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.Research progress on novel serum and urine biomarkers in early diagnosis of diabetic nephropathy
Journal of Public Health and Preventive Medicine 2026;37(4):146-150
Diabetic nephropathy (DN) is one of the main causes of chronic kidney disease and end-stage renal disease (ESRD) worldwide, especially in patients with type 2 diabetes mellitus (T2DM). Early diagnosis is crucial for slowing down the progression of DN and improving the prognosis of patients. Traditional diagnostic methods, such as measurement of urinary microalbumin (mALB) and estimated glomerular filtration rate (eGFR), often fail to detect early renal injury because structural renal injury may occur before albumin excretion. This study aims to optimize clinical diagnostic methods for DN, reduce patient risk of onset, and provide a theoretical basis for further exploration of diagnostic biomarkers of DN by evaluating the diagnostic value of multiple novel serum and urine biomarkers in the early detection of DN.
3.Clinical Characteristics and Survival Analysis of 34 Patients with Aggressive NK-Cell Leukemia
Hui-Hui ZHANG ; Chun-Lan HUA ; Ping-Ping SUN ; Shuai LIU ; Wen-Juan FAN ; Xing-Wu LI ; Bao-Hong YUE
Journal of Experimental Hematology 2025;33(6):1577-1582
Objective:To explore the clinical characteristics and prognosis risk factors of aggressive NK-cell leukemia(ANKL).Methods:The clinical and laboratory data of 34 patients with ANKL and 15 patients with chronic lymphoproliferative disorders of NK cells(CLPD-NK)admitted to the First Affiliated Hospital of Zhengzhou University from September 2019 to December 2024 were retrospectively analyzed.The Kaplan-Meier method was used to calculate survival rates,and the Cox proportional hazards regression model was used to analyze prognostic factors.Results:Compared with CLPD-NK patients,ANKL patients had a younger median age of onset,a higher proportion patients with EBV-DNA≥500 copies/ml,hepatosplenomegaly and hemophagocytic syndrome.They also presented with a higher peak of fever,a shorter median survival time,lower WBC count,PLT count,ALB and Fib values,while having higher LDH,AST,TG,ferritin,CRP and PCT levels.There were statistically significant differences in the morphology and expression of HLA-DR,CD56,CD57,CD16 and CD158 on abnormall cells between ANKL patients and CLPD-NK patients.Multivariate survival analysis revealed that combined with asparaginase treatment could improve patients' survival,and CRP≥ 15 mg/L and Fib<2.0 g/L were independent risk factors affecting the overall survival of patients with ANKL.Conclusion:The differences in clinical features and laboratory tests between patients with ANKL and CLPD-NK aid in the diagnosis of ANKL.CRP and Fib levels can be used to predict the prognosis of patients,and combined asparaginase therapy can enhance the overall survival of patients.
4.Gene Mutation Analysis of an Individual with a RHD Variant RHD*DV.5 and RHD Negative Gene Heterozygote
Shi-Shi WU ; Juan PENG ; Li-Bo WU ; Hong-Xiao CHEN ; Dong-Mei ZHAN ; Yue-Mei DONG ; Wan-Qin WANG ; Liang WU
Journal of Experimental Hematology 2025;33(6):1758-1764
Objective:To perform RHD gene detection on a blood sample with serological weak D phenotype.Methods:A specimen received by the People's Hospital of Zhijin County was serologically identified by the microcolumn gel method and saline method.RHD gene detection was conducted by the PCR-SSP method,and the full sequence determination of the 10 exons amplified was performed.The sequencing results were compared with the ISBT database to determine the genotype.Bioinformatics tool was used to predict the functional damage of mutant proteins,and Alphafold-3 was used for tertiary structural modeling of wild-type and mutant RhD proteins,and the structures of the two proteins were compared and analyzed to explore the reasons why mutations lead to weak serological manifestations.Results:The patient's genotype was identified as RHD*DV.5/RHD*01N.01 heterozygote,with the complete deletion of RHD genes on one chromosome,unable to express the D antigen.On the other chromosome,a G>A mutation occurred at the 697th base of the 5th exon,resulting in a partial D phenotype.This mutation causes internal hydrogen bond changes at the 233 position of RhD protein,resulting in a change in the conformation of the protein,affecting binding to the corresponding antibody.Conclusion:The patient is a heterozygous mutant individual with RHD*DV.5/RHD*01N.01,exhibiting a partial D phenotype serologically.This variation is extremely rare and has been scarcely reported globally.
5.Mechanism of total flavonoids of Carthamus tinctorius L.against he-patic fibrosis based on LC-MS/MS combined with network pharma-cology and pharmacology experiments
Mingqi LI ; Yinghe WANG ; Xiaolu ZHAO ; Xiaomei BAO ; Xin YUE ; Guiqiang REN ; Yue-hong MA
Chinese Journal of Clinical Pharmacology and Therapeutics 2025;30(5):586-598
AIM:To elucidate the pharmacody-namic and network pharmacological mechanisms of total flavonoids of Carthamus tinctorius L.,to ex-plore their key targets and related pathways,and to clarify their mechanism of action against hepatic fibrosis.METHODS:The total flavonoids of Cartha-mus tinctorius L.were determined by LC-MS/MS and analysed for their compositions;the active in-gredients were screened by TCMSP database,SWISS ADME database and literature search;the targets related to total flavonoids of Carthamus tinctorius L.were screened by Swiss Target Predic-tion database;and the targets related to hepatic fi-brosis were screened by GeneCards database;the anti-hepatic fibrosis targets of total flavonoids of Carthamus tinctorius L.were obtained by taking the intersection of Venny.2.1.0;the protein interac-tions were analysed by STRING database;the visu-alization analysis was carried out by Cytoscape soft-ware;the GO function and KEGG pathway analysis was carried out by Metascape platform;and molec-ular docking was verified by using AutoDock soft-ware for the core targets and active ingredients.The mechanism of anti-hepatic fibrosis of total fla-vonoids of Carthamus tinctorius L.was verified by animal model and in vitro cell experiments.RE-SULTS:A total of 41 flavonoid components were identified in Carthamus tinctorius L.Through the network pharmacological analysis,149 anti-hepatic fibrosis targets of total flavonoids of Carthamus tinctorius L.were obtained,including 23 core tar-gets.The GO enrichment analyses involved a total of three aspects,namely,biological process(BP),cellular component(CC),and molecular function(MF).KEGG enrichment results showed that PI3K/Akt and MAPK are pathways involved in the devel-opment of hepatic fibrosis.Molecular docking veri-fied that the active ingredients Quercetin,Acacetin and Glabridin were tightly bound to Akt1 and HI-FIA,respectively.In animal model experiments,it was observed by HE and Masson staining that fibro-plasia was reduced,collagen deposition was re-duced,inflammatory cell infiltration was reduced,and fibrotic liver tissues were improved in total fla-vonoids of Carthamus tinctorius L.administration group.In isolated cell experiments:Western blot-ting results suggested that total flavonoids of Car-thamus tinctorius L.could decrease the hepatic fi-brosis marker factor α-SMA,Collagen1(P<0.01)and PI3K,Akt protein expression(P<0.01).CONCLU-SION:Total flavonoids of Carthamus tinctorius L.ex-erted anti-hepatic fibrosis effects through multi-components,multi-targets and multi-pathways,and their mechanism of action may be achieved by regulating the PI3K/Akt signalling pathway.
6.Influence of Oatp4c1-P-gp transmembrane transport system in the kidneys of obese mice on the pharmacokinetics of digoxin
Jing-wen MEN ; Lu SUN ; Hao-ran YUE ; Zhao-yue DUAN ; Hui-nan HOU ; Ting GUI ; Jun-hong XIN ; Zhi-bo GAI
Chinese Pharmacological Bulletin 2025;41(7):1318-1324
Aim To investigate the expression of or-ganic anion transporting polypeptide 4C1(Oatp4c1)-P-glycoprotein(P-gp)in the kidneys of obese mice in-duced by high-fat diet(HFD),and its impact on the pharmacokinetic changes of digoxin.Methods C57BL/6 mice were randomly divided into the Chow group and the HFD group.Body weight and blood glu-cose were recorded weekly.After successful model es-tablishment,digoxin was intraperitoneally injected,and blood was collected at different time points.Part of the blood samples was used for LC-MS/MS detection,and the other part was used for the detection of other bio-chemical indicators.After 16 weeks,the organs were removed and weighed.HE and immunohistochemical staining was used to observe the renal pathology and the expression of Villin,a marker of proximal tubules.Western blot and qPCR were combined to detect the expression of Villin,Oatp4c1 and P-gp.Results In the HFD group,body weight and blood glucose in-creased significantly.The blood concentration of digox-in rose,the area under the curve increased,and the half-life was prolonged.The proximal tubular epithelial cells shed,and the protein expression of Villin,Oatp4c1 and P-gp decreased significantly.Conclu-sions The down-regulation of Oatp4c1-P-gp expres-sion in the kidneys of HFD mice leads to an increase in the blood concentration of digoxin and a decrease in re-nal clearance.
7.Application of workshop-driven interactive teaching in clinical alarm training for nursing interns
Yue LI ; Dan HU ; Xin YANG ; Yuhan ZENG ; Chao HUANG ; Yueling HONG ; Xi SHI ; Juan LI
Chinese Journal of Medical Education Research 2025;24(10):1415-1422
Objective:To evaluate the effectiveness of a workshop-driven interactive teaching model in clinical alarm training for undergraduate nursing interns in the intensive care unit (ICU).Methods:A total of 120 undergraduate nursing students who interned in the ICU from November 2023 to April 2024 were enrolled and randomly assigned using a random number table into a control group ( n=60, traditional teaching) and an intervention group ( n=60, workshop-driven interactive teaching). Clinical alarm knowledge, attitudes, and practices (KAP); perception of patient safety culture; and training satisfaction were assessed before and after the training using validated questionnaires. Differences between groups were analyzed using independent sample t-test, paired sample t-test, chi-square test, and the Mann-Whitney U test with SPSS 22.0. Results:There were no significant differences between the two groups in clinical alarm KAP scores or patient safety culture perception scores before the training ( P>0.05). After the training, the intervention group showed significantly higher scores in clinical alarm KAP [(127.58±6.45) vs. (123.48±7.61), t=3.17, P=0.002] and patient safety culture perception [(99.44±9.17) vs. (95.45±12.03), t=-2.04, P=0.044] compared with the control group. Satisfaction with training content, teaching quality, and overall instructional design was significantly higher in the intervention group than in the control group ( P<0.05). Within-group comparisons showed that the intervention group had significant improvements in clinical alarm KAP [(127.58±6.45) vs. (120.10±10.25), t=-5.10, P<0.001] and patient safety culture perception [(99.44±9.17) vs. (94.46±12.12), t=-2.65, P=0.010] after training. No significant changes were observed in the control group after training ( P>0.05). Conclusions:The workshop-driven interactive teaching model can effectively enhance the clinical alarm KAP levels and patient safety culture perception among undergraduate nursing interns in the ICU. This teaching approach provides a scientific basis for optimizing clinical alarm education and cultivating high-quality nursing professionals.
8.Clinical features and short-medium term follow-up of children with severe multisystem inflammatory syndrome
Yue LIU ; Jian ZHANG ; Biru LI ; Botao NING ; Fang ZHANG ; Teng TENG ; Hong REN
Chinese Pediatric Emergency Medicine 2025;32(1):38-43
Objective:To analyze and summarize the clinical features and short-medium term follow-up results of children with multisystem inflammatory syndrome(MIS-C)following coronavirus infection.Methods:The data of six children with MIS-C admitted to the Intensive Care Unit of Shanghai Children's Medical Center from January to March 2023 were retrospectively analyzed.Results:All six cases were in shock,requiring vasoactive drugs,and one case required invasive mechanical ventilation.All the six patients had multiple organ function injury and increased inflammation indicators.After admission,they received organ support,glucocorticoids and gamma globulin treatment.Two patients were treated with biological agents.Both organ function and inflammation indicators showed significantly improvement after therapy.Six patients had mild coronary artery widening.All patients had good prognosis following short-medium term follow-up.Conclusion:Children with severe MIS-C may suffer life-threatening hemodynamic instability.Timely assessment,active anti-inflammatory and organ support therapy can obtain favorable prognosis.
9.Effect of the number of times to urinate on the modeling rate of neurogenic bladder model in rats after complete spinal cord transection
Roujun LIANG ; Lifen ZHAN ; Xuejiu ZENG ; Qiangsheng DING ; Xiaojing LUO ; Yue ZHUO ; Kun AI ; Shifeng DENG ; Ming XU ; Hong ZHANG
Chinese Journal of Tissue Engineering Research 2025;29(18):3840-3847
BACKGROUND:Spinal cord injury often leads to neurogenic bladder with hyperreflexia of the forced urethral muscle,but there is a lack of clear understanding of its pathogenesis and treatment,and establishing a stable and reliable animal model has an important impact on revealing its pathomechanisms and exploring therapeutic approaches.OBJECTIVE:To investigate the effect of the number of times to urinate on neurogenic model rats after complete spinal cord transection in order to improve the postoperative survival and modeling rate of neurogenic model rats.METHODS:Out of 46 female Sprague-Dawley rats,6 were selected as the sham-operated group using the random number table method,and the remaining 40 rats were randomly divided into 0,1,3,and 5 times daily urination groups after complete spinal cord transection modeling,with 10 rats in each group.The residual urine volume was measured every 3 days within 19 postoperative days,and the survival and modeling were observed on the 19th day after the operation,and urodynamics tests and contraction experiments of isolated forced urethra muscle strips were performed.RESULTS AND CONCLUSION:(1)Survival and modeling rate:there was 10%survival rate and 10%modeling rate in the group of 0 times daily urination;20%survival rate and 10%modeling rate in the group of 1 time daily urination;70%survival rate and 70%modeling rate in the groups of 3 and 5 times daily urination.(2)Residual urine volume:compared with the sham-operated group,the residual urine volume of the groups of 3 and 5 times daily urination was significant increased on postoperative days 3,6,9,12,and 15(P<0.01);the residual urine volume of the groups of 3 and 5 times daily urination was increased on the 18th day after surgery(P<0.05).Compared with the 3 times daily urination group,the residual urine volume was decreased in the 5 times daily urination group on the 6th day after surgery(P<0.05),while there was no significant difference in the residual urine volume between the 3 and 5 times daily urination groups on the 3rd,9th,12th,15th,and 18th days after surgery.(3)Urodynamics:Compared with the sham-operated group,the differential pressure at the point of leakage was significantly reduced(P<0.01)and the maximal volume was significantly increased(P<0.01)in the 3 and 5 times daily urination groups.There was no statistical difference in the differential pressure at the point of leakage and the maximal volume between the 3 and 5 times daily urination groups.(4)Muscle-strip contraction test of isolated detrusor muscles:Compared with the sham-operated group,the contraction amplitude and frequency of detrusor muscle strips were significantly reduced in the 3 and 5 times daily urination groups(P<0.01).There was no statistically significant difference in the contraction amplitude and frequency of detrusor muscle strips between the 3 and 5 times daily-urination groups.In conclusion,assisted urination is one of the keys to establish a successful neurogenic model of urethral reflexes,and there is no significant difference in the effects of urinating 3 or 5 times a day on the neurogenic model.It is recommended to urinate at least 3 times a day based on the actual workload and the modeling rate.
10.Advances in regulation of dysregulated bone remodeling by immune cells within rheumatoid arthritis synovial microenvironment
Jun-jie HE ; Zhong-liu YAO ; Ming-yue HU ; Hong HUANG ; Xiong CAI
Chinese Pharmacological Bulletin 2025;41(10):1801-1807
Rheumatoid arthritis(RA)is characterized by bidi-rectional bone remodeling imbalance,clinically termed the "high resorption-low formation" paradox,stemming not only from osteoclast hyperactivation but also critically involving pro-found suppression of osteoblast differentiation and function.No-tably,this suppression cannot be fully attributed to osteoclast hyperactivity;synovium-resident immune cells exert a pivotal regulatory influence through distinct mechanisms.This review systematically examines how synovial immune cells orchestrate bone remodeling in RA through both paracrine cytokine networks and direct cell-cell communication with bone lineage cells,thereby perturbing physiological homeostasis and driving patho-logical progression.These mechanistic revelations yield innova-tive perspectives on RA pathogenesis,positioning immune-medi-ated osteoimmune dysregulation as a promising therapeutic fron-tier for targeted intervention.


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