1.m6ATEpre: Predicting YTHDF1-mediated mRNA Translation Efficiency Regulated by m6A Sites via Multi-omics Data Integration
Teng ZHANG ; Ming ZHANG ; Shao-Wu ZHANG ; Lian LIU
Progress in Biochemistry and Biophysics 2026;53(4):1087-1102
ObjectiveThe most prevalent mRNA modification, N6-methyladenosine (m6A) plays an important role in various RNA metabolism, including gene expression and translation. By recruiting different “reader” proteins and their cofactors, m6A modification can affect messenger RNA (mRNA) degradation, splicing, nuclear export and translation. However, the selective mechanism by which m6A sites regulate mRNA translation through m6A reader YTHDF1 binding remains poorly understood, due to a lack of computational methods for identifying context-specific m6A sites that regulate translation. To address this, we developed a novel computational framework named m6ATEpre, the first tool designed to predict cell-specific m6A sites that regulate translation efficiency. Methodsm6ATEpre integrates multi-omics data, introduces a novel feature representation strategy for m6A site sequences, and employs an autoencoder to effectively capture embedded feature representations. Specifically, m6ATEpre first integrated MeRIP-seq data and PAR-CLIP data through overlapping m6A sites with YTHDF1 binding sites and identified YTHDF1-mediated m6A sites. Then, m6ATEpre detected the translation gene by analyzing the Ribo-seq data under YTHDF1 knockdown vs control condition. Genes whose translation is mediated by YTHDF1 in an m6A-dependent manner were identified by a significant decrease in translation efficiency upon YTHDF1 knockdown. Next, we proposed a binary vector indicating the presence or absence of YTHDF1 binding motifs to characterize each m6A site sequence. This represents a novel feature representation strategy for m6A sites. m6ATEpre utilized the autoencoder to extract the potentially important feature representations and constructed a multilayer perceptron neural networks model to predict potential m6A sites that regulating translation efficiency. ResultsA comprehensive evaluation of m6ATEpre was conducted through a series of experiments. We compared its performance against that of a similar prediction task model, as well as other classifiers. The results indicate that m6ATEpre achieved the best prediction performance. In addition, we analyzed different feature representation strategies and performed ablation experiments to validate the rationality of the model design. The results demonstrate that our proposed feature representation strategy has a greater advantage in improving prediction performance. In the HeLa cell line, bioinformatic analysis of the metagene distribution and sequence minimum free energy of m6A sites regulating translation efficiency (m6A-reg-TE sites) revealed their specific properties in translation regulation. Functional enrichment analysis indicated that m6A-reg-TE genes are associated with specific biological processes and KEGG pathways. By integrating the binding sites of YTHDF1 co-factors with m6A-reg-TE sites, we revealed that YTHDF1-mediated and m6A-dependent translation efficiency regulation requires the cooperation of multiple translation-regulatory RNA-binding proteins among its co-factors in the HeLa cell line. Furthermore, we extended our predictions to the dataset of the HEK293T cell line. Similarly, bioinformatic analysis of the metagene distribution and functional enrichment revealed the cell-specific characteristic of these predicted m6A-reg-TE sites in HEK293T cells. Likewise, integrated analysis of multiple YTHDF1 co-factors and m6A-reg-TE sites predicted in the HEK293T cell line reveals their m6A-dependent cooperation in regulating translation efficiency. Conclusionm6ATEpre is a timely tool that will advance our understanding of the mechanisms of m6A regulation in translation efficiency. The source code and datasets used in this work can be downloaded from
2.Construction of core outcome set for clinical research on traditional Chinese medicine treatment of simple obesity.
Tong-Tong WU ; Yan YU ; Qian HUANG ; Xue-Yin CHEN ; Fu-Ming-Xiang LIU ; Li-Hong YANG ; Chang-Cai XIE ; Shao-Nan LIU ; Yu CHEN ; Xin-Feng GUO
China Journal of Chinese Materia Medica 2025;50(12):3423-3430
Following the core outcome set standards for development(COS-STAD), this study aims to construct core outcome set(COS) for clinical research on traditional Chinese medicine(TCM) treatment of simple obesity. Firstly, a comprehensive review was conducted on the randomized controlled trial(RCT) and systematic review(SR) about TCM treatment of simple obesity that were published in Chinese and English databases to collect reported outcomes. Additional outcomes were obtained through semi-structured interviews with patients and open-ended questionnaire surveys for clinicians. All the collected outcomes were then merged and organized as an initial outcome pool, and then a preliminary list of outcomes was formed after discussion by the working group. Subsequently, two rounds of Delphi surveys were conducted with clinicians, methodology experts, and patients to score the importance of outcomes in the list. Finally, a consensus meeting was held to establish the COS for clinical research on TCM treatment of simple obesity. A total of 221 RCTs and 12 SRs were included, and after integration of supplementary outcomes, an initial outcome pool of 141 outcomes were formed. Following discussions in the steering advisory group meeting, a preliminary list of 33 outcomes was finalized, encompassing 9 domains. Through two rounds of Delphi surveys and a consensus meeting, the final COS for clinical research on TCM treatment of simple obesity was determined to include 8 outcomes: TCM symptom scores, body mass index(BMI), waist-hip ratio, waist circumference, visceral fat index, body fat rate, quality of life, and safety, which were classified into 4 domains: TCM-related outcomes, anthropometric measurements, quality of life, and safety. This study has preliminarily established a COS for clinical research on TCM treatment of simple obesity. It helps reduce the heterogeneity in the selection and reporting of outcomes in similar clinical studies, thereby improving the comparability of research results and the feasibility of meta-analysis and providing higher-level evidence support for clinical practice.
Humans
;
Obesity/therapy*
;
Medicine, Chinese Traditional
;
Randomized Controlled Trials as Topic
;
Treatment Outcome
;
Drugs, Chinese Herbal/therapeutic use*
3.Establishment of a nomogram for early risk prediction of severe trauma in primary medical institutions: A multi-center study.
Wang BO ; Ming-Rui ZHANG ; Gui-Yan MA ; Zhan-Fu YANG ; Rui-Ning LU ; Xu-Sheng ZHANG ; Shao-Guang LIU
Chinese Journal of Traumatology 2025;28(6):418-426
PURPOSE:
To analyze risk factors for severe trauma and establish a nomogram for early risk prediction, to improve the early identification of severe trauma.
METHODS:
This study was conducted on the patients treated in 81 trauma treatment institutions in Gansu province from 2020 to 2022. Patients were grouped by year, with 5364 patients from 2020 to 2021 as the training set and 1094 newly admitted patients in 2020 as the external validation set. Based on the injury severity score (ISS), patients in the training set were classified into 2 subgroups of the severe trauma group (n = 478, ISS scores ≥25) and the non-severe trauma group (n = 4886, ISS scores <25). Univariate and binary logistic regression analyses were employed to identify independent risk factors for severe trauma. Subsequently, a predictive model was developed using the R software environment. Furthermore, the model was subjected to internal and external validation via the Hosmer-Lemeshow test and receiver operating characteristic curve analysis.
RESULTS:
In total, 6458 trauma patients were included in this study. Initially, this study identified several independent risk factors for severe trauma, including multiple traumatic injuries (polytrauma), external hemorrhage, elevated shock index, elevated respiratory rate, decreased peripheral oxygen saturation, and decreased Glasgow coma scale score (all p < 0.05). For internal validation, the area under the receiver operating characteristic curve was 0.914, with the sensitivity and specificity of 88.4% and 87.6%, respectively; while for external validation, the area under the receiver operating characteristic curve was 0.936, with the sensitivity and specificity of 84.6% and 93.7%, respectively. In addition, a good model fitting was observed through the Hosmer-Lemeshow test and calibration curve analysis (p > 0.05).
CONCLUSION
This study establishes a nomogram for early risk prediction of severe trauma, which is suitable for primary healthcare institutions in underdeveloped western China. It facilitates early triage and quantitative assessment of trauma severity by clinicians prior to clinical interventions.
Humans
;
Nomograms
;
Male
;
Female
;
Wounds and Injuries/diagnosis*
;
Risk Factors
;
Middle Aged
;
Adult
;
Injury Severity Score
;
Risk Assessment
;
ROC Curve
;
Aged
;
Logistic Models
;
China
;
Glasgow Coma Scale
4.Explanation and interpretation of blood transfusion provisions for children with hematological diseases in the national health standard "Guideline for pediatric transfusion".
Ming-Yi ZHAO ; Rong HUANG ; Rong GUI ; Qing-Nan HE ; Ming-Yan HEI ; Xiao-Fan ZHU ; Jun LU ; Xiao-Jun XU ; Tian-Ming YUAN ; Rong ZHANG ; Xu WANG ; Jin-Ping LIU ; Jing WANG ; Zhi-Li SHAO ; Yong-Jian GUO ; Xin-Yin WU ; Jia-Rui CHEN ; Qi-Rong CHEN ; Jia GUO ; Ming-Hua YANG
Chinese Journal of Contemporary Pediatrics 2025;27(1):18-25
To guide clinical blood transfusion practices for pediatric patients, the National Health Commission has issued the health standard "Guideline for pediatric transfusion" (WS/T 795-2022). Blood transfusion is one of the most commonly used supportive treatments for children with hematological diseases. This guideline provides guidance and recommendations for blood transfusions in children with aplastic anemia, thalassemia, autoimmune hemolytic anemia, glucose-6-phosphate dehydrogenase deficiency, acute leukemia, myelodysplastic syndromes, immune thrombocytopenic purpura, and thrombotic thrombocytopenic purpura. This article presents the evidence and interpretation of the blood transfusion provisions for children with hematological diseases in the "Guideline for pediatric transfusion", aiming to assist in the understanding and implementing the blood transfusion section of this guideline.
Humans
;
Child
;
Hematologic Diseases/therapy*
;
Blood Transfusion/standards*
;
Practice Guidelines as Topic
5.Explanation and interpretation of the compilation of blood transfusion provisions for children undergoing hematopoietic stem cell transplantation in the national health standard "Guideline for pediatric transfusion".
Rong HUANG ; Qing-Nan HE ; Ming-Yan HEI ; Xiao-Fan ZHU ; Jun LU ; Xiao-Jun XU ; Tian-Ming YUAN ; Rong ZHANG ; Xu WANG ; Jin-Ping LIU ; Jing WANG ; Zhi-Li SHAO ; Ming-Yi ZHAO ; Yong-Jian GUO ; Xin-Yin WU ; Jia-Rui CHEN ; Qi-Rong CHEN ; Jia GUO ; Rong GUI ; Ming-Hua YANG
Chinese Journal of Contemporary Pediatrics 2025;27(2):139-143
To guide clinical blood transfusion practices for pediatric patients, the National Health Commission has issued the health standard "Guideline for pediatric transfusion" (WS/T 795-2022). Blood transfusion for children undergoing hematopoietic stem cell transplantation is highly complex and challenging. This guideline provides recommendations on transfusion thresholds and the selection of blood components for these children. This article presents the evidence and interpretation of the transfusion provisions for children undergoing hematopoietic stem cell transplantation, with the aim of enhancing the understanding and implementation of the "Guideline for pediatric transfusion".
Humans
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Hematopoietic Stem Cell Transplantation
;
Child
;
Blood Transfusion/standards*
;
Practice Guidelines as Topic
6.Explanation and interpretation of blood transfusion provisions for critically ill and severely bleeding pediatric patients in the national health standard "Guideline for pediatric transfusion".
Rong HUANG ; Qing-Nan HE ; Ming-Yan HEI ; Ming-Hua YANG ; Xiao-Fan ZHU ; Jun LU ; Xiao-Jun XU ; Tian-Ming YUAN ; Rong ZHANG ; Xu WANG ; Jin-Ping LIU ; Jing WANG ; Zhi-Li SHAO ; Ming-Yi ZHAO ; Yong-Jian GUO ; Xin-Yin WU ; Jia-Rui CHEN ; Qi-Rong CHEN ; Jia GUO ; Rong GUI
Chinese Journal of Contemporary Pediatrics 2025;27(4):395-403
To guide clinical blood transfusion practices for pediatric patients, the National Health Commission has issued the health standard "Guideline for pediatric transfusion" (WS/T 795-2022). Critically ill children often present with anemia and have a higher demand for transfusions compared to other pediatric patients. This guideline provides guidance and recommendations for blood transfusions in cases of general critical illness, septic shock, acute brain injury, extracorporeal membrane oxygenation, non-life-threatening bleeding, and hemorrhagic shock. This article interprets the background and evidence of the blood transfusion provisions for critically ill and severely bleeding children in the "Guideline for pediatric transfusion", aiming to enhance understanding and implementation of this aspect of the guidelines. Citation:Chinese Journal of Contemporary Pediatrics, 2025, 27(4): 395-403.
Humans
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Critical Illness
;
Blood Transfusion/standards*
;
Child
;
Hemorrhage/therapy*
;
Practice Guidelines as Topic
7.Explanation and interpretation of blood transfusion provisions for children undergoing cardiac surgery in the national health standard "Guideline for pediatric transfusion".
Rong HUANG ; Qing-Nan HE ; Ming-Yan HEI ; Ming-Hua YANG ; Xiao-Fan ZHU ; Jun LU ; Xiao-Jun XU ; Tian-Ming YUAN ; Rong ZHANG ; Xu WANG ; Jing WANG ; Zhi-Li SHAO ; Ming-Yi ZHAO ; Yong-Jian GUO ; Xin-Yin WU ; Jia-Rui CHEN ; Qi-Rong CHEN ; Jia GUO ; Rong GUI ; Jin-Ping LIU
Chinese Journal of Contemporary Pediatrics 2025;27(7):778-785
To guide clinical blood transfusion practices in pediatric patients, the National Health Commission has issued the health standard "Guideline for pediatric transfusion" (WS/T 795-2022). Children undergoing cardiac surgery are at high risk of bleeding, and the causes of perioperative anemia and coagulation disorders in neonates and children are complex and varied, often necessitating the transfusion of allogeneic blood components. This guideline provides direction and recommendations for specific measures in blood management for children undergoing cardiac surgery before, during, and after surgery. This article interprets the background and evidence for the formulation of the blood transfusion provisions for children undergoing cardiac surgery, hoping to facilitate the understanding and implementation of this guideline.
Humans
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Cardiac Surgical Procedures
;
Blood Transfusion/standards*
;
Child
;
Practice Guidelines as Topic
8.Efficacy and Safety of Yangxue Qingnao Pills Combined with Amlodipine in Treatment of Hypertensive Patients with Blood Deficiency and Gan-Yang Hyperactivity: A Multicenter, Randomized Controlled Trial.
Fan WANG ; Hai-Qing GAO ; Zhe LYU ; Xiao-Ming WANG ; Hui HAN ; Yong-Xia WANG ; Feng LU ; Bo DONG ; Jun PU ; Feng LIU ; Xiu-Guang ZU ; Hong-Bin LIU ; Li YANG ; Shao-Ying ZHANG ; Yong-Mei YAN ; Xiao-Li WANG ; Jin-Han CHEN ; Min LIU ; Yun-Mei YANG ; Xiao-Ying LI
Chinese journal of integrative medicine 2025;31(3):195-205
OBJECTIVE:
To evaluate the clinical efficacy and safety of Yangxue Qingnao Pills (YXQNP) combined with amlodipine in treating patients with grade 1 hypertension.
METHODS:
This is a multicenter, randomized, double-blind, and placebo-controlled study. Adult patients with grade 1 hypertension of blood deficiency and Gan (Liver)-yang hyperactivity syndrome were randomly divided into the treatment or the control groups at a 1:1 ratio. The treatment group received YXQNP and amlodipine besylate, while the control group received YXQNP's placebo and amlodipine besylate. The treatment duration lasted for 180 days. Outcomes assessed included changes in blood pressure, Chinese medicine (CM) syndrome scores, symptoms and target organ functions before and after treatment in both groups. Additionally, adverse events, such as nausea, vomiting, rash, itching, and diarrhea, were recorded in both groups.
RESULTS:
A total of 662 subjects were enrolled, of whom 608 (91.8%) completed the trial (306 in the treatment and 302 in the control groups). After 180 days of treatment, the standard deviations and coefficients of variation of systolic and diastolic blood pressure levels were lower in the treatment group compared with the control group. The improvement rates of dizziness, headache, insomnia, and waist soreness were significantly higher in the treatment group compared with the control group (P<0.05). After 30 days of treatment, the overall therapeutic effects on CM clinical syndromes were significantly increased in the treatment group as compared with the control group (P<0.05). After 180 days of treatment, brachial-ankle pulse wave velocity, ankle brachial index and albumin-to-creatinine ratio were improved in both groups, with no statistically significant differences (P>0.05). No serious treatment-related adverse events occurred during the study period.
CONCLUSIONS
Combination therapy of YXQNP with amlodipine significantly improved symptoms such as dizziness and headache, reduced blood pressure variability, and showed a trend toward lowering urinary microalbumin in hypertensive patients. These findings suggest that this regimen has good clinical efficacy and safety. (Registration No. ChiCTR1900022470).
Humans
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Amlodipine/adverse effects*
;
Drugs, Chinese Herbal/adverse effects*
;
Male
;
Female
;
Hypertension/complications*
;
Middle Aged
;
Treatment Outcome
;
Drug Therapy, Combination
;
Adult
;
Blood Pressure/drug effects*
;
Double-Blind Method
;
Aged
;
Antihypertensive Agents/adverse effects*
9.Significance of basophil levels in prognostic evaluation of intra-abdominal infection
Ming-min PANG ; Shao-hua FAN ; Mei-chen YAN ; Bao LIU ; Ju YANG ; Ya-nan LI ; Shi-han ZHANG ; Ting-yu MENG ; Tao GAO
Chinese Journal of Current Advances in General Surgery 2025;28(5):367-372
Objective:To assess the relationship between basophil levels and mortality in patients with intra-abdominal infection.Methods:Information on patients with intraperitoneal infection admitted to the intensive care unit were extracted from the MIMIC database.A time-dependent Cox regression model was used to adjust for confounders associated with 28-day mortality.Propensity score matching(PSM)was used to balance the baseline differences be-tween groups with different basophil levels,and a restricted cube chart(RCS)was used to show the relationship between basophil count and 28-day mortality in patients with intra-abdominal infection.Results:A total of 4403 patients with intra-abdominal infection were enrolled in the MIMIC database.Patients with high basophil levels have lower mortality than those with low basophil levels.There was an L-shaped curve between basophil level and 28-day mortality,with a cut-off value of 0.47×109/L.Cox regression analysis showed that basophil levels were an independent protective factor for mortal-ity in patients with intra-abdominal infection after adjusting for potential confounders(HR=0.586,95%CI:0.443-0.769).Protective factors for death at basophil levels remained after PSM adjusted for potential confounders(HR=0.628,95%CI:0.470-0.832).Conclusion:Basophil level is an independent protective factor for mortality in patients with intra-abdominal infection,and basophil levels should be dynamically monitored to better evaluate the prognosis of patients.
10.Relationship between internalized stigma and quality of life in patients with schizophrenia::the chain mediating role of self-esteem and severity of negative symptoms
Guiju AI ; Ming JIN ; Quanming SHAO ; Yanni LIU ; Xianzhen WANG ; Hong LUO
Sichuan Mental Health 2025;38(2):172-177
BackgroundPatients with schizophrenia experience low quality of life, and internalized stigma is considered an important indicator for quality of life, while the mediating role of self-esteem and severity of negative symptoms in the relationship between internalized stigma and quality of life remains underexplored. ObjectiveTo examine the mediating role of self-esteem and severity of negative symptoms in the relationship between internalized stigma and quality of life, so as to provide references for improving their quality of life. MethodsA total of 342 patients with schizophrenia who were hospitalized in 6 hospitals in Xiangyang City, Siping City and Changchun City from April to September 2023 were included, and all of whom met the diagnostic criteria for schizophrenia according to the International Classification of Diseases, tenth edition (ICD-10). Internalized Stigma of Mental Illness Scale (ISMI), Schizophrenia Quality of Life Scale (SQLS), Self-Esteem Scale (SES) and negative symptom subscale of Positive and Negative Symptom Scale (PANSS) were administered to all patients. Spearman correlation analysis was adopted to determine correlations between the different scales. A structural equation modeling was constructed using Amos 28.0, and Bootstrap method was employed to verify the mediating effect of self-esteem and negative symptom severity in the association between internalized stigma and quality of life. ResultsA total of 309 patients (90.35%) completed questionnaires in this study. The ISMI score of schizophrenia patients was positively correlated with both SQLS score and the PANSS negative symptom subscale score (r=0.612, 0.492, P<0.01), while was negatively correlated with SES score (r=-0.513, P<0.01). The SQLS score was negatively associated with the SES score (r=-0.555, P<0.01) and positively associated with PANSS negative symptom subscale score (r=0.672, P<0.01). The SES score was negatively correlated with PANSS negative symptom subscale score (r=-0.433, P<0.01).The total effect value of internalized stigma on quality of life was 0.746 (95% CI: 0.680~0.806). Self-esteem and severity of negative symptoms independently mediated the relationship between internalized stigma and quality of life, and the indirect effect values were 0.151 (95% CI: 0.062~0.254) and 0.126 (95% CI: 0.047~0.205), accounting for 20.24% and 16.89% of the total effect, respectively. In addition, a chained mediation effect of self-esteem and quality of life was also demonstrated, the indirect effect value was 0.102 (95% CI: 0.049~0.165), accounting for 13.67% of the total effect). ConclusionInternalized stigma in patients with schizophrenia patients can not only directly affect the quality of life, but also indirectly affect the quality of life of patients through either separate or chained mediation of self-esteem and the severity of negative symptoms. [Funded by Hubei Provincial Undergraduate Innovation and Entrepreneurship Project (number, S202410519027)]

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