1.Three-dimensional finite element analysis of molar distalization with clear aligners with different thicknesses and edges
Yanan CHENG ; Jiazhi YU ; Yinchang LIU ; Jie WU ; Tong YU ; Lu WANG ; Xiaoguang LI
Chinese Journal of Tissue Engineering Research 2026;30(2):310-318
BACKGROUND:One of the advantages of clear aligner treatment is molar distalization.However,tooth tilting movement and loss of anterior anchorage may occur during treatment.There are few studies on whether these problems can be improved by selecting clear aligners with different thicknesses and edges to improve the clinical treatment effect.OBJECTIVE:To analyze the control ability of clear aligners with different thickness and edges on the central incisor,lateral incisor,and second molar when pushing the maxillary second molar distally by three-dimensional finite element analysis.METHODS:Three-dimensional finite element analysis models of bilateral maxillary second molar distalization with clear aligner,maxillary dentition,periodontal ligament,and alveolar bone with different thicknesses and margins were established by Mimics,Geomagic Wrap,3-matic and SolidWorks software,respectively.There were 16 combinations of four thicknesses(0.4,0.5,0.625,and 0.75 mm)and four margins(scallop,straight,straight extension 2 mm and straight extension 4 mm).The data were imported into Ansys Workbench software for design and solution.The mean value,peak value and distribution of the periodontal ligament equivalent stress of the second molar,the equivalent stress and the maximum initial displacement of the second molar,and the control ability of each appliance on the second molar,central incisor,and lateral incisor were analyzed.RESULTS AND CONCLUSION:(1)The mean equivalent stress of periodontal ligament of the second molar,the equivalent stress of the second molar and the maximum initial displacement of the second molar increased with the extension of the appliance edge and the increase of the thickness of the appliance in the 16 groups of models.(2)When the thickness of appliances was the same,the maximum equivalent stress of the second molar in the linear appliance group was the highest,and the maximum equivalent stress of the second molar in the linear extended appliance group was greater than that in the scallop appliance group.When the edge of the appliance was the same,the periodontal ligament equivalent stress peak of the second molar increased with the increase of the thickness of the appliance.The equivalent stress distribution in the periodontal ligament of the second molar in the linear extendable appliance group was more uniform than that in the scallop appliance group and the linear appliance group.(3)When the thickness of the appliance was the same,the scallop-shaped appliance had the worst control on the second molar.When the edge of the appliance was the same,with the increase of the thickness of the appliance,the control of the second molar by the linear extender appliance was gradually stronger than that by the linear appliance.The control of the central incisor was stronger and more stable with the linear extended 2 mm appliance,while the control of the lateral incisor was stronger and more stable with the linear appliance.(4)The results showed that when using clear aligners to push molars distally,extending the edge of the appliance could improve the control of the molars and reduce the tilting movement of the teeth.The design of a straight extension margin of 2 mm for the central incisor and a straight edge for the lateral incisor can enhance the control of the anchorage incisor and reduce the labial inclination of the anterior teeth.
2.Bone marrow mesenchymal stem cell nanovesicles fusion neutrophil apoptotic bodies promote skin wound healing in diabetic mice
Zhanpeng SUN ; Sen LIU ; Ling SHI ; Kaiyuan CHEN ; Meichen SONG ; Yan WU ; Jing YU
Chinese Journal of Tissue Engineering Research 2026;30(1):34-42
BACKGROUND:Nanocell vesicles possess functions such as re-epithelialization,antioxidation,anti-inflammation,and regulation of extracellular matrix remodeling.Meanwhile,apoptotic bodies have the immunomodulatory effects.Therefore,the combination of the two to form nanofusion vesicles can synergistically promote the healing of diabetic skin wounds.OBJECTIVE:To elucidate the impact of nanofusion vesicles on skin wound healing in a diabetic murine model.METHODS:(1)Material preparation and characterization:The primary bone marrow mesenchymal stem cells of C57BL/6J neonatal mice and the neutrophil apoptotic bodies of C57BL/6J mice were isolated and extracted.The nanofusion vesicles were prepared by micro-extrusion mechanism.(2)In vitro experiment:MTT assay was used to detect the proliferative effect of different concentrations of nanofusion vesicles on NIH-3T3 cells and human umbilical vein endothelial cells.Reactive oxygen species fluorescence probe was used to detect the antioxidant effect of nano-fusion vesicles on NIH-3T3 cells treated with hydrogen peroxide(H2O2).The inhibitory effect of nanofusion vesicles on RAW 264.7 macrophage inflammation induced by lipopolyside was detected by real-time quantitative RT-qPCR.(3)In vivo experiment:36 male C57BL/6J mice were employed to develop a murine model of diabetes mellitus.Following the successful induction of diabetes,two circular full-thickness wounds,each with a diameter of 6 mm,were created on either side of the diabetic mice's spine using a skin punch.The mice were divided into three groups by random number table method.The control group was injected with 0.1 mL of phosphate buffer solution.The nanovesicle group was injected with 0.1 mL nanovesicles(25 μg/mL).The nanofusion vesicle group was injected with 0.1 mL nanofusion(25 μg/mL)vesicles.After treatment for three consecutive days,the wound healing and histomorphological changes were observed.RESULTS AND CONCLUSION:(1)In vitro experiment:nanofusion vesicles,when administered at concentrations ranging from 0 to 100 μg/mL,exhibited no toxic effects and promoted the proliferation of NIH-3T3 and HUVEC cell lines.Notably,a concentration of 25 μg/mL nanofusion vesicle significantly enhanced the proliferation of NIH-3T3 cells.Furthermore,the survival rate of human umbilical vein endothelial cells was observed to increase in correlation with escalating concentrations of nanofusion vesicles.Nanofusion vesicles had a good antioxidant effect.In comparison to the H2O2 group,the fluorescence signal indicative of reactive oxygen species was progressively diminished in both the nanovesicle group and the nanofusion vesicle group.Furthermore,nanofusion vesicles possessed anti-inflammatory capabilities,effectively mitigating the inflammatory response in macrophages triggered by lipopolysaccharide stimulation.(2)In vivo experiment:Hematoxylin-eosin and Masson's trichrome staining revealed that in comparison to the control group,both the nanovesicle group and the nanofusion vesicle group exhibited a significant increase in granulation tissue formation and collagen fiber deposition within the wounds by day 6.Notably,the nanofusion vesicle group displayed the most pronounced effects.On day 12,the wound of nanofusion vesicle group was significantly reduced,and the healing rate was significantly faster than that of other groups(P<0.01),and the effect of promoting wound healing was the most significant.Our findings demonstrated that nanofusion vesicles exhibited superior pro-cell proliferative,antioxidant,and anti-inflammatory properties,thereby exerting a beneficial effect on the promotion of skin wound healing in diabetic mouse models.
3.Three-dimensional finite element analysis of molar distalization with clear aligners with different thicknesses and edges
Yanan CHENG ; Jiazhi YU ; Yinchang LIU ; Jie WU ; Tong YU ; Lu WANG ; Xiaoguang LI
Chinese Journal of Tissue Engineering Research 2026;30(2):310-318
BACKGROUND:One of the advantages of clear aligner treatment is molar distalization.However,tooth tilting movement and loss of anterior anchorage may occur during treatment.There are few studies on whether these problems can be improved by selecting clear aligners with different thicknesses and edges to improve the clinical treatment effect.OBJECTIVE:To analyze the control ability of clear aligners with different thickness and edges on the central incisor,lateral incisor,and second molar when pushing the maxillary second molar distally by three-dimensional finite element analysis.METHODS:Three-dimensional finite element analysis models of bilateral maxillary second molar distalization with clear aligner,maxillary dentition,periodontal ligament,and alveolar bone with different thicknesses and margins were established by Mimics,Geomagic Wrap,3-matic and SolidWorks software,respectively.There were 16 combinations of four thicknesses(0.4,0.5,0.625,and 0.75 mm)and four margins(scallop,straight,straight extension 2 mm and straight extension 4 mm).The data were imported into Ansys Workbench software for design and solution.The mean value,peak value and distribution of the periodontal ligament equivalent stress of the second molar,the equivalent stress and the maximum initial displacement of the second molar,and the control ability of each appliance on the second molar,central incisor,and lateral incisor were analyzed.RESULTS AND CONCLUSION:(1)The mean equivalent stress of periodontal ligament of the second molar,the equivalent stress of the second molar and the maximum initial displacement of the second molar increased with the extension of the appliance edge and the increase of the thickness of the appliance in the 16 groups of models.(2)When the thickness of appliances was the same,the maximum equivalent stress of the second molar in the linear appliance group was the highest,and the maximum equivalent stress of the second molar in the linear extended appliance group was greater than that in the scallop appliance group.When the edge of the appliance was the same,the periodontal ligament equivalent stress peak of the second molar increased with the increase of the thickness of the appliance.The equivalent stress distribution in the periodontal ligament of the second molar in the linear extendable appliance group was more uniform than that in the scallop appliance group and the linear appliance group.(3)When the thickness of the appliance was the same,the scallop-shaped appliance had the worst control on the second molar.When the edge of the appliance was the same,with the increase of the thickness of the appliance,the control of the second molar by the linear extender appliance was gradually stronger than that by the linear appliance.The control of the central incisor was stronger and more stable with the linear extended 2 mm appliance,while the control of the lateral incisor was stronger and more stable with the linear appliance.(4)The results showed that when using clear aligners to push molars distally,extending the edge of the appliance could improve the control of the molars and reduce the tilting movement of the teeth.The design of a straight extension margin of 2 mm for the central incisor and a straight edge for the lateral incisor can enhance the control of the anchorage incisor and reduce the labial inclination of the anterior teeth.
4.Bone marrow mesenchymal stem cell nanovesicles fusion neutrophil apoptotic bodies promote skin wound healing in diabetic mice
Zhanpeng SUN ; Sen LIU ; Ling SHI ; Kaiyuan CHEN ; Meichen SONG ; Yan WU ; Jing YU
Chinese Journal of Tissue Engineering Research 2026;30(1):34-42
BACKGROUND:Nanocell vesicles possess functions such as re-epithelialization,antioxidation,anti-inflammation,and regulation of extracellular matrix remodeling.Meanwhile,apoptotic bodies have the immunomodulatory effects.Therefore,the combination of the two to form nanofusion vesicles can synergistically promote the healing of diabetic skin wounds.OBJECTIVE:To elucidate the impact of nanofusion vesicles on skin wound healing in a diabetic murine model.METHODS:(1)Material preparation and characterization:The primary bone marrow mesenchymal stem cells of C57BL/6J neonatal mice and the neutrophil apoptotic bodies of C57BL/6J mice were isolated and extracted.The nanofusion vesicles were prepared by micro-extrusion mechanism.(2)In vitro experiment:MTT assay was used to detect the proliferative effect of different concentrations of nanofusion vesicles on NIH-3T3 cells and human umbilical vein endothelial cells.Reactive oxygen species fluorescence probe was used to detect the antioxidant effect of nano-fusion vesicles on NIH-3T3 cells treated with hydrogen peroxide(H2O2).The inhibitory effect of nanofusion vesicles on RAW 264.7 macrophage inflammation induced by lipopolyside was detected by real-time quantitative RT-qPCR.(3)In vivo experiment:36 male C57BL/6J mice were employed to develop a murine model of diabetes mellitus.Following the successful induction of diabetes,two circular full-thickness wounds,each with a diameter of 6 mm,were created on either side of the diabetic mice's spine using a skin punch.The mice were divided into three groups by random number table method.The control group was injected with 0.1 mL of phosphate buffer solution.The nanovesicle group was injected with 0.1 mL nanovesicles(25 μg/mL).The nanofusion vesicle group was injected with 0.1 mL nanofusion(25 μg/mL)vesicles.After treatment for three consecutive days,the wound healing and histomorphological changes were observed.RESULTS AND CONCLUSION:(1)In vitro experiment:nanofusion vesicles,when administered at concentrations ranging from 0 to 100 μg/mL,exhibited no toxic effects and promoted the proliferation of NIH-3T3 and HUVEC cell lines.Notably,a concentration of 25 μg/mL nanofusion vesicle significantly enhanced the proliferation of NIH-3T3 cells.Furthermore,the survival rate of human umbilical vein endothelial cells was observed to increase in correlation with escalating concentrations of nanofusion vesicles.Nanofusion vesicles had a good antioxidant effect.In comparison to the H2O2 group,the fluorescence signal indicative of reactive oxygen species was progressively diminished in both the nanovesicle group and the nanofusion vesicle group.Furthermore,nanofusion vesicles possessed anti-inflammatory capabilities,effectively mitigating the inflammatory response in macrophages triggered by lipopolysaccharide stimulation.(2)In vivo experiment:Hematoxylin-eosin and Masson's trichrome staining revealed that in comparison to the control group,both the nanovesicle group and the nanofusion vesicle group exhibited a significant increase in granulation tissue formation and collagen fiber deposition within the wounds by day 6.Notably,the nanofusion vesicle group displayed the most pronounced effects.On day 12,the wound of nanofusion vesicle group was significantly reduced,and the healing rate was significantly faster than that of other groups(P<0.01),and the effect of promoting wound healing was the most significant.Our findings demonstrated that nanofusion vesicles exhibited superior pro-cell proliferative,antioxidant,and anti-inflammatory properties,thereby exerting a beneficial effect on the promotion of skin wound healing in diabetic mouse models.
5.Clinical Efficacy of Janus Kinase Inhibitors in Combination with Chinese Herbal Medicine for Rheumatoid Arthritis:A Retrospective Study and A Meta-analysis
Chenguang ZHAN ; Shengqin YANG ; Xin LI ; Yu WEN ; Peng ZHANG ; Xingrui YAN ; Haifang DU ; Maojie WANG ; Xiaodong WU ; Liyan MEI ; Xiumin CHEN ; Yanlin LI ; Runyue HUANG
Journal of Traditional Chinese Medicine 2026;67(5):534-543
ObjectiveTo evaluate the efficacy and safety of Janus kinase (JAK) inhibitors combined with Chinese herbal medicine (CHM) in treating rheumatoid arthritis (RA). MethodsClinical data from 169 RA patients were retrospectively collected. Among them, 71 cases received JAK inhibitors as the control group, while 98 cases received JAK inhibitors plus CHM as the observation group, both treated for 24 weeks. The rheumatoid factor (RF), cyclic citic peptide antibody (anti-CCP), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and white blood cell count (WBC) were recorded before and after treatment. Databases including CNKI, Wanfang, VIP, PubMed and Web of Science were searched from inception till August 31st, 2025 for randomized controlled trials (RCTs) on the combined use of JAK inhibitors and CHM for RA. The methodological quality of the included studies was evaluated using the risk of bias assessment tool. Meta-analyses were performed for RF, anti-CCP, ESR, CRP, 28-joint disease activity score (DAS28), overall clinical effective rate, and incidence of adverse events. Sensitivity analysis were also performed. ResultsThe retrospective study demonstrated that after treatment, ESR, CRP, and anti-CCP levels decreased in the observation group, while ESR and CRP levels decreased in the control group (P<0.05). Moreover, ESR and RF levels in the observation group were lower than those in the control group (P<0.05). A total of 9 RCTs involving 770 patients were included in the meta-analysis. The results indicated that the JAK inhibitors plus CHM group was superior to the JAK inhibitors group in reducing RF (MD=-8.97, 95%CI -15.01 to -2.94, P=0.004), CRP (MD=-3.34, 95%CI -3.82 to -2.86, P<0.001), ESR (MD=-5.33, 95%CI -7.98 to -2.69, P<0.001), and DAS28 score (MD=-0.54, 95%CI -0.74 to -0.34, P<0.001), as well as in improving the overall clinical effective rate (OR=4.53, 95%CI 2.55 to 8.03, P<0.001). No statistically significant differences were observed between groups in anti-CCP levels (SMD=-2.08, 95%CI -4.41 to 0.24, P=0.080) or incidence of adverse events (OR=0.93, 95%CI 0.55 to 1.57, P=0.790). ConclusionThe combination of JAK inhibitors and CHM demonstrates remarkable efficacy in treating RA, contributing to improved disease activity and reduced inflammatory markers with a favorable safety profile.
6.Research progress on the source and biosynthesis of tetrodotoxin
Wei WU ; Dunning YU ; Xingchi YANG ; Peng SUN ; Zhiyong CHU
Journal of Pharmaceutical Practice and Service 2026;44(1):1-6
Tetrodotoxin(TTX)is a potent neurotoxin known for its specific sodium channel blocking effects, widely used in biomedical research. While TTX has been identified in various marine organisms, its true origin remains unclear, and the specific biosynthetic pathways are yet to be elucidated. The reported sources of TTX and the progress in research on TTX biosynthesis were summarized, with a focus on potential microbial sources of TTX, which could provide scientific reference for the production and biosynthesis studies of TTX.
7.Rectal Administration of Leek and Konjac-derived Extracellular Vesicles Alleviates High-fat Diet-induced Obesity in Mice via Gut Microbiota Modulation
Ya-Ru ZHANG ; Yu-Jia WU ; Cheng-Bang LIANG ; Xin-He YU ; Yan MU ; Yan TAN
Progress in Biochemistry and Biophysics 2026;53(5):1224-1239
ObjectiveObesity, a global chronic metabolic disease, is closely associated with disruptions in lipid metabolism and gut microbiota. Current intervention strategies still have limitations in terms of safety and microecological regulation, necessitating the exploration of novel natural regulatory approaches. Based on the early pathological characteristics of obesity, this study innovatively employs a rectal delivery method alongside a high-fat diet (HFD)-induced obesity model to systematically evaluate the inhibitory effects, safety, and gut microbiota regulation mechanisms of leek-derived and konjac-derived extracellular vesicles on obesity development. By simulating early clinical intervention scenarios, this study aims to explore the preventive potential of plant-derived extracellular vesicles during the initial stages of obesity onset. MethodsExtracellular vesicles from leek and konjac were isolated using ultracentrifugation combined with density gradient centrifugation. Their nanoscale properties were characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM), and nanoparticle tracking analysis (NTA). Male C57BL/6J mice were randomly divided into four groups: normal control (NC), high-fat diet (HFD), leek-derived extracellular vesicles (LEVs), and konjac-derived extracellular vesicles (KEVs). Beginning simultaneously with HFD feeding, mice in the intervention groups received 20 g/L vesicles rectally every 3 d for 4 weeks. Body mass and body composition were monitored throughout. At endpoint, mouse serum, adipose tissue, and colonic contents were collected. Serum biochemical indices (lipid profile, liver and kidney function, cardiac markers) were assessed to evaluate safety and metabolic efficacy, while 16S rRNA sequencing was employed to analyze gut microbial structure and diversity. ResultsDLS, NTA, and TEM confirmed that both LEVs and KEVs exhibited typical cup-shaped nanostructures with average particle sizes of approximately 284 nm and 223 nm, respectively. LEVs and KEVs treatment significantly suppressed HFD-induced weight gain and elevation of body-fat percentage (P<0.05), and reduced accumulation of abdominal white and epididymal adipose tissue. Serological analyses showed that both vesicles lowered total cholesterol, triglycerides and LDL-cholesterol, and ameliorated liver enzyme profiles (ALT, AST), demonstrating lipid-metabolic regulation and hepatoprotective effects. No hepatic, renal or cardiac dysfunction was observed, indicating favorable safety. Gut microbiota analyses revealed that vesicle intervention partially restored HFD-depleted microbial diversity and reshaped community structure. Notably, LEVs markedly increased the relative abundance of the beneficial taxon Lachnospiraceae at the family level, which is known for producing short-chain fatty acids and enhancing intestinal barrier function. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional prediction suggested that LEVs and KEVs modulated gut microbial functions through distinct mechanisms: LEVs downregulated pathways related to ribosomes and DNA replication while enhancing xenobiotic degradation, whereas KEVs tended to upregulate energy metabolism and protein synthesis toward healthy levels. ConclusionRectally administered LEVs and KEVs exhibit excellent safety and pronounced metabolic benefits during the early phase of obesity, suppressing weight gain, correcting lipid dysregulation, and exerting effects via modulation of gut microbial composition and function. This study provides systematic experimental evidence supporting plant-derived exosome-like vesicles as an early intervention strategy against obesity.
8.Advancements in Gas-releasing Micro/Nanoplatforms for Overcoming MDR Bacterial Infections in Diabetic Wounds
Ruo-Can LIU ; Yu-Qian WANG ; Shuai ZHANG ; Shao-Zhi ZUO ; Yun-Di WU ; Xi-Long WU
Progress in Biochemistry and Biophysics 2026;53(5):1356-1375
Chronic diabetic wounds, severely complicated by multidrug-resistant (MDR) bacterial infections, represent a profound and escalating global health crisis. The intrinsically hostile microenvironment of diabetic wounds, characterized by localized hypoxia, persistent oxidative stress, and poor vascularization, creates an ideal niche for opportunistic pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa. These bacteria readily construct dense extracellular polymeric substance (EPS) biofilms, which not only physically shield the microbes from host immune responses but also actively trap the wound in a state of chronic, unresolved inflammation. Consequently, conventional systemic and topical antibiotic therapies are becoming increasingly futile, as poor perfusion at the wound site restricts drug bioavailability, while the rapid genetic evolution of bacteria and the impenetrable nature of biofilms lead to catastrophic treatment failures, often culminating in severe tissue necrosis and lower-extremity amputations. To circumvent the limitations of traditional antimicrobials, therapeutic gas delivery has emerged as a highly promising, paradigm-shifting strategy. Gaseous signaling molecules, particularly nitric oxide (NO), carbon monoxide (CO), hydrogen sulfide (H2S), and hydrogen (H2), possess unique physicochemical properties that allow them to seamlessly penetrate dense biofilm matrices and cellular membranes. Once inside, these gases operate via multi-targeted mechanisms that are incredibly difficult for bacteria to develop resistance against; for instance, NO induces severe lipid peroxidation and DNA cleavage in bacteria, CO downregulates pro-inflammatory cytokines, H2S significantly accelerates endothelial cell migration for neovascularization, and H2 acts as a powerful selective antioxidant to neutralize tissue-damaging reactive oxygen species (ROS). Together, these therapeutic gases not only exert broad-spectrum bactericidal effects but also actively reprogram the wound bed by promoting the critical M1-to-M2 macrophage polarization and stimulating angiogenesis. Despite their immense biological potential, the direct clinical translation of gas therapies is severely hindered by inherent physicochemical drawbacks, including extreme volatility, short physiological half-lives, poor aqueous solubility, and the high risk of off-target systemic toxicity, if applied indiscriminately. To conquer these immense pharmacokinetic barriers, cutting-edge advancements in materials science have driven the development of gas-releasing micro- and nanoplatforms. Utilizing sophisticated carriers such as metal-organic frameworks (MOFs), mesoporous silica, polymeric nanoparticles, liposomes, and injectable hydrogels, researchers can now encapsulate gas-donor molecules to achieve sustained, localized delivery. More importantly, these advanced nanoplatforms are ingeniously engineered to be stimuli-responsive. By exploiting the pathological hallmarks of the diabetic wound environment, such as elevated glucose concentrations, acidic pH, and overexpressed ROS, or by utilizing external triggers like near-infrared (NIR) light irradiation and ultrasound, these intelligent platforms ensure on-demand, precise spatio-temporal gas release. This often allows for powerful synergistic combinations, such as photothermal or photodynamic therapy coupled with gas release, thereby obliterating biofilms while sparing healthy tissue. While the therapeutic outcomes of these smart delivery systems in eradicating MDR infections and accelerating tissue repair are unprecedented, several critical challenges remain before widespread clinical adoption, as long-term biosafety profiles of the carrier nanomaterials, complexities in large-scale good manufacturing practice (GMP) production, and stringent regulatory hurdles must be rigorously addressed. Looking forward, the next frontier lies in the realm of precision medicine and theranostics, where future research must focus on the seamless integration of these gas-releasing platforms with flexible, wearable biosensors capable of continuously monitoring wound biomarkers (e.g., pH, temperature, uric acid) in real-time. Coupled with artificial intelligence algorithms to govern automated, closed-loop adaptive dosing, these next-generation smart dressings hold the ultimate potential to comprehensively transform the clinical management of complex, infected diabetic wounds.
9.A Computational Perspective on Differences Between MHC-I and MHC-II in TCR-pMHC Structure Prediction Resources: Review and Benchmarking
Xiao-Qin WU ; Da-Wei LIU ; Bin-Yu LI ; Yang LIU ; Yang CAO ; Wen-Tao DAI
Progress in Biochemistry and Biophysics 2026;53(5):1376-1399
The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.
10.Epidemiological investigation and analysis of a local dengue fever cluster outbreak in Qingpu District of Shanghai
Changpo LIN ; Wei WANG ; Zhangrui XU ; Yadong MA ; Zhicheng ZHANG ; Xueqin YU ; Chengcheng WANG ; Haoxuan WANG ; Yanli DAI ; Huanyu WU
Shanghai Journal of Preventive Medicine 2026;38(3):206-209
ObjectiveTo analyze the epidemiological characteristics of a local dengue fever cluster outbreak in Qingpu District of Shanghai in 2024, and to provide a reference for subsequent dengue fever prevention and control. MethodsSeven confirmed local dengue fever cases reported through the National Notifiable Infectious Diseases Surveillance System in Qingpu District of Shanghai in 2024 were selected as the research subjects. Descriptive epidemiological methods were used to conduct investigation and analysis from the aspects of onset, medical treatment and reporting, clinical symptoms, travel and contact history within 15 days before onset, and activity trajectories. ResultsA total of 7 cases were identified in this outbreak. None of the cases had a travel history to dengue-endemic areas within 15 days prior to onset, while all had shared exposure environments and mosquito bite histories, indicating a local clustered transmission pattern. The main clinical manifestations included fever (100.00%) and myalgia (42.86%). All 7 cases were positive for dengue virus serotype 2 (DENV-2) by nucleic acid testing. Genetic sequencing showed that the virus strains belonged to the Cosmopolitan genotype and were most closely related to the epidemic DENV strains circulating in southern China in recent years. ConclusionThis outbreak might be a local secondary infection caused by the short-term stay of dengue fever-infected individuals, and the possible source of importation was dengue fever endemic areas in southern China.

Result Analysis
Print
Save
E-mail