1.CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening.
Chao SHEN ; Hongyan DU ; Xujun ZHANG ; Shukai GU ; Heng CAI ; Yu KANG ; Peichen PAN ; Qingwei ZHAO ; Tingjun HOU
Acta Pharmaceutica Sinica B 2025;15(11):5758-5771
The interest in covalent drugs has resurged in recent decades, spurring the development of numerous specialized computational docking tools to facilitate covalent ligand design and screening. Herein, we present CarsiDock-Cov, a new paradigm distinguishing itself as the first deep learning (DL)-guided approach for covalent docking. CarsiDock-Cov retains the core components of its non-covalent predecessor, leveraging a DL model pretrained on millions of docking complexes to predict protein-ligand distance matrices, along with a dedicated-designed geometric optimization procedure to convert these distances into refined binding poses. Additionally, it incorporates several key enhancements specifically tailored to optimize the protocol for covalent docking applications. Our approach has been extensively validated on multiple public datasets regarding the docking and screening of covalent ligands, and the results indicate that our approach not only achieves comparably improved applicability compared to its non-covalent predecessor, but also exhibits competitive performance against various state-of-the-art covalent docking tools. Collectively, our approach represents a significant advance in covalent docking methodology, offering an automated and efficient solution that shows considerable promise for accelerating covalent drug discovery and design.
2.Bibliometric analysis of current status of global and Chinese anesthesiology research in 2023
Yuxiang MENG ; Zijie LING ; Sumin YUAN ; Li ZHANG ; Zhibiao XU ; Yuyun LIU ; Hongyan LIU ; Qingfeng WANG ; Linlin ZHAO
Chinese Journal of Anesthesiology 2024;44(10):1239-1246
Objective:To analyze the current status of anesthesiology research in the world and China in 2023 and to identify the anesthesiology research hotspots using bibliometrics.Methods:The literature related to anesthesiology published in PubMed in 2023 was searched, and the country and author of the literature, as well as the key words of the literature were visually analyzed by using the software CiteSpace6.2. R4.Results:A total of 22 473 articles were included, the country with the largest number of publications was the United States, and China ranked second. The author with the highest number of publications in the field of anesthesiology in the worldwide in 2023 was Kaye Alan D from the United States. Chronic pain, general anesthesia and pain management were the research hotspots in the field of anesthesiology worldwide in 2023. The research hotspots in the field of anesthesiology in China focused on general anesthesia, oxidative stress and neuropathic pain.Conclusions:The United States is the leader in the research in the field of anesthesiology, with China following behind. The keywords of the literature in the field of anesthesiology between China and the world are roughly the same, reflecting the convergence of Chinese scientific research with global scientific research. Domestic anaesthesia practitioners can refer to or learn from the research hotspots of related countries and strengthen communication and cooperation between teams while conducting academic research.
3.Changes in Drug Resistance and Cross-resistance Phenotype Analysis of Pseudomonas aeruginosa Clinical Isolates from 2016 to 2022 in Kunming
Zan LU ; Hongyan ZHAO ; Chunfu LI ; Daibi LI ; Yang HE ; Limin YIN
Journal of Modern Laboratory Medicine 2024;39(6):189-194
Objective To provide some evidence for early empirical treatment of infections caused by Pseudanonas aeruginosa(PA)and establish a certain foundation for further studies on its resistance mechanisms.Analyzed the resistance rate of PA and the phenotype characteristics for seven years at this hospital.Methods Using Whonet 5.6 software,the drug sensitivity data of PA isolated and reported from clinical specimens at Kunming First People's Hospital from 2016 to 2022 were analyzed annually.Imipenem,meropenem,ceftazidime,and cefepime were the main observation objects,statisticaly analyze the resistance of other antibiotics under different drug resistance combinations of the above-mentioned drugs Results A total of 1 920 strains of PA were detected in 7 years,with polymyxins exhibiting the lowest resistance rate at 1%.The average resistance rates for Amikacin,Gentamicin and Tobramycin were 6.4%,8.6%and 5.1%,respectively.The resistance rates of Quinolones,Piperacillin/Tazobactam,Ceftazidime,and Cefepime were similar,ranging from 10%~20%.Imipenem and Meropenem did not show better sensitivity,with resistance rates of 21.3%and 18.4%,respectively.The resistance rates of major antibiotics have fluctuated over the past 7 years,mostly increasing from 2017 to reaching a peak in 2018 and then falling back.And then stabilized with the domestic average level.1 393 strains were sensitive to Imipenem,and the sensitivity rate of Meropenem in this part was 96.2%.1 451 strains were sensitive to Imipenem,and 89%of them were sensitive to Meropenem at the same time.369 strains were both resistant to Imipenem and Meropenem,and 33.1%of them were sensitive to Ceftazidime.The more resistant to β-lactam,the lower the sensitivity rate to Amikacin and Ciprofloxacin.Conclusion The overall drug sensitivity of PA in this hospital is relatively good.Should adhere to strict management of antibiotic use.Aminoglycosides can be the preferred drugs for empirical treatment,followed by Quinolones,and Carbapenems and Ceftazidime are also candidates.PA has diverse resistance mechanisms to β-lactam antimicrobials,and carbapenem-resistant strains can be mediated by different mechanisms or jointly.
4.Application and evaluation of management mode for the use of antimicrobial drugs in county-level medical communities led by anti-infective clinical pharmacists
Xiaoqin DENG ; Chi ZHAO ; Zhaohong LI ; Hongyan YAN ; Dongfang SHEN ; Helang TAN ; Mingzhong JIANG ; Nanjun DENG
China Pharmacy 2024;35(1):95-100
OBJECTIVE To provide reference for improving the rational use of antimicrobial drugs in primary township medical institutions. METHODS Based on the county prescription pre-review center, a team led by anti-infective clinical pharmacists constructed the management mode for the use of antimicrobial drugs in county-level medical communities with clinical pharmacists as the main team by finding out the main problems in the use of antimicrobial drugs in primary township medical institutions, providing feedback on the problems, organizing relevant training for the problems, improving the customization rules of the prescription pre-review software, implementing the automatic interception and pharmacist online prescription review and other measures. Data on the use of antimicrobial drugs were collected and compared in the 15 primary township medical institutions between January-June in 2022 (before the implementation of the mode) and January-June in 2023 (after the implementation of the mode). RESULTS Compared with before the implementation of the mode, the utilization rate of antimicrobial drugs in outpatients of primary township medical institutions decreased from 24.97% before the implementation of the mode to 19.39% after the implementation of the mode; the utilization rate of antimicrobial injection in outpatients decreased from 66.10% to 46.80%; the utilization rate of intravenous drip of antimicrobial drugs in outpatients decreased from 52.33% to 40.35%; the rates of combined use of antimicrobial drugs in outpatients decreased from 12.70% to 8.19%; the reasonable rate of antimicrobial prescribing in outpatients increased from 55.28% to 73.93%. After the implementation of the mode, the proportion of antimicrobial prescriptions for each diagnosis was basically the same as before; the defined daily dose system (DDDs) and proportion of a few antimicrobial drugs changed compared with before according to the anatomical therapeutic chemical classification of drugs, among which DDDs of lincomycin, gentamicin and other drugs declined significantly; DDDs of antimicrobial drugs for each classification was basically the same as before according to AWaRe classification. CONCLUSIONS The management mode of the use of antimicrobial drugs led by anti-infective clinical pharmacists is constructed in the prescription pre-reviewing center of county-level medical communities, which can effectively improve the rational use of antimicrobial drugs in the primary township medical institutions.
5.The study on the effect of neuregulin-1 on myocardial injury in septic rats
Chao XU ; Rong HUANG ; Hongyan ZHAO ; Jing CAO
Chongqing Medicine 2024;53(2):165-170
Objective To study the effect of neuromodulatory protein-1(NRG-1)in inhibiting sepsis induced myocardial injury and its mechanism.Methods The rat sepsis model was established by cecal ligation and puncture(CLP).SD rats were divided into the sham operation group,sepsis group,sepsis+NRG group(rhNRG,10 μg/kg).After 12,24 h of successful modeling,the heart and peripheral serum of the surviving rats in each group were taken respectively.The HE staining was used to observe the changes of cardiac tissue morphology and structure,and ELISA was used to detect the expression levels of creatine kinase(CK),crea-tine kinase MB isoenzyme(CK-MB),sensitive troponin Ⅰ(cTnⅠ)in serum,tumor necrosis factor-α(TNF-α)in cardiac tissue and IL-6 expression level;Western blot was used to detect the phosphorylation protein ki-nase B(p-Akt),phosphorylation glycogen synthase kinaseβ(p-GSK3β),B-cell lymphoma/leukemia-2(Bcl-2)and Bax protein expression in rat myocardial tissue.Results After 12,24 h of modeling,compared with the sham group,the expression levels of CK,CK-MB and cTnⅠ in serum,TNF-α,IL-6 and Bax protein in myocar-dial tissue in the sepsis group all were significantly increased(P<0.05),while the expression levels of p-Akt and p-GSK3β in myocardial tissue were significantly decreased(P<0.05).After 12,24 h of modeling,com-pared with the sepsis group,the expression levels of CK,CK-MB,cTn Ⅰ in the serum and the expression levels of TNF-α,IL-6 in the myocardial tissue of the sepsis+NRG group were significantly decreased;after 24 h of modeling,compared with the sepsis group,the expression level of Bax protein in myocardial tissue of the sep-sis+NRG group was decreased,while the p-Akt,p-GSK3β expression levels were increased(P<0.05).The pathological results showed that compared with the sham operation group,the sepsis group produced signifi-cant lesions;compared with the sepsis group,the lesions in the sepsis+NRG group were alleviated.Conclusion The expression levels of related biomarkers in septic myocardial injury have change.NRG-1 could improve the cardiac function through Akt/GSK3β pathway,inhibit the related proinflammatory factors and reduce the myocardial tissue damage.
6.Clinical observation of areola approach endoscopic thyroidectomy and gasless axillary approach endoscopic thyroidectomy in the treatment of patients with papillary thyroid carcinoma
Hongyan SHEN ; Dandan HU ; Lei ZHAO ; Peiyou REN ; Guanlei ZHOU ; Zhen XU
Chinese Journal of Endocrine Surgery 2024;18(1):51-56
Objective:To explore the clinical efficacy of areola approach endoscopic thyroidectomy (AET) and gasless axillary approach endoscopic thyroidectomy (GAET) in the treatment of papillary thyroid carcinoma (PTC) patients.Methods:A total of 96 PTC patients from the Thyroid Surgery Department of Linyi People’s Hospital from May. 2019 to May. 2022 were selected and randomly divided into 48 patients using a random number table method. The areola group received AET, while the armpit group received GAET. The surgical situation, postoperative recovery, relevant biochemical indicators [white blood cell count (WBC), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), parathyroid hormone (PTH), blood calcium] before and after surgery, postoperative pain level, discomfort level, neck function, and complications were compared between the two groups.Results:The surgical time and extubation time of the armpit group were (125.71±15.73) minutes and (3.12±0.53) days, respectively, which were shorter than those of the areola group (137.94±20.02) minutes and (3.48±0.46) days. The intraoperative bleeding volume was (14.19±4.16) mL, which was less than that of the areola group (22.65±7.39) mL, and the number of lymph nodes cleaned was 5.06±1.02, which was more than that of the areola group (4.23±1.14) ( P<0.05) ; there was no significant difference in postoperative drainage volume and hospital stay between the two groups ( P>0.05) ; Peripheral blood WBC in the armpit group on the 1st and 3rd day after surgery [ (5.69±0.15) ×10 9/L, (5.52±0.14) ] ×10 9/L, ESR [ (8.21±0.55) mm/h, (7.64±0.60) mm/h], CRP [ (10.06±1.78) ng/L, (8.93±1.33) ng/L] were lower than those in the areola group [ (5.83±0.21) ×10 9/L, (5.70±0.23) ×10 9/L, (8.87±0.74) mm/h, (8.19±0.68) mm/h, (12.45±1.90) ng/L, (10.45±1.50) ng/L] ( P<0.05). There was no significant difference in the levels of the above biochemical indicators 5 days after surgery ( P>0.05). There was no significant difference in peripheral blood PTH and calcium levels between the two groups on the 1st, 3rd, and 5th postoperative days ( P>0.05). The pain level [ (3.25±0.32) scores, (2.53±0.27) scores, (1.82±0.22) scores] and discomfort level [ (6.85±0.71) scores, (5.24±0.66) scores, (3.51±0.57) scores] in the axillary group were lower than those in the areola group [ (3.78±0.40) scores, (2.89±0.34) scores, (2.06±0.26) scores, (7.46±0.84) scores, (6.09±0.73) scores, (4.16±0.60) scores] on the 1st, 3rd, and 5th postoperative days ( P<0.05). The neck flexion, lateral flexion, and extension range of motion in the axillary group on the 3rd day after surgery were (33.16±3.09) °, (27.63±2.57) °, and (30.44 2.73) °, respectively, which were greater than those in the areola group[ (30.08±2.76) °, (25.14±2.30) °, and (27.98±2.54) °], and the swallowing disorder index was (30.16±4.97) points lower than the (34.83±4.13) points in the areola group ( P<0.05). The incidence of complications in the axillary group was 4.17% (2/48), lower than the 16.67% (8/48) in the areola group. Conclusion:GAET treatment for PTC patients can improve the effect of lymph node dissection, reduce the degree of surgical trauma, postoperative pain and discomfort, accelerate early postoperative recovery of neck function, and reduce complications.
7.Cross-sectional study on working mode and human resource setting of PIVAS in national medical institutions
Ke LI ; Hongyan GU ; Dechun JIANG ; Lulu SUN ; Yingbo ZHAO
China Pharmacy 2024;35(18):2199-2202
OBJECTIVE To know about the working mode and human resource status of pharmacy intravenous admixture services (PIVAS) in national medical institutions. METHODS Through questionnaire survey, the national PIVAS was invited to fill out questionnaire and statistical analysis was performed on the effective sample data related to PIVAS working mode and human resources in the questionnaire. RESULTS In this study, 761 PIVAS from 722 medical institutions of 29 provinces were involved in the questionnaire survey, with 471 valid questionnaires for working mode and 441 valid questionnaires for human resources survey. In terms of working mode, among 471 PIVAS, 292 PIVAS (62.0%) were in pharmacist-alone mode, and 176 PIVAS (37.4%) were in pharmacist-nurse cooperative mode; there was no significant difference in the types of medical orders received by PIVAS between these two working modes except for the other medical orders (P>0.05). In terms of human resource setting, among 441 PIVAS, the average number of total staff of single PIVAS was 24(16,33), including 11(6,19) pharmacists, 7(2,13) nursing staff, and 3(1,5) workers; there was a statistically significant difference in the number of personnel among three groups (P< 0.01). The per capita income of PIVAS respondents in 2019 was [7.9(4.8,10.7)]×104 yuan, and in 2021 it was [8.8(5.8,11.7)]× 104 yuan, with an increase of 9.0% compared to 2019. The difference between the two groups was statistically significant (P< 0.01). CONCLUSIONS Medical institutions’ PIVAS in China had not fully implemented the pharmacist-alone work model, and some medical institutions had chosen a pharmacist-nurse cooperative mode. It is suggested that relevant departments formulate corresponding qualification requirements and training standards for nursing personnel as soon as possible based on sufficient research on PIVAS’s demand for nursing professionals.
8.Cross-sectional study on balance of payments in PIVAS of medical institutions nationwide
Ke LI ; Hongyan GU ; Dechun JIANG ; Lulu SUN ; Yingbo ZHAO
China Pharmacy 2024;35(20):2449-2452
OBJECTIVE To know about the pharmacy intravenous admixture charge and operation balance of pharmacy intravenous admixture services (PIVAS) in national medical institutions. METHODS Using questionnaire survey method, the national PIVAS leaders were invited to fill in the questionnaire, investigation and statistical analysis of the drug dispensing charge standard and the income and expenditure situations of PIVAS nationwide were conducted. RESULTS A total of 761 PIVAS completed the questionnaire, among which 466 PIVAS (61.2%) had already started implementing pharmacy intravenous admixture charge, mainly in tertiary hospitals. The charge standards for chemotherapy drugs and parenteral nutrition solutions were relatively high, while the standards for packaged drugs were the lowest, with differences in charge standards among provinces(P<0.05). Among the 25 provinces that reported annual drug preparation fee revenue, Hubei had the highest revenue in both 2019 and 2021. In 2019, the number of PIVAS with a balance of payments was more than that of PIVAS with an imbalance of payments, but the number of PIVAS with an imbalance of payments in 2021 exceeded the number of PIVAS with a balance of payments (P<0.05); among them, eight provinces were unbalanced in 2019 and 2021, such as Tianjin, Chongqing, Guizhou, etc. CONCLUSIONS PIVAS charge standards of the surveyed medical institutions in all provinces are not unified. It is suggested to improve the charge standard further, formulate the charge adjustment cycle, and promote a sustainable development of PIVAS.
9.Research Ideas on Human Experience in Medical Cases of Classic Formulas Based on Evidence-Based Concept
Hongyan CUI ; Mingyi SHAO ; Ruixia ZHAO ; Rongrong ZHANG ; Lanqing LYU ; Yuxuan FANG
Journal of Traditional Chinese Medicine 2024;65(22):2310-2315
The amount of data generated by the human experience in medical cases of classic formulas is large and the research value is high, but how to extract valuable information from these massive data is an important problem of researches on classical formulas. It is concluded that there are many problems in the current study of human experience in classical formulas, such as large amount of data, uneven quality, weak extrapolation and clinical application, which seriously affected the evidence strength of human experience in classical formulas and the contribution to experience accumulation and theoretical support. Therefore, from the structural perspective of the research questions, this paper proposed the research ideas of human experience in medical cases of classic formulas: firstly, according to the characteristics of traditional Chinese medicine (TCM) cases, based on the PICO model, which refers parti-cipants (P), intervention (I), comparisons (C), and outcomes (O), a TCM medical record evaluation tool in line with the evidence-based concept was constructed to evaluate the quality of medical cases; secondly, constructing a standardized database of human experience in classical formulas and using data mining algorithms to explore the deep relationship hidden in human experience; finally, the clinical value evaluation is carried out to verify the effectiveness of the diagnosis and treatment rules of classical formulas to achieve clinical transformation.
10.Association between the risk of increase in total cholesterol and the risk of cholelithiasis: A bidirectional Mendelian randomization study
Weiwei ZHAO ; Xiaoxu DU ; Hongyan GE
Journal of Clinical Hepatology 2024;40(3):573-580
ObjectiveTo investigate the association between the risk of increase in total cholesterol (TC) and the risk of cholelithiasis by using bidirectional Mendelian randomization (MR). MethodsThe open gwas public database was used to obtain the single nucleotide polymorphism data associated with TC and cholelithiasis, and a secondary data analysis was performed for all summary data of genome-wide association studies. The genetic loci closely associated with TC or cholelithiasis were selected as exposure or outcome variables, and the bidirectional MR analysis was performed using the methods such as Egger regression, Weighted median, IVW random effects model, and IVW fixed effects model, with odds ratio (OR) values for evaluating the causal relationship between TC and cholelithiasis. ResultsWith TC as the exposure and cholelithiasis as the outcome, TC-cholelithiasis had an overall OR value of 0.91 (95% confidence interval [CI]: 0.85 — 0.97) before elimination of heterogeneity and 0.93 (95%CI: 0.89 — 0.97) after elimination of heterogeneity. With cholelithiasis as the exposure and TC as the outcome, TC-cholelithiasis had an overall OR value of 0.20 (95%CI: 0.06 — 0.65) before elimination of heterogeneity and 0.28 (95%CI: 0.10 — 0.83) after elimination of heterogeneity. There was a bidirectional causal relationship between genetically predicted TC and cholelithiasis. ConclusionThis study confirms the bidirectional causal relationship between TC and cholelithiasis. The risk of cholelithiasis decreases with the increase in alleles associated with the elevation of TC level; on the contrary, the risk of elevated TC level decreases with the increase in alleles associated with the onset of cholelithiasis.

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