Prescription and medication rules of traditional Chinese medicine for prevention and treatment of diabetic microangiopathy based on literature mining / 中国中药杂志

This study explored the prescription and medication rules of traditional Chinese medicine(TCM) in the prevention and treatment of diabetic microangiopathy based on literature mining. Relevant literature on TCM against diabetic microangiopathy was searched and prescriptions were collected. Microsoft Excel 2021 software was used to establish a prescription database, and an analysis was conducted on the frequency, properties, flavors, meridian tropism, and efficacy classifications of drugs. Association rule analysis, cluster analysis, and factor analysis were performed using SPSS Modeler 18.0 and SPSS Statistics 26.0 software. The characteristic active components and mechanisms of action of medium-high frequency drugs in the analysis of medication rules were explored through li-terature mining. A total of 1 327 prescriptions were included in this study, involving 411 drugs, with a total frequency reaching 19 154 times. The top five high-frequency drugs were Astragali Radix, Angelicae Sinensis Radix, Poria, Salviae Miltiorrhizae Radix et Rhizoma, and Rehmanniae Radix. The cold and warm drugs were used in combination. Drugs were mainly sweet, followed by bitter and pungent, and acted on the liver meridian. The majority of drugs were effective in tonifying deficiency, clearing heat, activating blood, and resolving stasis. Association rule analysis identified the highly supported drug pair of Astragali Radix-Angelicae Sinensis Radix and the highly confident drug combination of Poria-Alismatis Rhizoma-Corni Fructus. The strongest correlation was found among Astragali Radix, Angelicae Sinensis Radix, Poria, and Salviae Miltiorrhizae Radix et Rhizoma through the complex network analysis. Cluster analysis identified nine categories of drug combinations, while factor analysis identified 16 common factors. The analysis of active components in high-frequency drugs for the treatment of diabetic microangiopathy revealed that these effective components mainly exerted their effects by inhibiting oxidative stress and suppressing inflammatory reactions. The study found that the pathogenesis of diabetic microangiopathy was primarily characterized by deficiency in origin, with a combination of deficiency and excess. Deficiency was manifested as Qi deficiency and blood deficiency, while excess as phlegm-heat and blood stasis. The key organ involved in the pathological changes was the liver. The treatment mainly focused on supplementing Qi and nourishing blood, supplemented by clearing heat, coo-ling blood, activating blood, and dredging collaterals. Commonly used formulas included Danggui Buxue Decoction, Liuwei Dihuang Pills, Erzhi Pills, and Buyang Huanwu Decoction. The mechanisms of action of high-frequency drugs in the treatment of diabetic microangiopathy were often related to the inhibition of oxidative stress and suppression of inflammatory reactions. These findings can provide references for the clinical treatment of diabetic microangiopathy and the development of targeted drugs.

Screening of active components from Chinese materia medica against SARS-CoV-2 based on literature mining and molecular docking / 中草药

Objective: To screen the active components from Chinese materia medica (CMM) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on literature mining and molecular docking. Methods: Candidate CMMs were collected from recently published prescriptions against COVID-19. The active components and protein targets of candidate CMMs were collected from TCMSP, CNKI and PubMed. SARS-CoV-2 3CL hydrolase (Mpro) has been determined by academician Zihe Rao’s team at Shanghai Technical University. The molecular docking was performed by AutoDock vina software. Results: A total of 11 high-frequency used candidate CMMs were obtained by literature mining, and 469 candidate components were found from TCMSP and literatures. The binding energy of all the components were calculated by molecular docking and 41 components of them were less than -33.44 kJ/mol. Among them, saikosaponin (E, B1, D, F, B2, C2, A) and glycyrrhizin had the lower binding energies. The results showed that Bupleuri Radix, Glycyrrhizae Radix et Rhizoma and Lonicerae Japonicae Flos contained more active components against SARS-CoV-2. Conclusion: The active components of CMMs against SARS-CoV-2 were screened based on literature mining and molecular docking, which provides a reference for exploration and discovery of new anti-SARS-CoV-2 drugs.

Traditional Chinese medicine for treatment of COVID-19 based on literature mining of targeting cytokine storm / 中草药

The primary clinical manifestations of coronavirus disease 2019 (COVID-19) are fever, fatigue and dry cough. Several clinical studies reported that some patients with low or medium fever, or even without obvious symptom, rapidly progressed to severe or critical illness, including severe acute respiratory syndrome, septic shock, coagulation disorders and intractable metabolic acidosis. These patients were usually associated with significant elevated serum levels of a profile of cytokines, which is similar to SARS-2003 and MERS-2015, indicating the occurrence of cytokine storm. In the present review, we summarized previous advances in the treatment of severe cases of SARS by using traditional Chinese medicines (TCM), especially those TCM targeting cytokine storm, based on literature mining. By using data mining and network pharmacology, we also investigated underlying mechanisms and biological pathways involved in the inhibitory effects of TCM against cytokine storm. This review not only provides novel insights in the precise application of TCM, appropriate integrative use of TCM in combination with western medicine, but also contributes to the discovery of novel drugs or new therapeutic strategies targeting cytokine storm to suppress progression of COVID-19 and to improve clinical prognosis and outcomes.

Research of characteristic spectrum of Qi deficiency syndrome based on literature mining technology / 中国中药杂志

As a basic syndrome of Chinese medicine, the study of characteristic syndrome spectrum of Qi deficiency syndrome is of great significance for the standardization of clinical diagnosis and modern material basis research. Suitable operators and algorithms were chosen to dig out the relationship between diseases, syndromes, symptoms, detection indicators and etiologist from the literature of Chinese clinical and basic research by literature mining method of frequency statistics, association rules and complex network analysis. Moreover, the information system of Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences was taken as the tools of data mining. The objective was to study the characteristic spectrum of Qi deficiency syndrome and to explore the characteristics of Qi deficiency syndrome. The results showed that the syndrome of fatigue, dietary were the main factors. The main pathogenesis of coronary heart disease, heart failure, chronic obstructive pulmonary disease, diabetes and stroke the disease were Qi deficiency. The clinical features of Qi deficiency syndrome were fatigue, shortness of breath and pale tongue. The biological indicators of Qi deficiency related were blood lipids, ECG, blood rheology, inflammatory reaction, NO, ET and NF-κB signalling pathway. The Qi deficiency syndrome on the level of syndrome spectrum was studied by the method of literature mining, which would provide reliable characteristic guidance data for the research on the substantial basis of Qi deficiency, the research on standard of diagnosis, establishment of syndrome model, the study on combination of disease and syndrome and the mechanism of prescriptions.

Effect of paper publication time on knowledge discovery in biomedical literature / 中华医学图书情报杂志

The effect of paper publication time on knowledge discovery in biomedical literature was studied by analyzing the role of time factor in indirect link mining and tested using the PubMed-covered data set,which showed that recently published papers played a better role than early published papers in knowledge discovery,indicating that the time factor plays a certain role in knowledge discovery in biomedical literature and can thus improve the efficiency of knowledge discovery in biomedical literature.

Knowledge Discovery-oriented Biomedical Literature Information Retrieval and Visualization Design / 医学信息学杂志

The paper discusses influence and effect of information retrieval process of biomedical literature and visualization design on user knowledge discovery,from the aspects of input and output,retieval process and information positioning,it introduces the interaction model of literature information retrieval process and analyzes approach of literature information visualization design,including color and font,statistical chart,list of categories and labels,layer structure and network pictures,etc.

Analysis and experimental evidence on interaction networks among PD-1 and other proteins / 国际检验医学杂志

Objective An interaction network among PD-1-ligands and other proteins were built to add deeper understanding of PD-1 signal pathway and to supply the theoretical data on the clinical application study of PD-1 and its ligands.Methods Searching the literature about PD-1 and its ligands in the PubMed,the result of which would be used to summarize the proteins that had been reported to have interactions with PD-1 and its ligands,and then,quadratic search would be performed on these proteins.Finally,the software Cytoscape would be used to build and analyze the interaction network and verified by PCR.Results There were 122 and 126 nodes in the PD-1/PD-L1 network and PD-1/PD-L2 network respectively.These proteins were involved in TCR signal path-way,cell adhesion,JAK-STAT signal pathway and interaction between cytokines.Meanwhile,a perspective that PD-L1 may influ-ence on CXCR4 through JAK-STAT pathway based on the network which had been supported by qPCR.Conclusion The bioinfor-matics suggested that there are differences between the mechanism of PD-1/PD-L1 and PD-1/PD-L2.Additionally,the method, which was based on the literature mining and bioinformatics,is good to put the biological literature to rational utilization and to pro-vide guidance for experiments.

The Effect of Strong-weak Connection on Medical Literature Knowledge Discovery / 医学信息学杂志

The paper analyzes different expressions of indirectly associated strong-weak connection in the process of biomedical literature knowledge discovery,defines the effect and function of strong-weak connection on literature knowledge discovery,and indicates that the accuracy rate of the discovery of potential connection through strong connection is obviously higher than the accuracy rate obtained through weak connection,and strong connection can serve as an important factor for improving the application effect of literature knowledge discovery.

Role of network characteristics in evaluation of literature-based indirect association discovery / 中华医学图书情报杂志

New scientific hypotheses detected by mining the potential indirect association inliterature according to the studies on literature-based knowledge discovery are increasinglyapplied in biomedical field and evaluation of literature-based indirect association discovery is a hot spot in recent studies on literature-based knowledge discovery . The role of network characteristics in evaluation of literature-based indirect association discovery during the litera-ture-based knowledge discovery was thus studied.The new indexes for evaluaing the literature-based indirect asso-ciation discovery were esatablished by integrating the co-ocurrent statistic information and the network charateris-tics, which are of greatimportance for improving literature-based knowledge discovery and constructing knowledge discovery system .

Preliminary Study on the Biological Basis of TCM Syndromes Based on Literature Mining / 中国中医药信息杂志

Objective To explore the biological basis of TCM syndromes from a biomolecules network perspective with qi deficiency syndrome as the breakthrough point. Methods A data dictionary of neuro-endocrine-immune (NEI) related genes and qi deficiency syndrome characterization terminology thesaurus were established. Literature about qi deficiency syndrome characterization was retrieved by using Genclip, to excavate the characteristic NEI gene, thereby to explore different bioactive substances of syndromes. Results The analysis of the genetic data, showed qi deficiency related cluster with the relevance of endocrine, signal transduction, hematopoietic cell and immune deficiencies etc. It is confirmed that the intrinsic biological features of TCM syndrome can effectively identify in the NEI level. Conclusion Literature mining method as a new way to discover syndromes biological indicators has certain feasibility, and it is recommended to be further expanded into other studies on syndromes to validate the universality and reliability of this method.

Knowledge discovery and data integration in biomedical literature / 中华医学图书情报杂志

Since it is one of the hotspots to discover the new knowledge in life science in data-intensive scientific discovery by integrating the biomedical literature and scientific data that can provide an open environment for their interactive operation , the mining of foreign and domestic biomedical literature and integration of scientific data were analyzed , the corresponding systems for different integration methods were investigated , the development trend in biomedical literature and scientific data integration was predicted .

Association Analysis of Reactive Oxygen Species-Hypertension Genes Discovered by Literature Mining

Oxidative stress, which results in an excessive product of reactive oxygen species (ROS), is one of the fundamental mechanisms of the development of hypertension. In the vascular system, ROS have physical and pathophysiological roles in vascular remodeling and endothelial dysfunction. In this study, ROS-hypertension-related genes were collected by the biological literature-mining tools, such as SciMiner and gene2pubmed, in order to identify the genes that would cause hypertension through ROS. Further, single nucleotide polymorphisms (SNPs) located within these gene regions were examined statistically for their association with hypertension in 6,419 Korean individuals, and pathway enrichment analysis using the associated genes was performed. The 2,945 SNPs of 237 ROS-hypertension genes were analyzed, and 68 genes were significantly associated with hypertension (p < 0.05). The most significant SNP was rs2889611 within MAPK8 (p = 2.70 x 10(-5); odds ratio, 0.82; confidence interval, 0.75 to 0.90). This study demonstrates that a text mining approach combined with association analysis may be useful to identify the candidate genes that cause hypertension through ROS or oxidative stress.