Artificial intelligence (AI) researchers and cheminformatics specialists strive to identify effective drug precursors while optimizing costs and accelerating development processes. Digital molecular representation plays a crucial role in achieving this objective by making molecules machine-readable, thereby enhancing the accuracy of molecular prediction tasks and facilitating evidence-based decision making. This study presents a comprehensive review of small molecular representations and AI-driven drug discovery downstream tasks utilizing these representations. The research methodology begins with the compilation of small molecule databases, followed by an analysis of fundamental molecular representations and the models that learn these representations from initial forms, capturing patterns and salient features across extensive chemical spaces. The study then examines various drug discovery downstream tasks, including drug-target interaction (DTI) prediction, drug-target affinity (DTA) prediction, drug property (DP) prediction, and drug generation, all based on learned representations. The analysis concludes by highlighting challenges and opportunities associated with machine learning (ML) methods for molecular representation and improving downstream task performance. Additionally, the representation of small molecules and AI-based downstream tasks demonstrates significant potential in identifying traditional Chinese medicine (TCM) medicinal substances and facilitating TCM target discovery.
Artificial Intelligence ; Drug Discovery/methods* ; Humans ; Machine Learning ; Medicine, Chinese Traditional ; Small Molecule Libraries/chemistry*

Periodontal bone defects, primarily caused by periodontitis, are highly prevalent in clinical settings and manifest as bone fenestration, dehiscence, or attachment loss, presenting a significant challenge to oral health. In regenerative medicine, harnessing developmental principles for tissue repair offers promising therapeutic potential. Of particular interest is the condensation of progenitor cells, an essential event in organogenesis that has inspired clinically effective cell aggregation approaches in dental regeneration. However, the precise cellular coordination mechanisms during condensation and regeneration remain elusive. Here, taking the tooth as a model organ, we employed single-cell RNA sequencing to dissect the cellular composition and heterogeneity of human dental follicle and dental papilla, revealing a distinct Platelet-derived growth factor receptor alpha (PDGFRA) mesenchymal stem/stromal cell (MSC) population with remarkable odontogenic potential. Interestingly, a reciprocal paracrine interaction between PDGFRA⁺ dental follicle stem cells (DFSCs) and CD31⁺ Endomucin⁺ endothelial cells (ECs) was mediated by Vascular endothelial growth factor A (VEGFA) and Platelet-derived growth factor subunit BB (PDGFBB). This crosstalk not only maintains the functionality of PDGFRA⁺ DFSCs but also drives specialized angiogenesis. In vivo periodontal bone regeneration experiments further reveal that communication between PDGFRA⁺ DFSC aggregates and recipient ECs is essential for effective angiogenic-osteogenic coupling and rapid tissue repair. Collectively, our results unravel the importance of MSC-EC crosstalk mediated by the VEGFA and PDGFBB-PDGFRA reciprocal signaling in orchestrating angiogenesis and osteogenesis. These findings not only establish a framework for deciphering and promoting periodontal bone regeneration in potential clinical applications but also offer insights for future therapeutic strategies in dental or broader regenerative medicine.
Receptor, Platelet-Derived Growth Factor alpha/metabolism* ; Humans ; Neovascularization, Physiologic/physiology* ; Dental Sac/cytology* ; Single-Cell Analysis ; Transcriptome ; Mesenchymal Stem Cells/metabolism* ; Bone Regeneration ; Animals ; Dental Papilla/cytology* ; Periodontium/physiology* ; Stem Cells/metabolism* ; Regeneration ; Angiogenesis

Objective:To explore the correlation between the ratio of C-reactive protein (CRP) to albumin (CAR) and the syndrome type of Wei-Qi-Ying-Xue in patients with severe coronavirus disease 2019 (COVID-19).Methods:A case-control study was conducted to select 63 severe patients with COVID-19 admitted to the Dongzhimen Hospital of Beijing University of Chinese Medicine from December 2022 to December 2023, including 50 severe cases and 13 critical cases. The clinical data of the patients were collected. According to the syndrome differentiation of Wei-Qi-Ying-Xue, there were 21 cases of Qi syndrome, 20 cases of Ying syndrome and 22 cases of Xue syndrome. The differences of CRP, ALB and CAR levels in patients with different Wei-Qi-Ying-Xue syndromes were compared. Spearman correlation test was used to test the correlation between CRP, ALB, CAR and the Wei-Qi-Ying-Xue syndrome type, and the receiver operating characteristic (ROC) curve was used to detect the diagnostic efficacy of CRP, ALB and CAR on the Wei-Qi-Ying-Xue syndrome type.Results:There was a statistically significant difference in the clinical classification of Western medicine among the three groups ( P<0.05). The CAR of the Ying group and the Xue group was higher than that of the Qi group ( P<0.05), while there was no statistically significant difference in age and comorbidities (all P>0.05). The CRP of the Xue group was higher than that of the Qi group ( P<0.05), and the ALB of the Ying group and the Xue group was lower than that of the Qi group (all P<0.05). Correlation analysis showed that there was a correlation between the Wei-Qi-Ying-Xue syndrome type and CRP, ALB and CAR ( P<0.05), among which CAR changed most significantly with the change of Wei-Qi-Ying-Xue syndrome type. ROC curve analysis showed that CRP, ALB and CAR had good diagnostic value for Qi syndrome and Xue syndrome ( P<0.05). The critical values of the diagnosis of Qi syndrome were 48.57 mg/L, 34.20 g/L and 2.97. The critical values of the diagnosis of Xue syndrome were 28.30 mg/L, 26.6 g/L and 5.96. Conclusions:CAR ratio is correlated with the Wei-Qi-Ying-Xue syndrome type of severe COVID-19 patients, and its level changes are in line with the evolution law of Wei-Qi-Ying-Xue syndrome. CAR≤2.97 is contributed to the diagnosis of Qi syndrome, and CAR>5.96 is contributed to the diagnosis of Xue syndrome. CAR may be an objective index related to the Wei-Qi-Ying-Xue syndrome type of severe COVID-19 patients.

Objective:To analyze the immune microenvironment characteristics of human dental follicle tissues from the third molars and to explore the mutual communication and the effects of innate immune cells and adaptive immune cells within the dental follicle.Methods:Sequencing data(GSA-Human:HRA008022)in the GSA database were analyzed.Bioinformatics tools were employed for gene identification and GO enrichment analysis was performed to define the biological function of innate and adaptive immune cells.CellChat analysis was used for explaining intercellular communication among immune cell populations.Results:Using t-SNE dimen-sionality reduction analysis for immune cell populations,innate immune cell populations were obtained,including innate lymphoid cells,dendritic cells,mast cells and macrophages,and adaptive immune cell populations including T cells and B cells.Pearson corre-lation analysis showed that innate immune cells,specifically innate lymphoid cells and macrophages,had a strong correlation with adap-tive immune cell populations.GO enrichment analysis revealed mutual coordination among innate immune cell populations and regulato-ry effects on adaptive immune cell populations.Further CellChat analysis indicated biological signal transmission between innate and a-daptive immune cell populations,with CLEC,MIF,ADGRE5,COLLAGEN and MIF signaling pathways is the most significant.Con-clusion:Dental follicle tissues are rich in immune cells and innate immune cell populations interact with adaptive immune cells to regulate immune responses and participate in maintaining the homeostasis of dental follicle.

Objective To systematically evaluate the effect of Xuebijing injection on lactic acid clearance in sepsis,and to provide the theoretical basis for the application of Xuebijing injection in the field of lactic acid clearance in sepsis.Methods Randomized controlled trials(RCT)of the effect of Xuebijing injection on lactic acid clearance in sepsis were retrieved in Chinese and English databases,including China National Knowledge Internet(CNKI),Wanfang Database,VIP Database,Chinese Biomedical Database(CBM),PubMed,Embase,Cochrane Library Database,and Web of Science.These trials were evaluated according to the Cochrane Handbook 5.1.0 standard and analyzed using RevMan 5.4 software for Meta-analysis.Funnel plots were used to assess publication bias in the included studies Results A total of 13 articles with 872 patients were included,including 446 patients in the experimental group(Xuebijing injection and conventional treatment group)and 426 patients in the control group(conventional treatment group).Meta-analysis showed that the blood lactic acid concentrations at 12 hours and 24 hours in the experimental group were lower than those of the control group[mean difference(MD)=-0.88,-0.73;95%confidence interval(95%CI)were-1.26 to-0.50,-0.89 to-0.57;P<0.000 1)].The experimental group exhibited a better 24 hours lactic acid clearance rate(MD=17.20,95%CI was 8.80 to 25.59;P<0.000 1),and a reduced sequential organ failure assessment(SOFA)score(MD=-2.41,95%CIwas-2.79 to-2.03,P<0.00001).Additionally,the experimental group demonstrated lower 28-day mortality rates compared to the control group[odds ratio(OR)=0.51,95%CI was 0.30-0.88,P=0.02];the differences were all statistically significant.Conclusion Xuebijing injection benefits by enhancing the lactic acid clearance capacity of sepsis patients,thereby alleviating the sepsis condition and improve improving the prognosis.

Objective:To analyze the distribution pattern of TCM syndrome elements in elderly patients with sepsis and septic shock, as well as the relationship between TCM syndrome elements, Sepsis Sequential Organ Failure Score (SOFA), Acute Physiology and Chronic Health Score Ⅱ (APACHE Ⅱ), and short-term mortality prognosis.Methods:A retrospective analysis was conducted on the clinical data of 58 patients treated in the Emergency Department and ICU of Dongzhimen Hospital of Beijing University of Chinese Medicine and the Third Affiliated Hospital of Beijing University of Chinese Medicine from January 1, 2021, to May 1, 2022. The patients were divided into a sepsis group of 38 cases and a septic shock group of 20 cases based on disease type. Basic information, TCM syndromes, SOFA score, and APACHE Ⅱ score of the two groups were collected. The survival and death statuses of the two groups within 28 days of admission were separately analyzed. Association rule analysis was used to investigate the distribution pattern of TCM syndromes in patients, and logistic regression analysis was performed to explore the relationship between TCM syndromes, SOFA score, APACHE Ⅱ score, and death prognosis.Results:In the sepsis group, the main TCM syndromes included yin deficiency, lung, phlegm, qi deficiency, blood stasis, heat, and yang deficiency; while in the septic shock group, the main TCM syndromes were yin deficiency, lung, yang deficiency, and qi deficiency. Multifactor logistic regression analysis showed that in the sepsis group, liver syndromes [ OR (95% CI)=0.080 (0.011, 0.578), P=0.012], meridians and collaterals [ OR (95% CI)=0.088 (0.011, 0.718), P=0.024], SOFA score [ OR (95% CI)=0.524 (0.310, 0.886), P=0.016], and APACHE Ⅱ score [ OR (95% CI)=0.426 (0.186, 0.977), P=0.044] were independent influencing factors for patient mortality prognosis. In the septic shock group, phlegm [ OR (95% CI)=0.014 (0.001, 0.267), P=0.005], meridians and collaterals [ OR (95% CI)=0.041 (0.003, 0.618), P=0.021], yang deficiency [ OR (95% CI)=0.028 (0.002, 0.427), P=0.010], SOFA score [ OR (95% CI)=0.543 (0.310, 0.950), P=0.032], and APACHE Ⅱ score [ OR (95% CI)=0.633 (0.408, 0.985), P=0.042] were independent influencing factors for patient mortality prognosis. Conclusions:The sepsis group mainly exhibits a mixture of deficiency and excess, while the septic shock group predominantly shows deficiency. Qi deficiency and yin deficiency are consistent throughout the disease progression. Meridians and collaterals, high SOFA score, and high APACHE Ⅱ score in elderly patients with sepsis and septic shock may indicate a poorer prognosis.

Objective:To evaluate the value of age-adjusted Charlson comorbidity index (aCCI) in the clinical prognosis of sepsis and septic shock in the elderly, and to further explore the role of aCCI in evaluating the timing of Shenfu injection in elderly patients with septic shock.Methods:Clinical data of elderly patients with sepsis and septic shock in Dongzhimen Hospital of Beijing University of Chinese Medicine from January 1, 2019 to January 1, 2022 were retrospectively analyzed. With the median aCCI score of all samples as the cutoff value, the patients were divided into the low aCCI score group and high aCCI score group. The prognosis of elderly patients with septic shock and the application timing of Shenfu injection with aCCI score and sequential organ failure assessment (SOFA) were compared.Results:A total of 61 patients were included, including 31 patients in the high aCCI score group. The proportion of septic shock in elderly sepsis patients was lower in the low aCCI score group ( P < 0.05). The aCCI score (95% CI: 1.229-2.615; P< 0.01) was more valuable than SOFA score (95% CI: 1.035-1.607; P< 0.05) in predicting septic shock in elderly patients with sepsis. The 28-day survival rate in the low aCCI score group was higher than that in the high aCCI score group ( P < 0.05). Both the SOFA score (95% CI: 1.010-1.364) and the aCCI score (95% CI: 1.072-10.501) were independent factors affecting the 28-day survival rate. The use of Shenfu injection was associated with 28-day survival outcome in elderly patients with septic shock (95% CI: 0.012-0.788; P < 0.05). Conclusions:aCCI score is more effective than SOFA score in assessing the risk of shock in elderly patients with septic shock, and has a certain predictive value for the survival and prognosis of elderly patients with sepsis. Shenfu injection may be beneficial to the survival and prognosis of elderly patients with septic shock, but it needs to be further verified by large-scale prospective studies.

Objective:To retrieve and summarize evidence on non-pharmacological sleep management in adult critically ill patients, providing reference for sleep intervention by ICU medical and nursing staff.Methods:The literature on non-pharmacological sleep management in adult critically ill patients was systematically searched in domestic and foreign databases and guideline websites. The search period was from the establishment of the database to February 2023. After screening the literature based on inclusion and exclusion criteria, two evidence-based trained researchers independently evaluated the quality of the included literature, extracted and summarized evidence.Results:A total of 13 articles were included, including 3 clinical guidelines, 9 systematic reviews, and 1 randomized controlled trial. A total of 21 best pieces of evidence were summarized, covering 5 aspects, including strengthening nurse education and training, improving ward environment, reducing sleep interruption, selecting mechanical ventilation modes reasonably, and promoting physical and mental relaxation.Conclusions:The evidence summarized can provide reference for the development of non-pharmacological sleep management plans for adult critically ill patients. ICU medical and nursing staff should carefully apply evidence in clinical practice based on evidence, fully consider the human resources and actual situation of the department, and combine it with the needs of patients.

ObjectiveTo investigate the effect of Bufeitang on intestinal flora of rats with lung Qi-deficiency syndrome of chronic obstructive pulmonary disease（COPD）， and to explore the mechanism of traditional Chinese medicine in regulating intestinal flora and thus restoring the balance of lung-gut axis. MethodA total of 84 rats were randomly divided into 7 groups， including blank group， model group， fecal bacterial transplantation（FMT） group， dexamethasone group and low， medium and high dose groups of Bufeitang， 12 rats in each group. Except for the blank group， cigarette and sawdust fumigation combined with intratracheal instillation of lipopolysaccharide（LPS） were used to establish the COPD rat model with lung Qi-deficiency syndrome in all other groups. The low， medium and high dose groups of Bufeitang were intragastric administrated with Bufeitang（3.645， 7.29， 14.58 g·kg^-1）， the FMT group was given fecal bacteria liquid enema（10 mL·kg^-1）， dexamethasone group was given dexamethasone acetate tablet suspension by gavage（0.135 mg·kg^-1）， the blank group and model group were given equal amount of distilled water. Fresh feces were collected after 28 d of continuous intervention for 16S rRNA gene sequencing. Lung and colon tissues were stained with hematoxylin-eosin（HE） for pathomorphological observation， and enzyme-linked immunosorbent assay （ELISA） was performed to detect the contents of tumor necrosis factor-α（TNF-α） and interleukin-8（IL-8） in lung tissues. ResultCompared with the blank group， the model group showed severe abnormal lung tissue structure with alveolar atrophy and collapse accompanied by severe inflammatory cell infiltration. Compared with the model group， the extent of injury was significantly improved， and inflammatory cell infiltration was reduced with basically normal alveolar structure in the high dose group of Bufeitang. Compared with the blank group， the model group had severely abnormal colonic tissue structure， the epithelial cells in the mucosal layer were eroded and shed， the number of inflammatory cells increased， the submucosal layer was edematous and the gap was enlarged. Compared with the model group， the extent of damage was significantly improved in the medium and high dose groups of Bufeitang， the epithelial cells in the mucosal layer were neatly and closely arranged， with only a small amount of inflammatory cell infiltration and no significant degeneration. Compared with the blank group， the TNF-α and IL-8 levels of lung tissue in the model group were significantly increased（P<0.01）. Compared with the model group， the TNF-α and IL-8 levels of lung tissues in the low， medium and high dose groups of Bufeitang were significantly decreased（P<0.01）. Bufeitang significantly modulated the number of bacteria species as well as alpha and beta diversity of model rats， corrected the return of intestinal flora to normal abundance and diversity， and positively regulated 4 differential phyla（such as Firmicutes， Proteobacteria） and 13 differential genera（such as Turicibacter， Lactobacillus， Anaerobiospirillum， Intestinimonas） in COPD model rats with lung Qi-deficiency syndrome， and down-regulated 2 carbohydrate metabolic pathway functions， including the pentose phosphate pathway（non-oxidative branch） Ⅰ and the Calvin-Benson-Bassham cycle. ConclusionBufeitang can modulate the abundance and diversity of intestinal flora species， affect the function of metabolic pathways， repair the structure of lung and colon tissues， regulate the level of inflammatory factors， and thus improve COPD with lung Qi-deficiency syndrome. The mechanism may be related to its regulation of inflammation-related intestinal flora to restore the balance of lung-gut axis in COPD with lung Qi-deficiency syndrome.

[摘 要] 目的：采用基于中国人群单核苷酸多态性位点开发的同源重组缺陷（HRD）检测工具评估云南地区卵巢癌患者的HRD状态和BRCA1/2基因突变频率并探讨其临床意义。方法：共纳入2021年1月至2023年5月间在云南省肿瘤医院收治的卵巢癌患者248例，HRD状态采用基因组瘢痕评分法（GSS）（主要依据拷贝数的长度、类型、位置及基因组断片）或HRD评分法（杂合性缺失、端粒等位基因失衡及大片段移位等基因组不稳定事件的总和）进行评估，当组织样本的GSS≥50分或HRD评分≥42分者或检测到有害的BRCA1/2基因突变时HRD被定义为阳性。分析患者HRD状态与临床病理特征的关系。结果：248名卵巢癌患者中70.97%的患者HRD呈阳性，其中BRCA1/2基因突变率为30.65%。Ⅲ~Ⅵ期、高级别浆液腺癌的卵巢癌患者具有更高的HRD阳性率（均P<0.01），HRD评分更高的患者其合并其他基因突变的频率也越高（P<0.05）。HRD状态与卵巢癌的病理类型、临床分期和其他基因突变均有关联（均P<0.01）。结论：云南地区卵巢癌患者HRD阳性率较高，HRD阳性的卵巢癌患者可以从聚ADP核糖聚合酶（PARP）抑制剂治疗中获得更大的收益。