This paper introduces a real-world cohort research model for community-acquired pneumonia （CAP） based on the Jiangsu Traditional Chinese Medicine （TCM） Dominant Diseases Diagnosis and Treatment Data Platform. Firstly， data cleaning is performed by standardizing diagnosis， symptoms， treatment and imaging， intelligently extracting unstructured information， and cleaning and constructing a standardized database. Secondly， for cohort establishment， CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly， in terms of protocol design， the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria， estimate sample size， define interventions， outcomes and economic evaluations， providing a reference for real-world TCM research on CAP.

This paper introduces a real-world cohort research model for community-acquired pneumonia （CAP） based on the Jiangsu Traditional Chinese Medicine （TCM） Dominant Diseases Diagnosis and Treatment Data Platform. Firstly， data cleaning is performed by standardizing diagnosis， symptoms， treatment and imaging， intelligently extracting unstructured information， and cleaning and constructing a standardized database. Secondly， for cohort establishment， CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly， in terms of protocol design， the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria， estimate sample size， define interventions， outcomes and economic evaluations， providing a reference for real-world TCM research on CAP.

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.

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 As climate change intensifies and extreme temperature events become more frequent, non-optimal temperature has emerged as a significant contributor to the global disease burden, representing a pressing public health challenge. Objective To analyze the disease burden, temporal trends, and health inequalities attributable to non-optimal, high, and low temperatures in China from 1990 to 2021, and to compare these findings with global levels to provide a scientific basis for targeted prevention strategies. Methods Using data from the Global Burden of Disease 2021 (GBD 2021), we extracted mortality rates and disability-adjusted life year (DALY) rates, and other indicators attributable to non-optimal, high, and low temperatures by sex, age, region, and cause. Joinpoint regression was applied to examine temporal trends. Decomposition analysis identified driving factors of change, while the slope index of inequality (SII) and concentration index (CI) quantified disparities across socio-demographic index (SDI) levels. Results From 1990 to 2021, the age-standardized mortality rates (ASMR) and age-standardized DALY rates (ASDR) attributable to non-optimal temperature in China exhibited a downward trend, decreasing from 66.48 (95%UI: 58.09, 76.56) to 32.70 (95%UI: 27.26, 39.26) per 100000 population, and from 1219.59 (95%UI: 1056.28, 1418.37) to 493.22 (95%UI: 403.88, 609.32) per 100000 population, respectively. Burdens attributable to non-optimal temperature and low temperature were higher than the global average, whereas the high temperature burden was lower. Males consistently experienced higher ASMR and ASDR attributable to non-optimal temperature than females. Cardiovascular diseases, chronic respiratory diseases, and respiratory infections and tuberculosis were the top three causes of non-optimal temperature-attributable burdens. Decomposition analysis revealed that population aging and growth were the primary drivers of increased burden, while epidemiological changes primarily drove the decline. Health inequalities were most predominant between extreme SDI regions but narrowed over time. Conclusion Despite the overall decline in burden attributable to non-optimal temperature in China, significant challenges remain, including high risks from cold exposure, gender disparities, and the compounding effects of an aging population with cardiovascular or respiratory diseases. Policy makers should prioritize climate change adaptation, focusing on elderly health and regional equity while strengthening the public health workforce.

Background As climate change intensifies and extreme temperature events become more frequent, non-optimal temperature has emerged as a significant contributor to the global disease burden, representing a pressing public health challenge. Objective To analyze the disease burden, temporal trends, and health inequalities attributable to non-optimal, high, and low temperatures in China from 1990 to 2021, and to compare these findings with global levels to provide a scientific basis for targeted prevention strategies. Methods Using data from the Global Burden of Disease 2021 (GBD 2021), we extracted mortality rates and disability-adjusted life year (DALY) rates, and other indicators attributable to non-optimal, high, and low temperatures by sex, age, region, and cause. Joinpoint regression was applied to examine temporal trends. Decomposition analysis identified driving factors of change, while the slope index of inequality (SII) and concentration index (CI) quantified disparities across socio-demographic index (SDI) levels. Results From 1990 to 2021, the age-standardized mortality rates (ASMR) and age-standardized DALY rates (ASDR) attributable to non-optimal temperature in China exhibited a downward trend, decreasing from 66.48 (95%UI: 58.09, 76.56) to 32.70 (95%UI: 27.26, 39.26) per 100000 population, and from 1219.59 (95%UI: 1056.28, 1418.37) to 493.22 (95%UI: 403.88, 609.32) per 100000 population, respectively. Burdens attributable to non-optimal temperature and low temperature were higher than the global average, whereas the high temperature burden was lower. Males consistently experienced higher ASMR and ASDR attributable to non-optimal temperature than females. Cardiovascular diseases, chronic respiratory diseases, and respiratory infections and tuberculosis were the top three causes of non-optimal temperature-attributable burdens. Decomposition analysis revealed that population aging and growth were the primary drivers of increased burden, while epidemiological changes primarily drove the decline. Health inequalities were most predominant between extreme SDI regions but narrowed over time. Conclusion Despite the overall decline in burden attributable to non-optimal temperature in China, significant challenges remain, including high risks from cold exposure, gender disparities, and the compounding effects of an aging population with cardiovascular or respiratory diseases. Policy makers should prioritize climate change adaptation, focusing on elderly health and regional equity while strengthening the public health workforce.

Aim To explore the mechanism of Jiawei Shaofu Zhuyu decoction in antagonizing endometriosis fibrosis by regulating mitophagy.Methods After the animal model was constructed,the syndrome was evalu-ated by general condition,organ water content and ther-mal imaging.The curative effect was evaluated by the weight of ectopic focus and the degree of adhesion.The pathological changes were compared using HE stai-ning,transmission electron microscopy,Masson and Sir-ius red staining.The expression of PINK1 and Parkin was detected by immunohistochemistry.The expression of mRNA and protein was determined by qPCR and Western blot,and the level of serum ROS was detected by ELISA.Results The autonomic activity of model mice was weakened,the water content of organs rose,and the temperature of limbs and lower abdomen was reduced by thermal imaging.HE staining showed obvi-ous hyperplasia of ectopic epithelium and glands.Transmission electron microscopy showed mitochondrial and endoplasmic reticulum structure damage,and nor-mal autophagy structure disappeared.Masson and Siri-us red staining showed increased collagen deposition;immunohistochemistry showed decreased expression of PINK1 and Parkin in ectopic foci.qPCR and Western blot showed that the expression of PINK1,Parkin,Bec-lin1,LC3 mRNA and protein in ectopic foci of model mice decreased,the expression of p62 mRNA and pro-tein increased,and serum ROS increased.The syn-drome performance of model mice was improved after the intervention of Jiawei Shaofu Zhuyu decoction;the inflammatory infiltration of ectopic foci was relieved,the morphology of mitochondria and endoplasmic retic-ulum was restored,and normal autophagy structure ap-peared.The degree of collagen deposition and fibrosis was reduced;the mRNA and protein expression of PINK1,Parkin,Beclin1 and LC3 increased.The ex-pression of p62 mRNA and protein decreased,and the level of ROS decreased.Conclusions Jiawei Shaofu Zhuyu decoction can improve the fibrosis of ectopic le-sions in mice with endometriosis of cold-dampness sta-sis syndrome,which may be related to the regulation of mitophagy.

Endometriosis(EMs)is a common estrogen-depend-ent clinical disease with the pathological characteristics of malig-nant tumors,which has great impact on women's physical and mental health.In recent years,experimental exploration has re-vealed that ectopic foci are in a hypoxic environment outside the uterine cavity,and mitochondria,as the"functional factories"of the cells,play an important role in the process of planting and in-vasion,and the mitochondrial quality control system,which in-cludes mitochondrial oxidative stress,kinetics,autophagy,bio-genesis and calcium homeostasis,is a key mechanism for the e-quilibrium of the mitochondrial function.The mitochondrial quality control system,including mitochondrial oxidative stress kinetics,autophagy,biogenesis and calcium homeostasis,is a key mechanism for mitochondrial functional balance.Therefore,to clarify the role of the mitochondrial quality control system in the development of EMs with the help of rational and rigorous experi-mental and clinical studies can not only help to clarify the patho-genesis of the disease,but also explore the key targets in the prevention and treatment of the disease.Therefore,this article summarizes the research progress of mitochondrial quality control system in endometriosis,with a view to providing reference and theoretical basis for the etiology,pathogenesis and prevention strategies of EMs.

Objective:To compare the impact of different treatment strategies on the survival outcomes in rectal cancer patients with poor response to neoadjuvant therapy, and to explore the survival-related influencing factors.Methods:A retrospective cohort study was conducted. Between January 2018 and November 2022, the clinical, pathological, and follow-up data of 106 rectal cancer patients who received neoadjuvant therapy and were evaluated as grade 4 or 5 based on the Magnetic Resonance Tumor Regression Grade (mrTRG) from the rectal cancer database at Peking Union Medical College Hospital were retrospectively collected. Based on the post-neoadjuvant therapy assessment, patients were classified into three groups: the chemotherapy-radiotherapy group (23 patients), the consolidation therapy group (18 patients), and the standard treatment group (65 patients). General condition, pathological findings, selection of neoadjuvant therapy, comorbidities, as well as 3-year expected DMFS and OS were observed in the three groups.Results:All 106 patients were followed up, with a median follow-up time of 28 (21, 38) months. The overall 3-year DMFS rate was 60%, and the 3-year OS rate was 74%. The 3-year DMFS in the standard treatment and consolidation therapy groups were 74% and 72%, respectively; the 3-year OS were 84%, 81%, respectively. The Log-rank test showed that there was no significant difference in the 3-year expected DMFS and OS between the standard treatment group and the consolidation therapy group (both P>0.05), but both groups had better survival outcomes than the chemotherapy-radiotherapy group (10% and 39%, respectively; all P<0.001). Multivariate Cox regression analysis indicated that the chemotherapy-radiotherapy only regimen was an independent risk factor for DMFS (HR=12.425, 95% CI: 4.436–34.594, P<0.001), and the independent risk factors for OS were chemotherapy-radiotherapy only regimen (HR=8.991, 95%CI:2.220–36.403, P=0.002) and age≥65 years (HR=3.495, 95%CI: 1.017–12.009, P=0.047). Stratified analysis showed that chemotherapy-radiotherapy only regimen was the independent risk factors for DMFS and OS in patients with extramural vascular invasion (EMVI) positive ( n=66) and mesorectal fascial invasion (MRF) positive (n=56) (all P<0.05). Whether consolidation therapy was added to the standard neoadjuvant treatment regimen was not an independent factor affecting 3-year expected DMFS or OS in rectal cancer patients with poor response to neoadjuvant therapy. Further comparisons between the standard neoadjuvant treatment and consolidation therapy groups showed no statistically significant differences in spincter-preservation rate or postoperative complication rates (both P>0.05). However, the consolidation therapy group had a longer interval between the end of radiotherapy and surgery [80.1 (50.8, 109.4) days vs. 61.8 (48.8, 74.8) days, P<0.001], and a higher incidence of chemotherapy-related adverse effects ([10/18] vs. 26.2% [17/65], P=0.018). Conclusion:In rectal cancer patients with poor response to neoadjuvant therapy and clear adverse prognostic features before surgery (locally advanced stage, MRF positive or EMVI positive), the addition of short- or long-course chemotherapy-based systemic therapy does not provide short- or long-term survival benefits. Moreover, an extended chemotherapy duration increases the incidence of chemotherapy-related adverse effects.

Objective:To analyze the types and characteristics of post-operative complications in colorectal cancer patients aged over 85 years undergoing laparoscopic surgery, and to summarize peri-operative management strategies.Methods:This was an observational study. Inclusion criteria: pathologically confirmed adenocarcinoma; tumor located in ileocecum, ascending colon, transverse colon, descending colon, sigmoid colon, or rectum; undergoing laparoscopic radical resection for colorectal cancer; complete clinical data. Exclusion criteria included distant metastasis, synchronous resection of multiple primary cancers, simultaneous liver metastasis surgery, and follow-up duration <1 month. A retrospective analysis was conducted on 191 patients of colorectal cancer patients aged over 85 years who underwent laparoscopic radical surgery in the General Surgery Department at Peking Union Medical College Hospital from January 2019 to January 2024. Among 191 patients, 107 patients (56.0%) had colon cancer and 84 (44.0%) rectal cancer. All patients received "home-based prehabilitation" and post-operative "enhanced recovery after surgery" protocols. Patient characteristics, peri-operative complication types, treatments, and outcomes were analyzed.Results:Post-operative complications occurred in 97 patients (50.8%), including 53 colon cancer patients (54.6%) and 44 rectal cancer patients (45.4%). Comorbidities existed in 88 patients (90.7%), with 93 patients (95.9%) classified as ASA II-III pre-operatively and 86 (88.7%) having nutritional risks. Surgical procedures included Dixon procedure (38 patients, 39.2%), right hemicolectomy (33 patients, 34.0%), sigmoidectomy (10 patients, 10.3%), and 17 patients (17.5%) received prophylactic stomas. Complication types comprised non-anastomotic infections (38 patients, 19.9%), intestinal flora disorder (26 patients, 13.6%), anastomotic/wound/stoma-related complications (16 patients, 8.4%), thrombotic/hemorrhagic events (6 patients, 3.1%), and others (11 patients, 5.8%). By Clavien-Dindo classification: Grade I (12 patients, 6.3%), Grade II (69 patients, 36.1%), Grade III (12 patients, 6.3%), and Grade IV (4 patients, 2.1%). Except for 5 patients (2.6%) requiring unplanned re-operation, all complications resolved with conservative treatment. The median duration of post-operative hospitalization was 9.5 days (7–13).Conclusion:Non-anastomotic infections and intestinal flora disorder constitute predominant complications after laparoscopic surgery in colorectal cancer patients aged over 85 years, mostly manageable with conservative treatment. Strengthened peri-operative management incorporating pre-operative prehabilitation and post-operative enhanced recovery after surgery protocols is crucial for patients aged over 85 years.