1.Brain Aperiodic Dynamics
Zhi-Cai HU ; Zhen ZHANG ; Jiang WANG ; Gui-Ping LI ; Shan LIU ; Hai-Tao YU
Progress in Biochemistry and Biophysics 2025;52(1):99-118
Brain’s neural activities encompass both periodic rhythmic oscillations and aperiodic neural fluctuations. Rhythmic oscillations manifest as spectral peaks of neural signals, directly reflecting the synchronized activities of neural populations and closely tied to cognitive and behavioral states. In contrast, aperiodic fluctuations exhibit a power-law decaying spectral trend, revealing the multiscale dynamics of brain neural activity. In recent years, researchers have made notable progress in studying brain aperiodic dynamics. These studies demonstrate that aperiodic activity holds significant physiological relevance, correlating with various physiological states such as external stimuli, drug induction, sleep states, and aging. Aperiodic activity serves as a reflection of the brain’s sensory capacity, consciousness level, and cognitive ability. In clinical research, the aperiodic exponent has emerged as a significant potential biomarker, capable of reflecting the progression and trends of brain diseases while being intricately intertwined with the excitation-inhibition balance of neural system. The physiological mechanisms underlying aperiodic dynamics span multiple neural scales, with activities at the levels of individual neurons, neuronal ensembles, and neural networks collectively influencing the frequency, oscillatory patterns, and spatiotemporal characteristics of aperiodic signals. Aperiodic dynamics currently boasts broad application prospects. It not only provides a novel perspective for investigating brain neural dynamics but also holds immense potential as a neural marker in neuromodulation or brain-computer interface technologies. This paper summarizes methods for extracting characteristic parameters of aperiodic activity, analyzes its physiological relevance and potential as a biomarker in brain diseases, summarizes its physiological mechanisms, and based on these findings, elaborates on the research prospects of aperiodic dynamics.
2.Enzyme-directed Immobilization Strategies for Biosensor Applications
Xing-Bao WANG ; Yao-Hong MA ; Yun-Long XUE ; Xiao-Zhen HUANG ; Yue SHAO ; Yi YU ; Bing-Lian WANG ; Qing-Ai LIU ; Li-He ZHANG ; Wei-Li GONG
Progress in Biochemistry and Biophysics 2025;52(2):374-394
Immobilized enzyme-based enzyme electrode biosensors, characterized by high sensitivity and efficiency, strong specificity, and compact size, demonstrate broad application prospects in life science research, disease diagnosis and monitoring, etc. Immobilization of enzyme is a critical step in determining the performance (stability, sensitivity, and reproducibility) of the biosensors. Random immobilization (physical adsorption, covalent cross-linking, etc.) can easily bring about problems, such as decreased enzyme activity and relatively unstable immobilization. Whereas, directional immobilization utilizing amino acid residue mutation, affinity peptide fusion, or nucleotide-specific binding to restrict the orientation of the enzymes provides new possibilities to solve the problems caused by random immobilization. In this paper, the principles, advantages and disadvantages and the application progress of enzyme electrode biosensors of different directional immobilization strategies for enzyme molecular sensing elements by specific amino acids (lysine, histidine, cysteine, unnatural amino acid) with functional groups introduced based on site-specific mutation, affinity peptides (gold binding peptides, carbon binding peptides, carbohydrate binding domains) fused through genetic engineering, and specific binding between nucleotides and target enzymes (proteins) were reviewed, and the application fields, advantages and limitations of various immobilized enzyme interface characterization techniques were discussed, hoping to provide theoretical and technical guidance for the creation of high-performance enzyme sensing elements and the manufacture of enzyme electrode sensors.
3.Constructing a model of degenerative scoliosis using finite element method:biomechanical analysis in etiology and treatment
Kai HE ; Wenhua XING ; Shengxiang LIU ; Xianming BAI ; Chen ZHOU ; Xu GAO ; Yu QIAO ; Qiang HE ; Zhiyu GAO ; Zhen GUO ; Aruhan BAO ; Chade LI
Chinese Journal of Tissue Engineering Research 2025;29(3):572-578
BACKGROUND:Degenerative scoliosis is defined as a condition that occurs in adulthood with a coronal cobb angle of the spine>10° accompanied by sagittal deformity and rotational subluxation,which often produces symptoms of spinal cord and nerve compression,such as lumbar pain,lower limb pain,numbness,weakness,and neurogenic claudication.The finite element method is a mechanical analysis technique for computer modelling,which can be used for spinal mechanics research by building digital models that can realistically restore the human spine model and design modifications. OBJECTIVE:To review the application of finite element method in the etiology and treatment of degenerative scoliosis. METHODS:The literature databases CNKI,PubMed,and Web of Science were searched for articles on the application of finite element method in degenerative scoliosis published before October 2023.Search terms were"finite element analysis,biomechanics,stress analysis,degenerative scoliosis,adult spinal deformity"in Chinese and English.Fifty-four papers were finally included. RESULTS AND CONCLUSION:(1)The biomechanical findings from the degenerative scoliosis model constructed using the finite element method were identical to those from the in vivo experimental studies,which proves that the finite element method has a high practical value in degenerative scoliosis.(2)The study of the etiology and treatment of degenerative scoliosis by the finite element method is conducive to the prevention of the occurrence of the scoliosis,slowing down the progress of the scoliosis,the development of a more appropriate treatment plan,the reduction of complications,and the promotion of the patients'surgical operation.(3)The finite element method has gradually evolved from a single bony structure to the inclusion of soft tissues such as muscle ligaments,and the small sample content is increasingly unable to meet the research needs.(4)The finite element method has much room for exploration in degenerative scoliosis.
4.Incidence rate and independent risk factors of synchronous multiple lesions in early gastric cancer
Yanqing ZHOU ; Yue YANG ; Yu XIAO ; Hongyong LI ; Zhen NI
Journal of Public Health and Preventive Medicine 2025;36(4):81-84
Objective To explore the incidence rate and independent risk factors of synchronous multiple early gastric cancer (SMEGC) in patients with early gastric cancer, and to provide evidence for early screening and intervention of high-risk population. Methods A retrospective analysis was performed on 308 patients with early gastric cancer who received treatment in the hospital from March 2019 to March 2024. The incidence rate of SMEGC was counted, and the risk factors were analyzed by univariate and multivariate Logistic regression analyses. Results Among the 308 patients with early gastric cancer in this study, 23 cases were SMEGC and 285 were single early gastric cancer, which were included in the SMEGC group and the single group respectively. The incidence rate of SMEGC was 7.47% (23/308). Compared with the single group, the proportions of male, smoking history, tumor diameter≤2 mm, chronic atrophic gastritis and intestinal metaplasia degree were higher in the SMEGC group (2=4.331、8.608、4.618、6.490、4.897,P=0.037、0.003、0.032、0.001、0.027). Logistic regression analysis suggested that chronic atrophic gastritis (OR=3.133, 95%CI: 1.240-7.918) and moderate-to-severe intestinal metaplasia (OR=3.171, 95%CI: 1.252-8.029) were independent risk factors for SMEGC (P<0.05). Conclusion Some patients with early gastric cancer are SMEGC. Chronic atrophic gastritis and moderate-to-severe intestinal metaplasia are independent risk factors affecting the occurrence of SMEGC. It is recommended to regularly screen high-risk patients and optimize management strategies to reduce the risk of SMEGC.
5.Analysis of T7 RNA Polymerase: From Structure-function Relationship to dsRNA Challenge and Biotechnological Applications
Wei-Chen NING ; Yu HUA ; Hui-Ling YOU ; Qiu-Shi LI ; Yao WU ; Yun-Long LIU ; Zhen-Xin HU
Progress in Biochemistry and Biophysics 2025;52(9):2280-2294
T7 RNA polymerase (T7 RNAP) is one of the simplest known RNA polymerases. Its unique structural features make it a critical model for studying the mechanisms of RNA synthesis. This review systematically examines the static crystal structure of T7 RNAP, beginning with an in-depth examination of its characteristic “thumb”, “palm”, and “finger” domains, which form the classic “right-hand-like” architecture. By detailing these structural elements, this review establishes a foundation for understanding the overall organization of T7 RNAP. This review systematically maps the functional roles of secondary structural elements and their subdomains in transcriptional catalysis, progressively elucidating the fundamental relationships between structure and function. Further, the intrinsic flexibility of T7 RNAP and its applications in research are also discussed. Additionally, the review presents the structural diagrams of the enzyme at different stages of the transcription process, and through these diagrams, it provides a detailed description of the complete transcription process of T7 RNAP. By integrating structural dynamics and kinetics analyses, the review constructs a comprehensive framework that bridges static structure to dynamic processes. Despite its advantages, T7 RNAP has a notable limitation: it generates double-stranded RNA (dsRNA) as a byproduct. The presence of dsRNA not only compromises the purity of mRNA products but also elicits nonspecific immune responses, which pose significant challenges for biotechnological and therapeutic applications. The review provides a detailed exploration of the mechanisms underlying dsRNA formation during T7 RNAP catalysis, reviews current strategies to mitigate this issue, and highlights recent progress in the field. A key focus is the semi-rational design of T7 RNAP mutants engineered to minimize dsRNA generation and enhance catalytic performance. Beyond its role in transcription, T7 RNAP exhibits rapid development and extensive application in fields, including gene editing, biosensing, and mRNA vaccines. This review systematically examines the structure-function relationships of T7 RNAP, elucidates the mechanisms of dsRNA formation, and discusses engineering strategies to optimize its performance. It further explores the engineering optimization and functional expansion of T7 RNAP. Furthermore, this review also addresses the pressing issues that currently need resolution, discusses the major challenges in the practical application of T7 RNAP, and provides an outlook on potential future research directions. In summary, this review provides a comprehensive analysis of T7 RNAP, ranging from its structural architecture to cutting-edge applications. We systematically examine: (1) the characteristic right-hand domains (thumb, palm, fingers) that define its minimalistic structure; (2) the structure-function relationships underlying transcriptional catalysis; and (3) the dynamic transitions during the complete transcription cycle. While highlighting T7 RNAP’s versatility in gene editing, biosensing, and mRNA vaccine production, we critically address its major limitation—dsRNA byproduct formation—and evaluate engineering solutions including semi-rationally designed mutants. By synthesizing current knowledge and identifying key challenges, this work aims to provide novel insights for the development and application of T7 RNAP and to foster further thought and progress in related fields.
6.Adolescent Smoking Addiction Diagnosis Based on TI-GNN
Xu-Wen WANG ; Da-Hua YU ; Ting XUE ; Xiao-Jiao LI ; Zhen-Zhen MAI ; Fang DONG ; Yu-Xin MA ; Juan WANG ; Kai YUAN
Progress in Biochemistry and Biophysics 2025;52(9):2393-2405
ObjectiveTobacco-related diseases remain one of the leading preventable public health challenges worldwide and are among the primary causes of premature death. In recent years, accumulating evidence has supported the classification of nicotine addiction as a chronic brain disease, profoundly affecting both brain structure and function. Despite the urgency, effective diagnostic methods for smoking addiction remain lacking, posing significant challenges for early intervention and treatment. To address this issue and gain deeper insights into the neural mechanisms underlying nicotine dependence, this study proposes a novel graph neural network framework, termed TI-GNN. This model leverages functional magnetic resonance imaging (fMRI) data to identify complex and subtle abnormalities in brain connectivity patterns associated with smoking addiction. MethodsThe study utilizes fMRI data to construct functional connectivity matrices that represent interaction patterns among brain regions. These matrices are interpreted as graphs, where brain regions are nodes and the strength of functional connectivity between them serves as edges. The proposed TI-GNN model integrates a Transformer module to effectively capture global interactions across the entire brain network, enabling a comprehensive understanding of high-level connectivity patterns. Additionally, a spatial attention mechanism is employed to selectively focus on informative inter-regional connections while filtering out irrelevant or noisy features. This design enhances the model’s ability to learn meaningful neural representations crucial for classification tasks. A key innovation of TI-GNN lies in its built-in causal interpretation module, which aims to infer directional and potentially causal relationships among brain regions. This not only improves predictive performance but also enhances model interpretability—an essential attribute for clinical applications. The identification of causal links provides valuable insights into the neuropathological basis of addiction and contributes to the development of biologically plausible and trustworthy diagnostic tools. ResultsExperimental results demonstrate that the TI-GNN model achieves superior classification performance on the smoking addiction dataset, outperforming several state-of-the-art baseline models. Specifically, TI-GNN attains an accuracy of 0.91, an F1-score of 0.91, and a Matthews correlation coefficient (MCC) of 0.83, indicating strong robustness and reliability. Beyond performance metrics, TI-GNN identifies critical abnormal connectivity patterns in several brain regions implicated in addiction. Notably, it highlights dysregulations in the amygdala and the anterior cingulate cortex, consistent with prior clinical and neuroimaging findings. These regions are well known for their roles in emotional regulation, reward processing, and impulse control—functions that are frequently disrupted in nicotine dependence. ConclusionThe TI-GNN framework offers a powerful and interpretable tool for the objective diagnosis of smoking addiction. By integrating advanced graph learning techniques with causal inference capabilities, the model not only achieves high diagnostic accuracy but also elucidates the neurobiological underpinnings of addiction. The identification of specific abnormal brain networks and their causal interactions deepens our understanding of addiction pathophysiology and lays the groundwork for developing targeted intervention strategies and personalized treatment approaches in the future.
7.Causal association between periodontitis and hepatobiliary diseases: genetic insights from Mendelian randomization
ZHAO Li ; CHEN Shaopeng ; CHEN Zhen ; CHEN Yueqi ; YU Ting
Journal of Prevention and Treatment for Stomatological Diseases 2025;33(10):873-883
Objective:
To investigate the reciprocal causal relationships between periodontitis and hepatobiliary diseases through Mendelian randomization (MR) analyses, to provide evidence for joint prevention and clinical decision-making in patients with concurrent periodontitis and hepatobiliary diseases.
Methods:
Single nucleotide polymorphisms (SNPs) were extracted from the largest genome-wide association study on periodontitis (17 353 cases, 28 210 controls) and hepatobiliary diseases within the European ancestry and used as instrumental variables (IVs). The strength of the associations was examined by calculating the F-statistic. The SNPs significantly associated with the outcome were removed by scanning on Phenoscanner platform. Bidirectional causal associations between periodontitis and hepatobiliary diseases were estimated using inverse variance weighted (IVW), MR-Egger, and Weighted Median methods. The robustness of the findings was further verified through additional sensitive MR approaches, including Cochran’s Q statistic (IVW), Rucker’s Q statistic (MR-Egger), MR-PRESSO and Leave-one-out analysis. Further MR analyses, utilizing other available genome-wide association studies (GWAS) on hepatobiliary diseases, were conducted to validate the results.
Results:
The IVW method found that periodontitis had a causal impact on acalculous cholecystitis (odds ratio = 1.277, 95% CI 1.097-1.485, P=0.002), implying an increased risk of acalculous cholecystitis associated with periodontitis, while the MR-Egger regression and Weighted Median failed to observe significant causal effects of periodontitis on acalculous cholecystitis. However, no bidirectional causal associations between periodontitis and nonalcoholic fatty liver disease, cirrhosis or liver cancer were observed using IVW, MR-Egger regression and Weighted Median. The bidirectional causal relationships were deemed unlikely to be influenced by horizontal pleiotropy. Further, the validation analysis based on alternative GWAS data suggested parallel results.
Conclusions
The MR analyses suggest that periodontitis may elevate the risk of acalculous cholecystitis. Further investigations, including clinical studies and mechanistic explorations, are warranted to validate these findings. However, the MR analyses do not support bidirectional causal associations between periodontitis and nonalcoholic fatty liver disease, cirrhosis or liver cancer.
8.Risk factors and epidemiological characteristics of hospital-acquired pneumonia in elderly diabetes mellitus
Huan YU ; Zhen NI ; Ling DUAN ; Hongyong LI
Journal of Public Health and Preventive Medicine 2025;36(5):159-162
Objective To understand the epidemiological characteristics and risk factors of hospital-acquired pneumonia in elderly diabetic patients. Methods Elderly patients with diabetes mellitus who were hospitalized in the hospital were selected from October 2020 to October 2023 as the research subjects. The epidemiological characteristics of hospital-acquired pneumonia were analyzed, and the risk factors affecting hospital-acquired pneumonia in elderly patients with diabetes mellitus were analyzed . Results There were 65 cases of hospital-acquired pneumonia in 388 elderly patients with diabetes mellitus, with an incidence of 16.75%, of which 56.92% were males and 43.08% were females. The proportion of patients aged≥80 years was higher than that of patients aged<80 years. There were no significant differences in gender, body mass index, education level, course of diabetes mellitus, smoking history, drinking history, hypertension, coronary heart disease and anemia between groups (P>0.05), but significant differences were shown in age, hospitalization time, tracheal invasive operation, types of antibacterial drug use and dysphagia between both groups (P<0.05). Logistic multivariate analysis showed that age≥80 years old, hospitalization time≥30 d, tracheal invasive operation, use of antibacterial drugs≥ 2 types, and dysphagia were independent risk factors for hospital-acquired pneumonia in elderly diabetic patients (P<0.05). Conclusion The risk of hospital-acquired pneumonia is high in elderly patients with diabetes mellitus. Patients with age≥80 years old, hospitalization time≥30 days, tracheal invasive operation, abuse of antibacterial drugs and dysphagia are high-risk population. It is necessary to take active intervention measures for such patients.
9.Risk factors and epidemiological characteristics of hospital-acquired pneumonia in elderly diabetes mellitus
Huan YU ; Zhen NI ; Ling DUAN ; Hongyong LI
Journal of Public Health and Preventive Medicine 2025;36(5):159-162
Objective To understand the epidemiological characteristics and risk factors of hospital-acquired pneumonia in elderly diabetic patients. Methods Elderly patients with diabetes mellitus who were hospitalized in the hospital were selected from October 2020 to October 2023 as the research subjects. The epidemiological characteristics of hospital-acquired pneumonia were analyzed, and the risk factors affecting hospital-acquired pneumonia in elderly patients with diabetes mellitus were analyzed . Results There were 65 cases of hospital-acquired pneumonia in 388 elderly patients with diabetes mellitus, with an incidence of 16.75%, of which 56.92% were males and 43.08% were females. The proportion of patients aged≥80 years was higher than that of patients aged<80 years. There were no significant differences in gender, body mass index, education level, course of diabetes mellitus, smoking history, drinking history, hypertension, coronary heart disease and anemia between groups (P>0.05), but significant differences were shown in age, hospitalization time, tracheal invasive operation, types of antibacterial drug use and dysphagia between both groups (P<0.05). Logistic multivariate analysis showed that age≥80 years old, hospitalization time≥30 d, tracheal invasive operation, use of antibacterial drugs≥ 2 types, and dysphagia were independent risk factors for hospital-acquired pneumonia in elderly diabetic patients (P<0.05). Conclusion The risk of hospital-acquired pneumonia is high in elderly patients with diabetes mellitus. Patients with age≥80 years old, hospitalization time≥30 days, tracheal invasive operation, abuse of antibacterial drugs and dysphagia are high-risk population. It is necessary to take active intervention measures for such patients.
10.Expert Consensus on Clinical Diseases Responding Specifically to Traditional Chinese Medicine: Pulmonary Nodules
Mingwei YU ; Huairui ZHANG ; Xinghan ZHANG ; Xiao LI ; Rengui WANG ; Zhiqiang LONG ; Zhen WANG ; Bo PANG ; Jianwei HUO ; Wei CHEN ; Yong ZHU ; Baoli LIU ; Yanni LOU ; Ganlin ZHANG ; Jiayun NIAN ; Mei MO ; Xiaoxiao ZHANG ; Guowang YANG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(6):238-245
In recent years, the incidence of pulmonary nodules has kept rising. To give full play to the advantages of traditional Chinese medicine (TCM) in the treatment of pulmonary nodules and identify the breakthrough points of integrating TCM with Western medicine, the China Association of Chinese Medicine organized medical experts in TCM and western medicine to carry out in-depth discussion regarding this disease. The discussion encompassed the modern medical advances, TCM theories of etiology and pathogenesis, the role and advantages of TCM in the whole course management of pulmonary nodules, contents and methods of research on pulmonary nodules, and science popularization work, aiming to provide a reference for clinical practice and scientific research. After discussion, the experts concluded that the occurrence of pulmonary nodules was rooted in the deficiency of the lung and spleen and triggered by phlegm dampness, blood stasis, and Qi stagnation. TCM can treat pulmonary nodules by controlling and reducing nodules, improving physical constitution, ameliorating multi-system nodular diseases, reducing anxiety and avoiding excessive diagnosis and treatment, and serving as an alternative for patients who are unwilling or unfit for surgical treatment. At present, the optimal diagnosis and treatment strategy for pulmonary nodules has not been formed, which needs to be further studied from multiple perspectives such as clinical epidemiology, biology, and evidence-based medicine. The primary task of current research is to find out the advantages, effective prescriptions, and target populations and determine the effective outcomes of TCM in the treatment of pulmonary nodules. At the same time, basic research should be carried out to explore the etiology and biological behaviors of pulmonary nodules. The expert consensus on the diagnosis and treatment of pulmonary nodules with integrated TCM and Western medicine needs to be continuously revised to guide clinicians to conduct standardized, scientific, and accurate effective diagnosis and treatment.


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