1.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.
2.Transcatheter aortic valve replacement for aortic regurgitation complicated by Takayasu arteritis: A case report
Jianbin GAO ; Jian LI ; Yu YANG ; Mier MA ; Kairui YANG ; Wei LUO ; Ning WANG ; Da ZHU ; Wenbin OUYANG ; Xiangbin PAN
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(01):163-166
Patients with Takayasu arteritis combined with aortic valve disease often have a poor prognosis following surgical valve replacement, frequently encountering complications such as perivalvular leakage, valve detachment, and anastomotic aneurysm. This article presents a high-risk case wherein severe aortic valve insufficiency associated with Takayasu arteritis was successfully managed through transcatheter aortic valve implantation via the transapical approach. The patient had satisfactory valve function with no complications observed during the six-month postoperative follow-up. This case provides a minimally invasive and feasible alternative for the clinical management of such high-risk patients.
3.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.
4.Clinical Efficacy and Scalp Microbiome Changes Induced by AMPamide-Containing Shampoo in Patients With Seborrheic Dermatitis
Yi Na YOON ; Sae Hee KIM ; Ji Won LIM ; Myeong Jae KIM ; Hye-Jin KIM ; Woo Jun SUL ; Daehwan KIM ; Wonseok JEONG ; Jeonghwan HWANG ; Da-Ae YU ; Yong Beom CHOE ; Yang Won LEE
Annals of Dermatology 2026;38(3):237-247
Background:
Seborrheic dermatitis (SD) is a chronic inflammatory scalp disorder associated with Malassezia dysbiosis and increased sebum production. AMPamide has been suggested to have anti-inflammatory and sebum-regulating effects, but its clinical efficacy and microbiome-modulating effects in SD remain unclear.
Objective:
To evaluate the clinical efficacy and scalp microbiome changes following 4 weeks of use of an AMPamide-containing shampoo in patients with SD.
Methods:
In this observational study, 30 patients with SD applied an AMPamide-containing shampoo for 4 consecutive weeks. Clinical outcomes, including sebum levels and overall severity scores, were assessed. Scalp bacterial and fungal communities were analyzed to evaluate α- and β-diversity and changes in Malassezia composition.
Results:
Treatment resulted in significant reductions in sebum levels and clinical severity scores, particularly in erythema, dandruff, and pruritus. Bacterial community composition remained largely stable, while fungal α-diversity increased, and β-diversity analysis revealed a decrease in the ratio of Malassezia restricta to Malassezia globosa.
Conclusion
AMPamide-containing shampoo was associated with improved clinical symptoms and a shift toward a more balanced fungal community composition in patients with SD, supporting its potential as a non-steroidal therapeutic option for SD.
5.Symptoms and quality of life benefits of successful percutaneous coronary intervention in left main disease and/or 3-vessel disease patients with diabetes
Bo-da ZHU ; Tian-tong YU ; Peng HAN ; Bo-hui ZHANG ; Xi ZHANG ; Ping YUAN ; Gang WANG ; Yi YANG ; Hui-li ZHU ; Pan-pan SUN ; Tong-tong LI ; Shuai ZHAO ; Cheng-xiang LI ; Kun LIAN
Chinese Journal of Interventional Cardiology 2025;33(2):93-100
Objective To investigate whether successful percutaneous coronary intervention(PCI)could improve symptoms and quality of life(QOL)in left main disease and/or 3-vessel disease patients with diabetes.Methods Patients with left main disease and/or 3-vessel disease who underwent PCI in the First Affiliated Hospital of Air Force Medical University from April 2018 to May 2021 were consecutively enrolled and subdivided into 2 groups:diabetes and no diabetes.Detailed baseline characteristics,symptoms,including dyspnea and angina,assessed with the Rose dyspnea scale(RDS),Seattle angina questionnaire(SAQ),the European quality of life-5 dimensions(EQ-5D)and 12-item short-form health survey(SF-12)questionnaire respectively,procedural details,and 1 month and 1 year follow-up data were collected.Results Among 440 left main disease and/or 3-vessel disease patients,disease was present in 176(40.00%),who had more hypertension,peripheral artery disease,and LCX lesion(all P<0.05).The incidence of major adverse cardiovascular events(MACE)and all-cause mortality were similar between the two groups(both P>0.05)at 1 month follow-up,while all-cause mortality in diabetes patients was significantly higher than those without diabetes at 1 year follow-up(P=0.013).Low left ventricular ejection fraction was an independent risk factor for MACE and all-cause mortality at 1 month and 1 year follow-up after successful revascularization(all P<0.05).Most importantly,symptoms,including dyspnea and angina,and QOL were markedly improved regardless of diabetes both at 1 month and 1 year follow-up(all P<0.05).Diabetes patients showed improved dyspnea and QOL at similar degree to the non-diabetes patients(all P>0.05)and a more significantly relieved angina(P=0.013).Additionally,the number of chronic total occlusion(CTO)per patient was identified as an independent risk factor of dyspnea(OR 0.723,95%CI 0.525~0.997,P=0.048)and angina relief(OR 0.686,95%CI 0.473~0.995,P=0.047),and the contrast volume(OR 0.995,95%CI 0.992~0.999,P=0.008)as an independent risk factor of QOL improvement in diabetic patients.Conclusions Successful PCI is beneficial for relieving symptoms and improving quality of life in patients with diabetes who have left main disease and/or 3-vessel disease.
6.Comparative effectiveness of small optical zone orthokeratology lenses and repeated low-level red-light therapy for controlling myopia in adolescents
Shi-mei LIU ; Li CHEN ; Da LUO ; Qi-hui LUO ; Yu CHENG ; Ren-xiang TANG ; Wei YANG ; Bo LIU
Journal of Regional Anatomy and Operative Surgery 2025;34(11):972-976
Objective To compare the effect of small optical zone orthokeratology lenses(OK lenses)and repeated low-level red-light(RLRL)therapy in controlling myopia progression for adolescents,and the therapeutic effectiveness of RLRL is evaluated.Methods A retrospective analysis was conducted on the clinical data of 80 adolescent myopic patients in the First Affiliated Hospital of Army Medical University.The patients were divided into the RLRL group and the OK lenses group according to different intervention methods,with 40 cases in each group.Patients in the RLRL group received RLRL therapy combined with single-vision spectacles,and patients in the OK lenses group were treated with OK lenses.The changes of spherical equivalent(SE),axial length and subfoveal choroidal thickness(SFCT)1,3,6,and 12 months after treatment compared with the baseline,and color vision of patients were assessed.Based on the mean baseline axial length of the RLRL group,the patients in this group were subdivided into the short axial group and the long axial group,and the changes of the axial length and SFCT were further analyzed.Results The diopter 1,3,6,and 12 months after treatment in the RLRL group were not significantly different from the baseline(P>0.05).Axial lengths of patients in the RLRL group progressively shortened after treatment and returned close to the baseline 12 months after treatment.In contrast,axial lengths of patients in the OK lens continued to grow within 12 months after treatment;the axial lengths at each time point after treatment of patients in the two groups were significantly different from the baseline(P<0.05).The changes of axial length of patients in the RLRL group at each time point after treatment were significantly smaller than those in the OK lenses group(P<0.05).The SFCT changes of patients in the RLRL group at each time point after treatment were all greater than those in the OK lenses group(P<0.05).The SFCT at each time point after treatment in the RLRL group were significantly different from the baseline(P<0.05),whereas the SFCT at each time point after treatment in the OK lenses group were not significantly different from the baseline(P>0.05).The changes of axial length at each time point after treatment of patients in the long axial group were all greater than those in the short axial group(P<0.05);the SFCT changes 6 months after treatment of patients in the long axial group was greater than that in the short axial group(P<0.05);the SFCT at each time point after treatment of patients in the two groups were signifi-cantly different from the baseline(P<0.05).Color vision tests revealed no abnormities after treatment in the RLRL group and the OK lenses group.Conclusion RLRL therapy is effective in controlling myopia progression and demonstrates superior axial length control compared to orthokeratology lenses.
7.CiteSpace-based literature visualization analysis of brain-computer interface technology applied in rehabilitation of stroke patients
Yu-wei HAN ; Da HUO ; Li-gang CHEN ; Xin-yu YANG ; Hai JIN ; Xiao-ming LI ; Guo-biao LIANG ; Chun-yong YU
Chinese Medical Equipment Journal 2025;46(9):65-69
Relevant China's literature on the application of brain-computer interface technology in the field of rehabilita-tion of stroke patients was retrieved in the China Knowledge Network database from its establishment to December 31,2024,and CiteSpace visual analysis software was used to analyze the selected literature in terms of trend of annual publica-tion number,author collaboration network,keyword co-occurrences and emergences and to generate a corresponding knowledge map.It's pointed out brain-computer interface technology showed significant application potential for motor function recovery and neurorehabilitation,which had the research hotspots of the cross technologies covering motor imagina-tion,rehabilitation training and virtual reality and the research frontiers of the fusion application of intelligent algorithms of deep learning and pattern recognition.The challenges and future development directions of the field were investigated,and references were provided for promoting the application of brain-computer interface technology to rehabilitation of sroke patients in China.[Chinese Medical Equipment Journal,2025,46(9):65-69]
8.Investigation of Effects of Ultrasound on Red Blood Cell Membranes Using Cryo-Electron Tomography
Yang YU ; Si-Hang CHENG ; Guan-Fang ZHAO ; Hui-Li WANG ; Hai-Jiao XU ; Hong-Da WANG
Chinese Journal of Analytical Chemistry 2025;53(1):74-83
Ultrasound technology has been applied in the biomedical field,particularly in drug delivery and cell processing.In this study,the effects of different ultrasound power levels(40 W to 100 W)and time durations(1 min,5 min,or 5 min discontinuously)on the morphology of human red blood cells(hRBCs)membranes were systematically investigated using cryo-electron tomography(Cryo-ET).The hRBCs membranes were firstly subjected to ultrasound at power levels of 40 W and 60 W for 5 min each.Cryo-ET observations revealed minimal morphological changes in the hRBCs membranes following the 40 W treatment,with the membrane structure remaining relatively intact and only minor undulations appearing on the membrane surface.These undulations might result from the mild mechanical stress induced by ultrasound,which was insufficient to disrupt the overall membrane structure.At power of 60 W,the hRBCs membranes largely preserved their structural integrity.When the ultrasonic power was increased to 80 W,the structural damage to the hRBCs membranes became more severe.Cryo-ET images showed irregular ruptures and larger pores on the membrane surface,indicating a significant compromise in membrane integrity.At ultrasound power of 100 W,the hRBCs membranes were completely disrupted,resulting in the formation of numerous membrane fragments,and a complete loss of membrane continuity.To further explore the effects of ultrasound duration on erythrocyte membrane morphology,the ultrasonic power was fixed at 100 W and the impacts of varying treatment durations(1 min,5 min,and intermittent ultrasound)on the membrane structure were systematically investigated.After 1 min of ultrasonic treatment,Cryo-ET images showed minimal changes in erythrocyte membrane morphology.Although some small pores and undulations appeared on the membrane surface,the overall structure remained relatively intact.As the ultrasound duration extended to 5 min,the degree of membrane damage increased significantly.Cryo-ET images revealed extensive rupture and detachment of the membrane,with continuity being severely compromised.As to treatment alternating 1 min of ultrasound with 1 min of rest,for a total of 5 min of ultrasound exposure,Cryo-ET observations showed the integrity of the membrane-cytoskeleton attachment remained.Under intermittent ultrasound treatment,although some pores and ruptures were observed on the membrane surface,the overall structure remained more intact compared to continuous ultrasonic treatment.This preservation might be due to the intermittent treatment providing buffer periods for the membrane,allowing partial recovery after mechanical stress,thereby reducing the cumulative damage caused by continuous ultrasound.This work provided experimental basis for further understanding of mechanism of ultrasound induced change of cell membrane and cytoskeleton.
9.Advances in Nanozymatic Colorimetric Sensing Technology in the Field of Environmental,Food and Drug Safety Detection
Zhi-Chao YANG ; Rui-Ting FENG ; Hong-Da LI ; Yu-Mu LIU
Chinese Journal of Analytical Chemistry 2025;53(9):1435-1446
Food,drug and environment related cases are becoming more and more frequent,and the demand for on-site rapid detection is also increasing.Nanozymes are nanomaterials with enzyme-like catalytic activity,which have the advantages of high catalytic efficiency,good stability,economy,adjustability,multifunctionality and large-scale preparation.The colorimetric sensing technology based on nanozymes combined with smart phones has wide range of applications in the field of food,drugs and environment detection,and is expected to become an important means for relevant departments to combat crime.This paper summarized the progresses of nanozymes in the field of environmental,food and drug crime(EFDC)detection,focusing on the detection mechanism of different types of nanozymes and the current status of research on the detection of EFDC,and prospected the future development of nanozymes.The possible future prospects of machine learning(ML)in the field of nanozymes colorimetric sensing technology and the challenges in detection of EFDC were also discussed.
10.Comparative effectiveness of small optical zone orthokeratology lenses and repeated low-level red-light therapy for controlling myopia in adolescents
Shi-mei LIU ; Li CHEN ; Da LUO ; Qi-hui LUO ; Yu CHENG ; Ren-xiang TANG ; Wei YANG ; Bo LIU
Journal of Regional Anatomy and Operative Surgery 2025;34(11):972-976
Objective To compare the effect of small optical zone orthokeratology lenses(OK lenses)and repeated low-level red-light(RLRL)therapy in controlling myopia progression for adolescents,and the therapeutic effectiveness of RLRL is evaluated.Methods A retrospective analysis was conducted on the clinical data of 80 adolescent myopic patients in the First Affiliated Hospital of Army Medical University.The patients were divided into the RLRL group and the OK lenses group according to different intervention methods,with 40 cases in each group.Patients in the RLRL group received RLRL therapy combined with single-vision spectacles,and patients in the OK lenses group were treated with OK lenses.The changes of spherical equivalent(SE),axial length and subfoveal choroidal thickness(SFCT)1,3,6,and 12 months after treatment compared with the baseline,and color vision of patients were assessed.Based on the mean baseline axial length of the RLRL group,the patients in this group were subdivided into the short axial group and the long axial group,and the changes of the axial length and SFCT were further analyzed.Results The diopter 1,3,6,and 12 months after treatment in the RLRL group were not significantly different from the baseline(P>0.05).Axial lengths of patients in the RLRL group progressively shortened after treatment and returned close to the baseline 12 months after treatment.In contrast,axial lengths of patients in the OK lens continued to grow within 12 months after treatment;the axial lengths at each time point after treatment of patients in the two groups were significantly different from the baseline(P<0.05).The changes of axial length of patients in the RLRL group at each time point after treatment were significantly smaller than those in the OK lenses group(P<0.05).The SFCT changes of patients in the RLRL group at each time point after treatment were all greater than those in the OK lenses group(P<0.05).The SFCT at each time point after treatment in the RLRL group were significantly different from the baseline(P<0.05),whereas the SFCT at each time point after treatment in the OK lenses group were not significantly different from the baseline(P>0.05).The changes of axial length at each time point after treatment of patients in the long axial group were all greater than those in the short axial group(P<0.05);the SFCT changes 6 months after treatment of patients in the long axial group was greater than that in the short axial group(P<0.05);the SFCT at each time point after treatment of patients in the two groups were signifi-cantly different from the baseline(P<0.05).Color vision tests revealed no abnormities after treatment in the RLRL group and the OK lenses group.Conclusion RLRL therapy is effective in controlling myopia progression and demonstrates superior axial length control compared to orthokeratology lenses.

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