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.

Objective To understand the epidemiological characteristics of newly reported occupational diseases and provide a basis for the formulation of occupational disease prevention and control plans in Nanjing. Methods A descriptive analysis was conducted on newly reported occupational disease cases in Nanjing from 2014 to 2024. Results A total of 325 new cases of occupational diseases were reported in Nanjing, primarily concentrated in occupational otorhinolaryngological and oral diseases, as well as pneumoconiosis. Male cases outnumbered female cases across all types of occupational diseases. The median age at diagnosis was 53 (44, 65) years, and the median length of employment was 13 (6, 24) years. The distribution of occupational diseases varied significantly by gender and age at diagnosis (P<0.01). The distribution of occupational diseases also showed significant differences based on the length of exposure to hazards (χ²=120.63, P<0.01). Large enterprises, state-owned enterprises, and manufacturing industries accounted for the majority of cases (120 cases, 36.92%; 154 cases, 47.38%; 232 cases, 71.38%). The distribution of newly reported occupational diseases across different age groups at diagnosis was statistically significant (H=97.66, P<0.01; H=84.06, P<0.01; H=34.64, P<0.01; H=20.05, P<0.01; H=21.70, P<0.01). Except for occupational diseases caused by physical factors, the distribution of other newly reported occupational diseases across different employment length groups was also statistically significant (H=105.45, P<0.01; H=97.05, P<0.01; H=34.14, P<0.01; H=42.69, P<0.01). Conclusion The prevention and control of newly reported occupational diseases in Nanjing remain challenging. Attention should be paid to key occupational otorhinolaryngological and oral diseases, as well as pneumoconiosis. It is necessary to strengthen supervision and management of medium and large state-owned enterprises and manufacturing industries.

Objective This study investigated the diversity of rodent populations and the infection status of Bartonella at three ports along the China-Mongolia border in 2022. Methods Rodents at three Belt and Road ports along the China-Mongolia border, namely Ganqimaodu, Erenhot, and Zhuengadabuqi, were morphologically identified. The Bartonella citrate synthase(gltA)gene was amplified by nested polymerase chain reaction(PCR), and PCR-positive products were sequenced. The resulting sequences were then analyzed for genetic characteristics. Phylogenetic analysis was performed using MEGA 11.0 software using Neighbor-Joining and Maximum-Likelihood method. Results A total of 94 rodents were captured, representing seven species from five families and six genera: Mus musculus, Meriones unguiculatus, Meriones meridianus, Spermophilus dauricus, Allactaga sibirica, Dipus sagitta, and Phodopus roborovskii. Among them, M. unguiculatus was the most abundant species, with 58 rodents, accounting for 61.70% of the total. Overall,11 positive Bartonella pathogen sequences were obtained from the three ports, with a positive detection rate of 11.70%(11/94). The infected rodent species included M. unguiculatus, M. meridianus, and A. sibirica, and two species of Bartonella were detected. Conclusions Rodents at Ganqimaodu, Erenhot, and Zhuengadabuqi ports along the China-Mongolia border were naturally infected with Bartonella. Rodent monitoring and pathogen prevention and control in this area should be strengthened.

Objective This study reports on the obligatory parasitism of water mites Arrenurus sp. on Anopheles messeae at the Manzhouli Port, Inner Mongolia, China. Methods Duing July 2024, a survey on the mosquito diversity was conducted at the Manzhouli Port. Captured mosquitoes and their ectoparasites were identified to species level. Results A total of 1840 adult mosquitoes were collected, representing species from three genera: Culex(Cx. modestus, Cx. pipiens pallens), Aedes(Ae. dorsalis, Ae. flavidorsalis, Ae. flavescens), and Anopheles (An. messeae). Among all the mosqutioes specimens,3 out of 150 captured An. messeae were found to carry ectoparasitic mites, with number of 2,4,27 mites separately. Morphological and molecular identification reached the same result as water mites(Hydrachnidiae, Hydracrina). COI gene sequence showed 94% similarity with the closest species Arrenurus truncatellus. Conlusions Literature review suggests water mites are host-specific parasitism of mosquito species and herein with the first record of Arrenurus sp. parasiting on An. Messeae in the most high-latitude region globally.

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.

Background/Aims: Data from Asia regarding the short-term and long-term outcomes for acute severe ulcerative colitis (ASUC) are limited. We assessed the outcomes of ASUC, identified the risk factors for colectomy, and compared colectomy rates between the pre-biologics and post-biologics eras in Taiwan. Methods: The patients with an ASUC diagnosis between January 2013 and March 2022 at 5 tertiary medical centers were retrospectively analyzed. Results: In total, 98 patients were enrolled, with 68.4% diagnosed in the post-biologics era. In 78.6% of the ASUC patients initially received intravenous steroid therapy, for which the success rate was 74.1%. As for rescue therapy, 15 patients (93.8%) received biologics and 1 (6.3%) received cyclosporin. Biologics rescue therapy had a 93.3% success rate. One (1%) mortality due to septic shock occurred. The colectomy rate for index ASUC admission was 11.2%. Patients receiving colectomy were predominantly male (P= 0.012) and at older age (P= 0.016). Higher C-reactive protein (P= 0.035), lower albumin (P= 0.017), and hemoglobin (P= 0.023) levels were associated with colectomy risk. During a median follow-up of 24 months, 13 patients (15.1%) had recurrent ASUC and 23.1% of patients received colectomy. The accumulated colectomy rate at 3 years did not differ between the pre- and post-biologics eras (16.1% vs. 13.4%, P= 0.270). Conclusions This is the first Asian study on ASUC to compare colectomy rates between the prebiologics and post-biologics eras, revealing no significant difference. The recurrent ASUC had a higher colectomy rate than the index ASUC.

Objective To examine the changing prevalence and antimicrobial resistance profiles of Burkholderia cepacia in 52 hospitals across China from 2015 to 2021.Methods A total of 9 261 strains of B.cepacia were collected from 52 hospitals between January 1,2015 and December 31,2021.Antimicrobial susceptibility of the strains was tested using Kirby-Bauer method or automated antimicrobial susceptibility testing systems according to a unified protocol.The results were interpreted according to the breakpoints released in the Clinical & Laboratory Standards Institute(CLSI)guidelines(2023 edition).Results A total of 9 261 strains of B.cepacia were isolated from all age groups,especially elderly patients.The proportion was 11.1％(1 032 strains)in children,significantly lower than the proportion in adults.About half(46.5％,4 310/9 261)of the strains were isolated from patients at least 60 years old and 42.3％(3 919/9 261)of the strains were isolated from young adults.Most isolates(71.1％)were isolated from sputum and respiratory secretions,followed by urine(10.7％)and blood samples(8.1％).B.cepacia isolates were highly susceptible to the five antimicrobial agents recommended in the CLSI M100 document(33rd edition,2023).B.cepacia isolates showed relatively higher resistance rates to meropenem and levofloxacin.However,the resistance rates to ceftazidime,trimethoprim-sulfamethoxazole,and minocycline remained below 8.1％.The percentage of B.cepacia strains resistant to levofloxacin was the highest compared to other antibiotics in any of the three age groups(from 12.4％in the patients＜18 years old to 20.6％in the patients aged 60 years or older).Conclusions B.cepacia is one of the clinically important non-fermenting gram-negative bacteria.Accurate and timely reporting of antimicrobial susceptibility test results and ongoing antimicrobial resistance surveillance are helpful for rational prescription of antimicrobial agents and proper prevention and control of nosocomial infections.

Objective To explore the efficacy and safety of pegylated doxorubicin liposome(PLD)in neoadjuvant chemotherapy(NAC)for breast cancer.Methods A total of 126 breast cancer patients treated with the NAC regimen containing PLD in the Third Xiangya Hospital of Central South University from Janu-ary 2018 to December 2022 were selected as the research subjects.The clinical efficacy,pathological efficacy and occurrence of adverse reactions of the patients were observed,and total pathological complete response(tpCR)rates of different molecular subtypes were analyzed.The changes in left ventricular ejection fraction(LVEF)were compared between before and after treatment.Results Among 126 patients,the clinical efficacy of NAC in 119 cases was evaluated,and the objective response rate(ORR)was 67.2％(80/119).A total of 123 patients were evaluated for the pathological efficacy,breast cancer pathological complete response(bpCR)rate was 13.8％(17/123);tpCR rate was 12.2％(15/123),in which the the human epidermal growth factor receptor 2(HER2)positive[hormone receptor(HR)negative]type had the highest rate(33.3％),followed by triple-negative(21.7％).There was no hand-foot syndrome occurred,and only one case developed the grade 2 oral mucositis.LVEF showed no statistically significant difference between before and after treatment[69.9％(51.0％,87.0％)vs.69.0％(57.0％,85.0％)](P＞0.05).Conclusion The NAC regimen containing PLD has a better effect on HER2—positive and triple-negative breast cancer.

Objective To analyze risk factors for poor postoperative wound healing in spinal tuberculo-sis patients and construct prediction models along with a risk scoring table using machine learning algorithms,providing references for early prevention and management.Methods Clinical data from 420 spinal tuberculo-sis patients treated at four tertiary hospitals in Guizhou Province between January 2017 and February 2024 were retrospectively analyzed.Risk factors were identified through univariate and multivariate analyses.Logis-tic regression,random forest,and support vector machine prediction models were constructed.Model perform-ance was evaluated using receiver operating characteristic(ROC)curves,precision,recall,accuracy,and F1-score.A risk prediction scoring table for poor postoperative wound healing was subsequently developed.Re-sults Among the 420 patients with spinal tuberculosis,132 experienced poor postoperative wound healing,with an incidence rate of 31.43%.Logistic regression analysis showed that BMI≤18.5 kg/m2,preoperative albumin≤30 g/L,combined surgical procedure,intraoperative blood loss>1 000 mL,direct bilirubin>8 μmol/L within 3 days after surgery,neutrophil count≤75×109/L within 3 days after surgery,and postopera-tive drainage volume>500 mL were risk factors for poor postoperative wound healing(P<0.05).In the comparison among the three risk prediction models constructed based on machine learning algorithms,the ran-dom forest model demonstrated the best predictive performance.A risk prediction scoring table was construc-ted based on the partial regression coefficients from the multivariate analysis,with a total score range from 0 to 11 points.A score>6 points indicated an increased risk of poor postoperative wound healing.The area un-der the ROC curve(AUC)for this risk prediction scoring table was 0.846(95%CI:0.769 to 0.923),indica-ting good predictive performance.Conclusion The random forest model based on machine learning algorithms and the risk prediction scoring table have certain predictive value for assessing the risk of poor postoperative wound healing in patients with spinal tuberculosis;they can assist healthcare professionals in early identifica-tion of high-risk patients.

Objective To investigate the effects and underlying mechanisms of down-regulating m6A demethylase fat mass and obesity-associated protein(FTO)on proplatelet formation in the MEG-01 megakaryocytic cells.Methods ①MEG-01 cells were treated with 1 nmol/L phorbol myristate acetate(PMA)(treatment group)or DMSO(control group)for 72 h.FTO expression was measured by Western blotting and RT-qPCR.② MEG-01 cells were infected with targeted FTO shRNA(knockdown group,sh-FTO)or negative control shRNA(negative control group,sh-NC)viruses.FTO knockdown group and negative control group MEG-1 cells were treated with 1 nmol/L PMA for 72 h,and the protein and mRNA expression levels of FTO were detected by Western blotting and RT-qPCR.Cell cycle,viability and apoptosis were assessed by propidium iodide(PI)DNA staining,CCK-8 assay and Annexin V-FITC/PI double staining and TUNEL staining.The expression of cleaved Caspase-3 protein was determine by Western blotting.Megakaryocyte maturation was assessed by CD41/CD61 staining.Proplatelet formation was observed under bright field and detected by CD61 immunofluorescence assay.The expression of apoptosis-related molecules(Caspase3,BAD,BAK1,BCL2 and MCL1)was detected by RT-qPCR,and the protein change of BCL2 was further verified by Western blotting.The dataset was screened out from the gene expression omnibus(GEO)database,and then analyzed with University of California,Santa Cruz(UCSC)genome browser to compare the methylation sequencing peaks on BCL2 mRNA,and m6A methylated RNA immunoprecipitation(m6A-RIP)was used to assess the m6A methylation levels of BCL2 target gene mRNAs in MEG-01 megakaryocytes.Then,the changes in the m6A methylation enrichment level of BCL2 mRNA were observed between the sh-NC group and the sh-FTO group.mRNA stability and ribosome profiling assays were performed to assess translational efficiency of target genes.Results ①PMA treatment upregulated the expression of FTO at protein(P＜0.05)and mRNA(P＜0.01)levels.② FTO shRNA resulted in reduced FTO expression at both mRNA and protein levels(P＜0.01).Compared to the negative control group,the FTO knockdown group showed more cells arrested at the G1/S phase[(60.80±1.29)%vs(72.13±1.18)%,P＜0.01],significantly reduced cell viability[(1.17±0.03)%vs(0.69±0.05)%,P＜0.01],increased Annexin V-FITC/PI positive cells[(12.87±0.83)%vs(17.45±1.58)%,P＜0.01],more TUNEL positive cells[(1.03±0.27)%vs(17.49±9.91)%,P＜0.01],enhanced protein level of cleaved Caspase-3(P＜0.01),decreased proportion of CD41/CD61 positive cells[(51.63±1.13)%vs(34.08±0.53)%,P＜0.01],and less proplatelet formation in MEG-01 megakaryocytes[(26.49±6.73)%vs(13.31±5.97)%,P＜0.01].③Compared to sh-NC group,the FTO knockdown group had significantly decreased protein and mRNA expression of anti-apoptotic molecule BCL2(P＜0.01).UCSC GEO sequencing data revealed there were m6A methylation modification sites on BCL2 mRNA,which was verified through m6A-RIP experiment in MEG-01 megakaryocytes.Compared with GAPDH mRNA,BCL2 mRNA exhibited a significantly enriched m6A signal(P＜0.01).Compared to sh-NC group,a significant increase in m6A methylation modification was observed on BCL2 mRNA.BCL2 mRNA stability was significantly decreased,and its translation efficiency significantly was decreased(P＜0.01).Conclusion m6 A demethylase FTO rgulates BCL2 mRNA stability and translation efficiency,thereby promoting proplatelet formation in MEG-01 megakaryocytes.