate the feasibility and optimal expansion width of replacing the left anterior descending coronary artery (LADCA) with the region of heart sparing (RHS) to reduce cardiac radiation dose during breast cancer radiotherapy.Methods:Retrospective analysis was conducted on data from 88 patients with left-sided breast cancer who underwent radiotherapy at 2 centers: Nanfang Hospital of Southern Medical University (50 cases for the training set, 15 cases for the internal test set) and Ganzhou Hospital of Nanfang Hospital (23 cases for the external test set) from March 2022 to January 2024. All patients had left-sided invasive ductal carcinoma with axillary lymph node metastasis, and had undergone modified radical mastectomy and chemotherapy. Based on simulation CT images, 2 radiation oncologists delineated the LADCA and 8 RHSs. The RHSs were delineated by expanding the LADCA contour by 0.5 cm increments, totaling 8 expansions. The RHS widths were defined as 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4.0 cm. The nnU-Net model was trained for 3D automatic segmentation of the LADCA and RHSs. Model performance was evaluated using the Dice similarity coefficient (DSC), relative volume error (RVE), sensitivity, specificity, and 95% Hausdorff distance (HD95). Additionally, the minimum, maximum, and average relative dose variations (RDV) as well as V5% and V20% indicators were calculated for the LADCA and each RHS. Correlation analysis was performed using the least squares regression, with the slope and coefficient of determination ( R2) employed to evaluate the accuracy of the model fitting, the relationship between the LADCA and RHS, and the degree of their correlation, thereby assessing the substitutive effect of the RHS for the LADCA. Results:The DSC for the LADCA was 0.415, while the DSCs for RHS widths of 0.5 cm and 4.0 cm were 0.718 and 0.835, respectively. Overall, the automatic segmentation performance improved with increasing RHS width. The DSC, RVE, sensitivity, specificity, and HD95 for the external test set were largely consistent with those of the internal test set, demonstrating the model's good robustness across different datasets. All RDVmin values were negative, while RDVmax and RDVmean showed a positive correlation with RHS width. RDVmean increased from 39.01% to 75.89% as the RHS width increased. In the correlation analysis, the slopes for RHS widths of 1.5 cm and 2.0 cm were 0.95 and 1.05, respectively, with R2 values and coefficients of variation of 0.79 and 0.73, and 21.11% and 24.03%, respectively. Conclusions:The automatic segmentation model trained on nnU-Net can accurately segment RHSs. Based on geometric and dosimetric indicators, a 1.5 cm-wide RHS is the most suitable substitute for the LADCA, effectively limiting the radiation dose to the LADCA without compromising target dose coverage.
10.Global research status,hotspot analysis and trend outlook of tick-borne encephalitis
Xing-zhi FENG ; Yi-jia XU ; Qian-feng XIA ; Ya-jun LU
Chinese Journal of Zoonoses 2025;41(4):434-440
This study explored the current status,hotspots,and research trends in tick-borne encephalitis(TBE)worldwide.The bibliometric analysis and knowledge mapping software,VOSviewer,was used to conduct a comprehensive study of the literature in the field of TBE in the Web of Science database and the CNKI database,and to construct a research framework of the TBE field in order to demonstrate the association between the main keywords,research countries,research institutions and published journals in this field.A total of 2 046 English-language and 582 Chinese-language publications were included in this study,with an increasing trend of publication year by year.Keyword co-occurrence analysis showed that TBE and its viruses were the focus of research,along with infection,epidemiology,pathogen classification,prevalence,transmission,and clinical symptoms.The United States,Germany,and other countries were at the top of the list of publications and citations.Institutions such as the Russian Academy of Sciences and Medical University of Vienna were prominent contributors to TBE research.Journals represented by Ticks and Tick-borne Diseases were in the lead in terms of publications and citations and were important publications for research in this field.TBE research showed wide and vigorous trends worldwide.The study displayed the current status of research and the evolution of hot trends in this field,which provided us with strong support for examining TBE as a public health problem from a broader perspective and was also of great significance for promoting future in-depth research and formulating precise prevention and control strategies.

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