1.The Structure and Function of The YopJ Family Effectors in The Bacterial Type III Secretion System
Ao-Ning LI ; Wen-Bo LI ; Yu-Ying LU ; Min-Hui ZHU ; Yu-Long QIN ; Yong ZHAO ; Zhao-Huan ZHANG
Progress in Biochemistry and Biophysics 2026;53(3):516-533
The Type III Secretion System (T3SS) serves as a pivotal virulence apparatus for numerous Gram-negative bacterial pathogens, enabling them to infect both animal and plant hosts. Functioning as a molecular syringe, the T3SS directly translocates bacterial effector proteins from the bacterial cytoplasm into the interior of eukaryotic host cells. These effectors are central weapons that precisely manipulate a wide spectrum of host cellular physiological processes, ranging from cytoskeletal dynamics to immune signaling, to establish a favorable niche for bacterial survival and proliferation. Among the diverse arsenal of T3SS effectors, the YopJ family constitutes a critical group of virulence factors. Members of this family are characterized by a conserved catalytic triad structure—a hallmark of the CE clan of cysteine proteases that has been evolutionarily repurposed to confer acetyltransferase activity. A defining and intriguing feature of these enzymes is their stringent dependence on a host-derived eukaryotic cofactor, inositol hexakisphosphate (IP6), for allosteric activation. This requirement acts as a sophisticated molecular safeguard, ensuring enzymatic activity only within the appropriate host environment, thereby preventing detrimental effects on the bacterium itself. While seminal studies on individual members such as Yersinia’s YopJ and Salmonella’s AvrA have provided deep mechanistic insights, a systematic and integrative understanding of the structure-function relationships across the entire family remains fragmented. Key questions persist regarding how a conserved catalytic core has diverged to recognize distinct host substrates in different kingdoms of life. To address this gap, this article provides a systematic review of the YopJ family, focusing on three interconnected aspects: their structural features, their catalytic mechanism, and their divergent immunosuppressive strategies in animal versus plant hosts. By conducting a comparative analysis of the sequences and resolved three-dimensional structures of three representative members (e.g., HopZ1a, PopP2, AvrA), we elucidate regions of significant variation embedded within the conserved core catalytic architecture. These variable regions, often involving surface loops and substrate-binding interfaces, are crucial determinants of target specificity and functional specialization. The functional divergence of this effector family is most apparent when comparing their modes of action in different hosts. In animal hosts, YopJ-family effectors primarily sabotage innate immune signaling pathways. They achieve this by acetylating key serine and threonine residues within the activation loops of critical kinases in the MAPK and NF‑κB pathways. This post-translational modification blocks the phosphorylation and subsequent activation of these kinases, leading to potent suppression of inflammatory cytokine production. Conversely, in plant hosts, the strategy broadens to dismantle the two-tiered plant immune system. YopJ homologs target a more diverse set of substrates, including immune-associated receptor-like cytoplasmic kinases (RLCKs), microtubule networks via tubulin acetylation (which disrupts cellular trafficking and signaling), and transcription factors central to defense gene regulation. This multi-target approach effectively suppresses both Pattern-Triggered Immunity (PTI) and Effector-Triggered Immunity (ETI). In conclusion, this synthesis aims to deepen the mechanistic understanding of YopJ family-mediated pathogenesis by integrating structural biology with cellular function across host kingdoms. Elucidating the precise molecular basis for substrate selection—how conserved platforms achieve target diversity—is a major frontier. Furthermore, this knowledge provides a vital theoretical foundation for developing novel anti-virulence strategies. Targeting the conserved IP6-binding pocket or the catalytic acetyltransferase activity itself represents a promising avenue for designing broad-spectrum inhibitors that could disarm this critical family of bacterial effectors, potentially offering new therapeutic approaches against a range of pathogenic bacteria.
2.Epidemiological characteristics and disease burden of liver cancer in Guangdong Province
Ying ZHANG ; Yixuan CHEN ; Rong CAO ; Yue GAO ; Yutong HAN ; Ye WANG ; Ruilin MENG ; Xueyan ZHENG ; Yu LIAO ; Zhuanping ZENG
Journal of Public Health and Preventive Medicine 2026;37(1):68-72
Objective To analyze the epidemiological characteristics and disease burden of liver cancer in Guangdong Province in 2020, and to provide a scientific foundation for the development of regionalized prevention and control strategies for liver cancer. Methods According to the cancer registry data of Guangdong Province, the incidence, mortality and age-standardized rate by Chinese standard population in 2020 were calculated to analyze the epidemiological characteristics of liver cancer. The disability adjusted life years (DALYs), year of life loss (YLL), year of lived with disability (YLD), and cause-eliminated life expectancy were used to assess the disease burden of liver cancer. Results In 2020, the crude incidence rate and the age-standardized incidence rate of liver cancer in Guangdong Province were 27.79/100 000 and 20.84/100 000,respectively, and the crude mortality rate and the age-standardized mortality rate of liver cancer were 25.49/100,000 and 17.64/100 000, respectively. The total DALY and DALY rate of liver cancer in Guangdong Province were 515 311 person-years and 513.83/100 000, respectively. After eliminating the causes of death from liver cancer, the life expectancy in Guangdong Province increased from 84.60 years to 84.99 years. All indicators consistently demonstrated that the burden of liver cancer was higher in males than that in females, and the burden of liver cancer was higher in rural areas than that in urban areas. Conclusion Liver cancer in Guangdong Province exhibits a high incidence, mortality and disease burden level in 2020. There are obvious differences of gender, age and region in cancer burden. It is necessary to strengthen liver cancer screening and diagnosis and treatment in men, the elderly and those in rural areas to reduce the burden of liver cancer gradually in Guangdong Province.
3.Exploring Biological Characteristics of Rat Model of Atrial Fibrillation with Phlegm-heat and Blood Stasis Pattern Based on Metabolomics
Ailin HOU ; Yuxuan LIU ; Wenxi YU ; Xing JI ; Chan WU ; Dazhuo SHI ; Ying ZHANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(5):245-255
ObjectiveTo establish an animal model of atrial fibrillation(AF) that accurately reflects the phlegm-heat and blood stasis(TRYZ) pathogenesis in traditional Chinese medicine. MethodsForty SPF-grade SD rats were randomly assigned using a random number table to the following groups:the control group, the TRYZ+AF group,the AF group and the TRYZ group, with ten rats in each group. The TRYZ+AF and TRYZ groups underwent a high-fat diet combined with intraperitoneal lipopolysaccharide(LPS) injection to simulate the pathological alterations of TRYZ syndrome. Groups TRYZ+AF and AF were induced with acetylcholine-calcium chloride(Ach-CaCl2) via caudal vein injection to induce AF. The control group received no intervention and was maintained under normal conditions. The modeling period lasted 3 weeks. Electrocardiography was used to assess AF episodes and duration, echocardiography evaluated left atrial dimensions and cardiac function, fully automated biochemical analyzer measured the levels of total cholesterol(TC), triglycerides(TG), high-density lipoprotein cholesterol(HDL-C) and low-density lipoprotein cholesterol(LDL-C), hemoreometer analyzed the whole blood viscosity, plasma viscosity, and whole blood reduced viscosity, a coagulation analyzer assessed prothrombin time(PT), activated partial thromboplastin time(APTT), thrombin time(TT), and fibrinogen(FIB), enzyme-linked immunosorbent assay(ELISA) was used to determine the levels of C-reactive protein(CRP), interleukin(IL)-1β, IL-6, IL-17, tumour necrosis factor(TNF)-α, matrix metalloproteinase-9(MMP-9), galectin-3(Gal-3), Collagen Ⅰ, and α-smooth muscle actin(α-SMA). Hematoxylin-eosin(HE) staining and Masson's trichrome staining were used to analyze pathological changes in atrial myocardium, Western blot was employed to detect MMP-9, Collagen Ⅰ and α-SMA protein expression in myocardial tissue, real-time quantitative polymerase chain reaction(Real-time PCR) evaluated fibrous factor gene expression levels. Changes in the TRYZ syndrome were assessed via body weight, tongue color[red(R), green(G), and blue(B)], and rectal temperature. Ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS) was employed to detect differential metabolites between the control group and the TRYZ+AF group. ResultsFollowing three weeks of sustained modeling, compared with the control group, rats in the TRYZ+AF and the TRYZ groups exhibited reduced body weight, dry faeces, elevated rectal temperature, dark red tongue, decreased RGB values on the tongue surface, and markedly elevated TC and LDL-C levels(P<0.05, P<0.01). The TRYZ+AF, TRYZ, and AF groups exhibited significantly decreased TT, APTT and PT, along with markedly elevated whole blood viscosity and FIB(P<0.05, P<0.01). Rats in the TRYZ+AF and AF groups exhibited AF rhythm, markedly decreased heart rate, prolonged RR intervals, enlarged left atrium, and significantly reduced ejection fraction and shortening fraction(P<0.05, P<0.01). Serum levels of CRP, IL-1β, IL-6, IL-17, TNF-α, MMP-9, Gal-3, Collagen Ⅰ, and α-SMA were elevated in rats from the TRYZ+AF, TRYZ, and AF groups compared to the control group, with the most pronounced increase observed in the TRYZ+AF group(P<0.05, P<0.01). Histopathology revealed that the collagen fiber deposition in the atrial of rats in the TRYZ+AF, TRYZ and AF groups was higher than that in the control group(P<0.05, P<0.01). Western blot and Real-time PCR results further demonstrated that the protein and mRNA expression levels of MMP-9, Collagen Ⅰ and α-SMA in the myocardial tissue of the TRYZ+AF group were higher than those in the other three groups(P<0.05, P<0.01). Metabolomic analysis revealed 173 differentially expressed metabolites in the TRYZ+AF group and the control group, primarily enriched in pathways such as glycerophospholipid metabolism and glycolysis/gluconeogenesis. ConclusionThis study successfully establishes a rat model of AF integrated with the TRYZ syndrome, demonstrating the pathological process where the interactions of phlegm, heat and stasis jointly trigger tremor, this provides a reliable experimental tool for in-depth research into the biological basis of this disease syndrome.
4.Empirical study of input, output, outcome and impact of community-based rehabilitation stations
Xiayao CHEN ; Ying DONG ; Xue DONG ; Zhongxiang MI ; Jun CHENG ; Aimin ZHANG ; Didi LU ; Jun WANG ; Jude LIU ; Qianmo AN ; Hui GUO ; Xiaochen LIU ; Zefeng YU
Chinese Journal of Rehabilitation Theory and Practice 2026;32(1):83-89
ObjectiveTo investigate the present situation of input, output, outcome and impact of all registered community-based rehabilitation stations in Inner Mongolia in China, and analyze how the input predict the output, outcome and impact. MethodsFrom March 1st to April 30th, 2025, a questionnaire survey was conducted on all registered community-based rehabilitation stations in Inner Mongolia, covering four dimensions: input, output, outcome and impact. A total of 1 365 questionnaires were distributed. The input included four items: laws and policies, human resources, equipment and facilities, and rehabilitation information management. The output included two items: technical paths and benefits/effectiveness. The outcome included three items: coverage rates, rehabilitation interventions and functional results. The impact included two items: health and sustainability. Each item contained several questions, all of which were described in a positive way. Each question was scored from one to five. A lower score indicated that the situation of the community-based rehabilitation station was more in line with the content described in the question. Regression analysis was performed using the total score of each item of input dimension as independent variables, and the total scores of the output, outcome and impact dimensions as dependent variables. ResultsA total of 1 262 valid questionnaires were collected. The mean values of input, output, outcome and impact of community-based rehabilitation stations were 1.827 to 1.904, with coefficient of variation of 45.892% to 49.239%. The regression analysis showed that, rehabilitation information management, human resources, and laws and policies significantly predicted the output dimension (R² = 0.910, P < 0.001). Meanwhile, all four items in the input dimension predicted both the outcome (R² = 0.850, P < 0.001) and impact dimensions (R² = 0.833, P < 0.001). ConclusionInput, output, outcome and impact of the community-based rehabilitation stations in Inner Mongolia were generally in line with the content of the questions, although some imbalances were observed. Additionally, the input of community-based rehabilitation stations could significantly predict their output, outcome and impact.
5.Evaluation of CARIFS Score and Negative Antigen Conversion Rate of Qingxuan Daozhi Formula in Treatment of Influenza in Children (Heat Accumulation in Lung and Stomach Syndrome):A Multi-center Randomized Controlled Clinical Study
Jing WANG ; Liqun WU ; Tiegang LIU ; Yongning CAO ; Jing QIU ; Jing LI ; Huaqing TAN ; Ying ZHANG ; Xulei GOU ; Jia WANG ; Jing LI ; Haipeng CHEN ; Xueying QIN ; Yuanshuo TIAN ; Yang WANG ; Chen BAI ; Zhendong WANG ; Qianqian LI ; He YU ; Xueyan MA ; Fei DONG ; Lin JIANG ; Yingqi XU ; Jianping LIU ; Xiaohong GU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(13):188-196
ObjectiveThis paper aims to observe the syndrome improvement and negative antigen conversion rate of Qingxuan Daozhi formula in the treatment of influenza in children (heat accumulation in the lung and stomach syndrome). MethodsThrough a multi-center randomized controlled methodology design,confirmed influenza cases were collected from October 2022 to April 2023 in the pediatrics department of eight hospitals,such as Dongfang Hospital of Beijing University of Chinese Medicine. A total of 180 children with influenza and heat accumulation in the lung and stomach syndrome conforming to the standard were recruited through the clinic. The sick children meeting the inclusion criteria were randomly divided into groups by a block-randomized method. The children in the experimental group were treated with Qingxuan Daozhi formula for five days,and those in the control group were treated with Oseltamivir Phosphate Granules for five days. The primary efficacy indicator was the negative conversion rate of influenza antigen detection. Secondary efficacy indicators were the Canadian acute respiratory illness and flu scale (CARIFS) and the incidence of complications,severe cases, and critical cases. Follow-up observation was conducted on the day of enrollment,48 hours after medication,72 hours after medication, and (6+1) d after medication. ResultsOne hundred and eighty participants were randomly assigned to the experimental group (90 cases) or the control group (90 cases). All participants were followed up during the study. Comparison of influenza antigen detection results in the primary efficacy indicators showed that the average time of negative influenza antigen conversion in the experimental group was (5.29±1.25) d,and that in the control group was (5.40±1.68) d,without a statistically significant difference. After five days of intervention,52 cases in the experimental group and 51 cases in the control group converted to negative,without a statistically significant difference. CARIFS score results in the secondary efficacy indicators showed that during 72 hours after intervention,there were statistically significant differences between the experimental group and the control group in three dimensions, including headache,muscle soreness, and the need for extra care (P<0.05). On the (6+1) days after the intervention,the differences in both the experimental group and the control group were statistically significant in 10 dimensions, including sore throat,bad sleep,uncomfortable feeling,poor spirit and fatigue,crying more than usual,the need for extra care,symptom,function,influence on parents,and total score (P<0.05). The comparison results within the group in the dimensional scores of symptom, function, and influence on parents,as well as the CARIFS total score showed that with the delay of follow-up time,scores of both groups decreased significantly,with a statistically significant difference (P<0.01). Inter-group comparison results showed that the mean score of the experimental group was higher than that of the control group at the time of enrollment. With the progress of intervention,the score of the experimental group was significantly decreased compared with that of the control group. At the end of follow-up,the mean score of the experimental group was lower than that of the control group,with no statistically significant difference. In terms of the incidence of complications,severe cases, and critical cases, there were no complications,severe cases, and critical cases in the two groups,without a statistically significant difference. ConclusionThe symptom improvement effect and negative antigen conversion rate of Qingxuan Daozhi formula in the treatment of influenza in children (heat accumulation in the lung and stomach syndrome) are not inferior to Oseltamivir Phosphate granules, and children's acceptance is better. It can be more widely used in clinical treatment of influenza in children (heat accumulation in the lung and stomach syndrome).
6.Analysis of the safety of intravascular lithotripsy and rotational atherectomy in the management of coronary artery calcification
Zhang-ying WU ; Li ZHU ; Su LI ; Jia HUANG ; Yu-xiang DAI
Chinese Journal of Interventional Cardiology 2025;33(11):634-639
Objective To investigate the safety of intravascular lithotripsy(IVL)and coronary rotational atherectomy(RA)in the management of coronary artery calcification(CAC).Methods In this retrospective,matched-pair cohort study,210 patients with severe CAC treated at Zhongshan Hospital,Fudan University between December 2021 and April 2025 were enrolled.The cohort was equally divided into two interventional groups:IVL group(n=105)and RA group(n=105),based on the revascularization strategy employed.Procedure parameters,postoperative biochemical markers of myocardial injury,and incidence of in-hospital major adverse cardiovascular events(MACE)were compared between the two groups.Results Before propensity score matching(PSM),statistically significant differences were observed in terms of the proportions of the left anterior descending artery(77.1%vs.63.8%,P=0.034),the right coronary artery(14.3%vs.30.5%,P=0.005),and the percentage of target vessel stenosis[85%(80%,90%)vs.80%(80%,90%),P=0.014]between the IVL and RA groups.After PSM,these differences became insignificant(all P>0.05).There is no statistically significant differences in stent implantation rate,drug-coated balloon usage rate,stent diameter,or total stent length between the IVL and RA groups(all P>0.05).Compared to the RA group,although the IVL group had a higher utilization of tirofiban after the procedure,and a lower rate of intravenous nitrate during the procedure,these differences were not statistically significant(all P>0.05).cTnT levels increased significantly after the procedure in both the IVL and RA groups(all P<0.001).Before PSM,the preoperative cTnT levels were comparable between the IVL and RA groups(P=0.525),while a statistically significant difference emerged postoperatively(P=0.038).The incidence of in-hospital myocardial infarction showed no significant intergroup difference(8.6%vs.16.2%,P=0.094),and no events of death or target vessel revascularization occurred in either group.After PSM,despite no significant difference in preoperative cTnT levels between the IVL and RA groups(P=0.235),a significant difference was observed postoperatively(P=0.014).Furthermore,while no deaths or target vessel revascularization occurred in either group,the IVL group demonstrated a significantly lower incidence of in-hospital myocardial infarction compared to the RA group(9.9%vs.23.9%,P=0.025).Conclusions The use of intravascular lithotripsy for the pretreatment in patients with severe CAC is safe and promising.
7.The level of serum soluble vascular cell adhesion molecule-1 in patients with multiple myeloma and its effect on the therapeutic effect ofdaletumab
Yu HUANG ; Qian HUANG ; Ying LI ; Linlin LYU ; Wenjuan ZHANG
Chinese Journal of Postgraduates of Medicine 2025;48(8):697-701
Objective:To investigate the serum level of soluble vascular cell adhesion molecule-1 (sVCAM-1) in patients with multiple myeloma (MM) and its effect on the therapeutic effect of daletumab.Methods:A total of 126 MM patients admitted to the Affiliated Hospital of Jining Medical College from June 2019 to June 2021 were retrospectively selected as the observation group, and 120 healthy subjects in the same period were selected as the control group. The observation group was treated with daletumab. The level of sVCAM-1 in the observation group and the control group was compared, and the relationship between serum sVCAM-1 level and clinicopathological features, different Durie-Salmon (DS) stages, different International Staging System(ISS) stages and treatment outcome of MM patients were analyzed.Results:The serum level of sVCAM-1 in the observation group was higher than that in the control group: (797.69 ± 119.73) μg/L vs. (210.55 ± 73.77) μg/L, there was statistical difference ( P<0.01). There were no statistical differences in serum sVCAM-1 level among MM patients with different sex, body mass index, blood calcium, serum albumin, hemoglobin, lactate dehydrogenase and diagnostic type ( P>0.05). The serum level of sVCAM-1 in MM patients DS stage Ⅰ, Ⅱ and Ⅲ were (649.29 ± 101.02), (694.36 ± 109.88) and (729.66 ± 120.44) μg/L, there was statistical difference ( F = 5.12, P<0.01). The serum level of sVCAM-1 in MM patients with ISS stage Ⅰ, Ⅱ and Ⅲ were (648.73 ± 99.77), (701.05 ± 107.83) and (765.82 ± 111.07) μg/L, there was statistical difference ( F = 11.46, P<0.01). After treatment, the serum level of sVCAM-1 in MM patients with complete remission, partial remission and relapse were (234.05 ± 90.73), (445.36 ± 97.11) and (793.05 ± 121.03) μg/L, there was statistical difference ( F = 245.15, P<0.01). The results of receiver operating characteristic (ROC) curve analysis showed that when the cut-off value of serum sVCAM-1 level was 58.50 μg/L, the area under the curve (AUC) was 0.762 (95% CI 0.699 - 0.825, P<0.01), the sensitivity was 80.95%, the specificity was 67.50%, and the accuracy was 74.39%. Conclusions:The level of serum sVCAM-1 in MM patients is significantly increased, and the higher the level of SVCAM-1, the worse the prognosis of patients, which can be used as one of the indicator to predict the therapeutic effect of MM patients.
8.Retrospective study on adverse prognosis of neonates with late onset sepsis and invasive procedures in neonatal intensive care unit
Mengwen CHEN ; Chengyi FENG ; Jianfang WANG ; Ying LIU ; Hui WANG ; Haiying SONG ; Rongping ZHU ; Lin ZHANG ; Yu WANG ; Lijuan GAO ; Fang HE
Chinese Journal of Infection Control 2025;24(6):782-788
Objective To investigate the incidence and adverse prognosis of late onset sepsis(LOS)in neonates in neonatal intensive care unit(NICU).Methods A retrospective study was conducted to collect and analyze the peri-natal condition,underlying diseases,invasive procedures,and adverse prognosis of neonates in NICU of a regional maternal and child healthcare hospital from 2019 to 2023.According to whether LOS occurred during hospitaliza-tion,neonates were divided into LOS group and non-LOS group.The LOS group was divided into 5 subgroups based on whether invasive procedures were performed:LOS plus umbilical vein catheter(UVC)group,LOS plus peripherally inserted central catheter(PICC)group,LOS plus sequential catheter group,LOS plus tracheal intuba-tion group,and LOS plus lumbar puncture group,the relationship between LOS and adverse prognosis was ana-lyzed.Results Among 2 945 neonates in NICU,354(12.02%)developed LOS.Comparison between LOS groups and non-LOS group were as follows:in term of perinatal condition of neonates,there were statistically significant difference in weight,gestational age,and whether they were twins between the two groups(all P<0.001);in term of underlying diseases,there were statistically significant differences in the number of cases of maternal gestational hypertension,neonatal asphyxia,neonatal congenital heart disease,neonatal ventricular dilation,neonatal pneumo-nia,neonatal hyperthyrotropinemia,and neonatal anemia,as well as five invasive procedures between the two groups(all P<0.05).Compared with the non-LOS group,the incidences of retinopathy of prematurity(ROP),neonatal necrotizing enterocolitis(NNEC),bronchopulmonary dysplasia(BPD),and neonatal respiratory distress syndrome(NRDS)in LOS group were all higher(all P<0.001).Regression analysis showed that compared with the non-LOS groups,the risk of ROP increased in the LOS group and its subgroups,with the LOS plus sequential catheter group having a 2.27-fold higher risk of ROP than non-LOS group;the risk of NNEC increased in the LOS group and its subgroups,with the LOS plus UVC group having an 8.29-fold higher risk of NNEC than the non-LOS group.Except for the LOS plus UVC group,the risk of BPD increased in the LOS group and other subgroups,with the LOS plus PICC group and LOS plus sequential catheter group having 4.68-and 4.64-fold higher risk of BPD than the non-LOS group,respectively;the risk of NRDS in the LOS plus PICC group was 6.84-fold higher than the non-LOS group(all P<0.05).The top three pathogens causing LOS were coagulase negative Staphylococcus,Klebsiella pneumoniae,and Escherichia coli.Conclusion LOS can significantly increase the risks of ROP,NNEC,BPD,and NRDS.LOS plus invasive procedures can further increase the risk of adverse prognosis.
9.Performance comparison of 5 automatic cell type annotation methods in scRNA-seq data
Jinghui NI ; Yu GAO ; Qiyue CHEN ; Ying ZHANG ; Yan LIU
Chinese Journal of Endemiology 2025;44(11):931-936
Objective:This study aims to analyze the performance of five automatic cell type annotation methods in single cell RNA sequencing (scRNA-seq) data.Methods:Simulated data were generated using the Splatter package in R language, taking into account two data characteristics: the number of cells and the number of genes. The actual data came from the GSE10245 scRNA seq dataset of non-small cell lung cancer in Gene Expression Omnibus (GEO) database, the data had been pre-processed and batch effects had been eliminated. The automatic cell type recognition (ACTINN) of neural networks, the single-cell type annotation method based on deep learning (scDeepSort), the reference batch transcriptome annotation scRNA seq R-package (SingleR), the cross platform and cross species scRNA seq data classifier (SingleCellNet), and the cross scRNA seq dataset projection (scMap-cell) were implemented using the Tensorflow library in Python. The performance evaluation indicators for cell type annotation included accuracy (ACC), F1-score, and Matthews correlation coefficient (MCC). Each method was validated using ten fold cross validation, and the average value was taken after 50 repeated runs for performance comparison between methods. The Dunnett's t-test in the DescTools package of R language was used for multiple comparisons between ACTINN and other four methods. Results:Under 12 different scenarios (3 levels of cell numbers × 4 levels of gene numbers), simulated data analysis showed that compared with scDeepSort, SingleR, SingleCellNet, and scMap-cell, the percentage increase in ACC value of ACTINN ranged from 3.31% to 14.59%, 1.38% to 13.03%, 12.98% to 25.25%, and 20.72% to 29.62%, respectively; the range of F1 score improvement percentages were 2.75% - 22.74%, 2.46% - 23.68%, 5.07% - 27.47%, and 10.27% - 31.47%, respectively; the percentage increase ranges for MCC values were 3.42% - 9.75%, 2.26% - 7.61%, 5.41% - 11.11%, and 8.27% - 15.22%, respectively. Actual data analysis showed that the ACC value of ACTINN was 81.0%, which was increased by 2.1%, 5.2%, 7.9%, and 8.9% compared with the above four methods, respectively; the F1-score value was 80.5%, which was increased by 2.3%, 5.9%, 2.4%, and 6.0%, respectively; the MCC value was 83.3%, which was increased by 0.9%, 2.5%, 3.4%, and 11.2%, respectively. The results of Dunnett's t-test showed that the difference was not statistically significant in ACC values between scDeepSort and ACTINN ( P = 0.821), in F1-score values between scDeepSort and ACTINN ( P = 0.498), and in MCC values between scDeepSort, SingleCellNet and ACTINN ( P = 0.904, 0.134). However, the differences were statistically significant in other multiple comparisons ( P < 0.05). Conclusions:ACTINN and scDeepSort have good performance in cell type annotation, with ACTINN showing outstanding performance and SingleR showing robust performance, while SingleCellNet and scMap-cell have relatively limited performance. This suggests that self-attention mechanism algorithm based on Transformer framework is expected to promote further development of automatic cell annotation methods.
10.Two-Dimensional Speckle Tracking Echocardiography in Distinguishing Fabry Disease in Patients with Left Ventricular Hypertrophy
Chonghui WANG ; Han WANG ; Ying YANG ; Lin LIU ; Fangfang FAN ; Yawen ZHAO ; Wei ZHANG ; Yang YU ; Wei MA
Chinese Journal of Medical Imaging 2025;33(8):848-853,879
Purpose To explore the diagnostic value of two-dimensional speckle tracking echocardiography(2D-STE)in differentiating left ventricular hypertrophy(LVH)caused by Fabry disease from other etiologies.Materials and Methods A total of 23 patients clinically confirmed Fabry disease with LVH(Fabry disease group)in Peking University First Hospital from August 2014 to February 2023,retrospectively.23 patients with hypertensive LVH(hypertensive LVH group)and 23 with hypertrophic cardiomyopathy(HCM)(HCM group)were also included.Conventional echocardiographic parameters and 2D-STE-derived left atrial strain and left ventricular longitudinal strain were analyzed and compared among the three groups.LASSO regression was used to select variables and construct a diagnostic model to differentiate hypertensive LVH,HCM and Fabry disease group.Results The Fabry disease group showed significantly reduced left ventricular global longitudinal strain and segmental left ventricular longitudinal strain in the basal anterior wall,basal anterolateral wall and mid inferior wall compared to the hypertensive LVH group(P<0.05).There were no significant differences in left atrial strain,left ventricular global longitudinal strain and segmental left ventricular longitudinal strain between the Fabry disease and HCM groups(P>0.05).Compared to the conventional echocardiography-based model,the combined model did not significantly improve diagnostic accuracy for differentiating the three etiologies(Z=-1.314--0.594,all P>0.05).Conclusion Compared to patients with hypertensive LVH,HCM and Fabry disease group exhibit varying degrees of decrease in global and segmental longitudinal strain of the left atrium and left ventricle.Additional measurements of left ventricular longitudinal strain and left atrial strain do not provide significant incremental diagnostic value over conventional echocardiography in distinguishing among Fabry disease,hypertensive LVH and HCM.


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