OBJECTIVES: To develop a heterogeneous graph prediction method based on the fusion of multi-layer semantics and topological information for addressing the challenges in drug-target interaction prediction, including insufficient modeling of high-order semantic dependencies, lack of adaptive fusion of semantic paths, and over-smoothing of node features. METHODS: A heterogeneous graph network with multiple types of entities such as drugs, proteins, side effects, and diseases was constructed, and graph embedding techniques were used to obtain low-dimensional feature representations. An adaptive metapath search module was introduced to automatically discover semantic path combinations for guiding the propagation of high-order semantic information. A semantic aggregation mechanism integrating multi-head attention was designed to automatically learn the importance of each semantic path based on contextual information and achieve differentiated aggregation and dynamic fusion among paths. A structure-aware gated graph convolutional module was then incorporated to regulate the feature propagation intensity for suppressing redundant information and redcuing over-smoothing. Finally, the potential interactions between drugs and targets were predicted through an inner product operation. RESULTS: Compared with existing drug-target interaction prediction methods, the proposed method achieved an average improvement of 3.4% and 2.4%, 3.0% and 3.8% in terms of the area under the receiver operating characteristic curve (AUC) and the area under the precision-recall curve (AUPRC) on public datasets, respectively. CONCLUSIONS The drug-target interaction prediction method developed in this study can effectively extract complex high-order semantic and topological information from heterogeneous biological networks, thereby improving the accuracy and stability of drug-target interaction prediction. This method provides technical support and theoretical foundation for precise drug target discovery and targeted treatment of complex diseases.
Semantics ; Humans ; Drug Interactions ; Neural Networks, Computer ; Algorithms

Objectives:To investigate the effect of the expression of low-density lipoprotein receptor associated protein (LDLR) on the vascular abnormalities in hepatocellular carcinoma (HCC) and its mechanisms.Methods:Based on the information of Oncomine Cancer GeneChip database, we analyzed the correlation between the expression level of LDLR and the expression level of carcinoembryonic antigen (CEA) and CD31 in hepatocellular carcinoma tissues. Lentiviral transfection of short hairpin RNA target genes was used to construct LDLR-knockdown MHCC-97H and HLE hepatocellular carcinoma cells. The differential genes and their expression level changes in LDLR-knockdown hepatocellular carcinoma cells were detected by transcriptome sequencing, real-time fluorescence quantitative polymerase chain reaction, and protein immunoblotting. The gene-related signaling pathways that involve LDLR were clarified by enrichment analysis. The effect of LDLR on CEA was assessed by the detection of CEA content in conditioned medium of hepatocellular carcinoma cells. Angiogenesis assay was used to detect the effect of LDLR on the angiogenic capacity of human umbilical vein endothelial cells, as well as the role of CEA in the regulation of angiogenesis by LDLR. Immunohistochemical staining was used to detect the expression levels of LDLR in 176 hepatocellular carcinoma tissues, and CEA and CD31 in 146 hepatocellular carcinoma tissues, and analyze the correlations between the expression levels of LDLR, CEA, and CD31 in the tissues, serum CEA, and alanine transaminase (ALT).Results:Oncomine database analysis showed that the expressions of LDLR and CEA in the tissues of hepatocellular carcinoma patients with portal vein metastasis were negatively correlated ( r=-0.64, P=0.001), whereas the expressions of CEA and CD31 in these tissues were positively correlated ( r=0.46, P=0.010). The transcriptome sequencing results showed that there were a total of 1 032 differentially expressed genes in the LDLR-knockdown group and the control group of MHCC-97H cells, of which 517 genes were up-regulated and 515 genes were down-regulated. The transcript expression level of CEACAM5 was significantly up-regulated in the cells of the LDLR-knockdown group. The Gene Ontology (GO) function enrichment analysis showed that the differential genes were most obviously enriched in the angiogenesis function. The Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis showed that the relevant pathways involved mainly included the cellular adhesion patch, the extracellular matrix receptor interactions, and the interactions with the extracellular matrix receptors. The CEA content in the conditioned medium of the LDLR-knockdown group was 43.75±8.43, which was higher than that of the control group (1.15±0.14, P＜0.001). The results of angiogenesis experiments showed that at 5 h, the number of main junctions, the number of main segments, and the total area of the lattice formed by HUVEC cells cultured with the conditioned medium of MHCC-97H cells in the LDLR-knockdown group were 295.3±26.4, 552.5±63.8, and 2 239 781.0±13 8211.9 square pixels, which were higher than those of the control group (113.3±23.5, 194.8±36.5, and 660 621.0±280 328.3 square pixels, respectively, all P＜0.01).The number of vascular major junctions, the number of major segments, and the total area of the lattice formed by HUVEC cells cultured in conditioned medium with HLE cells in the LDLR-knockdown group were 245.3±42.4, 257.5±20.4, and 2 535 754.5±249 094.2 square pixels, respectively, which were all higher than those of the control group (113.3±23.5, 114.3±12.2, and 1 565 456.5±219 259.7 square pixels, respectively, all P＜0.01). In the conditioned medium for the control group of MHCC-97H cells,the number of main junctions, the number of main segments, and the total area of the lattice formed by the addition of CEA to cultured HUVEC cells were 178.9±12.0, 286.9±12.3, and 1 966 990.0±126 249.5 spixels, which were higher than those in the control group (119.7±22.1, 202.7±33.7, and 1 421 191.0±189 837.8 square pixels, respectively). The expression of LDLR in hepatocellular carcinoma tissues was not correlated with the expression of CEA, but was negatively correlated with the expression of CD31 ( r=-0.167, P=0.044), the level of serum CEA ( r=-0.061, P=0.032), and the level of serum ALT (r=-0.147, P=0.05). The expression of CEA in hepatocellular carcinoma tissues was positively correlated with the expression of CD31 ( r=0.192, P=0.020). The level of serum CEA was positively correlated with the level of serum ALT ( r=0.164, P=0.029). Conclusion:Knocking down LDLR can promote vascular abnormalities in HCC by releasing CEA.

Objective To explore the clinical value of laparoscopic radical cystectomy based on fascia anatomy for bladder cancer treatment.Methods The clinical data of 51 patients with bladder cancer who underwent 3D laparoscopic radical cystectomy during Jan.2015 and Jun.2022 were retrospectively analyzed.The surgery was performed based on membrane anatomy technology along four longitudinal and two transverse planes to complete the radical cystectomy.The pelvic plexus was preserved for patients with normal preoperative sexual function.Results All surgeries were completed without conversion to open operation.The mean operation time was(502.52±108.99)min,mean intraoperative blood loss was(275.96±155.18)mL,mean postoperative drainage time was(4.14±2.41)d,and the mean postoperative hospital stay was(16.37±4.85)d.The mean number of lymph nodes removed was(17.98±11.48).The mean postoperative follow-up was(30.27±19.39)months.At the last follow-up,no Clavien ≥grade 3 complications were observed.The estimated overall survival(OS),tumor-specific survival(TSS),and recurrence-free survival(RFS)were 82.4％,92.2％,and 88.2％,respectively.The lymph node positive patients had shorter OS and RFS(60.0％,60.0％)than the lymph node negative patients(84.8％,91.3％).Among the 19 male patients who underwent radical cystectomy with pre-exposure and preservation of pelvic plexus,daytime and nocturnal continence rate were 83.3％and 72.2％,respectively,and 17 patients recovered potency within 6 months postoperatively.Conclusion Laparoscopic radical cystectomy based on fascia anatomy is safe and effective in laparoscopic radical cystectomy,with standardized surgical procedure,satisfactory oncological outcomes,little hemorrhage,few complications and fast recovery.

Objectives:To investigate the effect of the expression of low-density lipoprotein receptor associated protein (LDLR) on the vascular abnormalities in hepatocellular carcinoma (HCC) and its mechanisms.Methods:Based on the information of Oncomine Cancer GeneChip database, we analyzed the correlation between the expression level of LDLR and the expression level of carcinoembryonic antigen (CEA) and CD31 in hepatocellular carcinoma tissues. Lentiviral transfection of short hairpin RNA target genes was used to construct LDLR-knockdown MHCC-97H and HLE hepatocellular carcinoma cells. The differential genes and their expression level changes in LDLR-knockdown hepatocellular carcinoma cells were detected by transcriptome sequencing, real-time fluorescence quantitative polymerase chain reaction, and protein immunoblotting. The gene-related signaling pathways that involve LDLR were clarified by enrichment analysis. The effect of LDLR on CEA was assessed by the detection of CEA content in conditioned medium of hepatocellular carcinoma cells. Angiogenesis assay was used to detect the effect of LDLR on the angiogenic capacity of human umbilical vein endothelial cells, as well as the role of CEA in the regulation of angiogenesis by LDLR. Immunohistochemical staining was used to detect the expression levels of LDLR in 176 hepatocellular carcinoma tissues, and CEA and CD31 in 146 hepatocellular carcinoma tissues, and analyze the correlations between the expression levels of LDLR, CEA, and CD31 in the tissues, serum CEA, and alanine transaminase (ALT).Results:Oncomine database analysis showed that the expressions of LDLR and CEA in the tissues of hepatocellular carcinoma patients with portal vein metastasis were negatively correlated ( r=-0.64, P=0.001), whereas the expressions of CEA and CD31 in these tissues were positively correlated ( r=0.46, P=0.010). The transcriptome sequencing results showed that there were a total of 1 032 differentially expressed genes in the LDLR-knockdown group and the control group of MHCC-97H cells, of which 517 genes were up-regulated and 515 genes were down-regulated. The transcript expression level of CEACAM5 was significantly up-regulated in the cells of the LDLR-knockdown group. The Gene Ontology (GO) function enrichment analysis showed that the differential genes were most obviously enriched in the angiogenesis function. The Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis showed that the relevant pathways involved mainly included the cellular adhesion patch, the extracellular matrix receptor interactions, and the interactions with the extracellular matrix receptors. The CEA content in the conditioned medium of the LDLR-knockdown group was 43.75±8.43, which was higher than that of the control group (1.15±0.14, P＜0.001). The results of angiogenesis experiments showed that at 5 h, the number of main junctions, the number of main segments, and the total area of the lattice formed by HUVEC cells cultured with the conditioned medium of MHCC-97H cells in the LDLR-knockdown group were 295.3±26.4, 552.5±63.8, and 2 239 781.0±13 8211.9 square pixels, which were higher than those of the control group (113.3±23.5, 194.8±36.5, and 660 621.0±280 328.3 square pixels, respectively, all P＜0.01).The number of vascular major junctions, the number of major segments, and the total area of the lattice formed by HUVEC cells cultured in conditioned medium with HLE cells in the LDLR-knockdown group were 245.3±42.4, 257.5±20.4, and 2 535 754.5±249 094.2 square pixels, respectively, which were all higher than those of the control group (113.3±23.5, 114.3±12.2, and 1 565 456.5±219 259.7 square pixels, respectively, all P＜0.01). In the conditioned medium for the control group of MHCC-97H cells,the number of main junctions, the number of main segments, and the total area of the lattice formed by the addition of CEA to cultured HUVEC cells were 178.9±12.0, 286.9±12.3, and 1 966 990.0±126 249.5 spixels, which were higher than those in the control group (119.7±22.1, 202.7±33.7, and 1 421 191.0±189 837.8 square pixels, respectively). The expression of LDLR in hepatocellular carcinoma tissues was not correlated with the expression of CEA, but was negatively correlated with the expression of CD31 ( r=-0.167, P=0.044), the level of serum CEA ( r=-0.061, P=0.032), and the level of serum ALT (r=-0.147, P=0.05). The expression of CEA in hepatocellular carcinoma tissues was positively correlated with the expression of CD31 ( r=0.192, P=0.020). The level of serum CEA was positively correlated with the level of serum ALT ( r=0.164, P=0.029). Conclusion:Knocking down LDLR can promote vascular abnormalities in HCC by releasing CEA.

Objective:To establish and validate a gallstones classification method based on deep learning.Methods:A total of 618 gallstones samples were collected from East Hospital Affiliated to Tongji University, and 1 023 high-definition cross-sectional gallstones profile images were captured to construct a cross-sectional gallstones profile image dataset. Based on the traditional eight-category gallstones classification method, a lightweight network model, MobileNet V3, was trained using deep learning and transfer learning methods. The classification performance of MobileNet was evaluated using a confusion matrix with metrics such as accuracy rate, precision rate, F1 score, and recall rate. The MobileNet V3 was improved and further validated using accuracy and loss values.Results:The accuracy rate (94.17%), precision rate (94.03%), F1 score (92.96%) and recall rate (92.99%) of the improved MobileNet V3 model were better than other networks. The improved MobileNet V3 model achieved the highest accuracy rate (94.17%) in gallstones profile classification and was validated by the test set. The confusion matrix showed a weighted average of accuracy rate (92.0%), precision rate (92.6%), and F1 score (92.2%) for each category of gallstones.Conclusions:Based on deep learning, a high-accuracy gallstones classification method is proposed, which provides a new idea for the intelligent identification of gallstones.

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas.
Animals ; China ; Genomics ; Humans ; Male ; Pesticides ; Spodoptera/genetics* ; Transcriptome

Most carcinogenic mutations, including those causing a loss of function, are not directly "druggable" with traditional small-molecule inhibitors, such as targeted drugs. Thus, despite our growing cognition of carcinogenic mutations that drive tumor progres-sion, there are still problems regarding targeted therapy for tumors. The application of synthetic lethality effects is expected to be-come a new breakthrough in tumor-targeted therapy. Therefore, identifying a combination of genetic mutations that generate synthet-ic lethality effects plays important roles in targeted therapy for tumors. This article reviews the origin and development of synthetic le-thality effects, the forms of interaction, related screening techniques, clinical treatment strategies, and significance and challenges.

Objective: To investigate the changes of C-reactive protein(CRP), fibrinogen(FIB) and erythrocyte sedimentation rate(ESR) in patients with obstructive sleep apnea-hypopnea syndrome(OSAHS), and their relationship with sleep respiratory parameters. Methods: From June 2015 to August 2018, 70 OSAHS patients[observation group, apnea hypopnea index(AHI)≥5/h]and 20 persons in the snoring control group(control group, AHI<5/h) who received the monitor of polysomnography in the Pingxiang People′s Hospital were enrolled.The levels of CRP, FIB and ESR were measured and compared between the two groups.The correlations were analyzed between the levels of inflammatory markers and sleep breathing parameters. Results: The two groups had no statistically significant differences in age, gender and BMI(all P>0.05). The CRP, FIB and ESR of the observation group were (4.5±3.0)mg/L, (3.3±0.9)g/L, (11.4±5.4)mm/h, respectively, which were significantly higher than those of the control group[(2.0±1.5)mg/L, (2.9±0.5)g/L, (7.6±2.6)mm/h](t=5.12, 2.68, 4.36, all P<0.05). The level of CRP was positively correlated with AHI, oxygen desaturation index(ODI)(r=0.285, P<0.05 and r=0.282, P<0.05), and negatively correlated with the lowest SaO₂ and the average SaO₂(r=-0.257, P<0.05 and r=-0.259, P<0.05). The level of FIB was positively correlated with AHI, ODI(r=0.430, P<0.01 and r=0.311, P<0.01), and negatively correlated with the lowest SaO₂(r=-0.287, P<0.01). There were no correlations between ESR and sleep breathing parameters. Conclusion The levels of CRP, FIB and ESR are increased in OSAHS patients, and the levels of CRP and FIB are proportional to the severity of OSAHS, suggesting that OSAHS patients has systemic inflammatory response.