1.EvoNB:A protein language model-based workflow for nanobody mutation prediction and optimization
Danyang XIONG ; Yongfan MING ; Yuting LI ; Shuhan LI ; Kexin CHEN ; Jinfeng LIU ; Lili DUAN ; Honglin LI ; Min LI ; Xiao HE
Journal of Pharmaceutical Analysis 2025;15(6):1334-1343
The identification and optimization of mutations in nanobodies are crucial for enhancing their thera-peutic potential in disease prevention and control.However,this process is often complex and time-consuming,which limit its widespread application in practice.In this study,we developed a work-flow,named Evolutionary-Nanobody(EvoNB),to predict key mutation sites of nanobodies by combining protein language models(PLMs)and molecular dynamic(MD)simulations.By fine-tuning the ESM2 model on a large-scale nanobody dataset,the ability of EvoNB to capture specific sequence features of nanobodies was significantly enhanced.The fine-tuned EvoNB model demonstrated higher predictive accuracy in the conserved framework and highly variable complementarity-determining regions of nanobodies.Additionally,we selected four widely representative nanobody-antigen complexes to verify the predicted effects of mutations.MD simulations analyzed the energy changes caused by these mu-tations to predict their impact on binding affinity to the targets.The results showed that multiple mu-tations screened by EvoNB significantly enhanced the binding affinity between nanobody and its target,further validating the potential of this workflow for designing and optimizing nanobody mutations.Additionally,sequence-based predictions are generally less dependent on structural absence,allowing them to be more easily integrated with tools for structural predictions,such as AlphaFold 3.Through mutation prediction and systematic analysis of key sites,we can quickly predict the most promising variants for experimental validation without relying on traditional evolutionary or selection processes.The EvoNB workflow provides an effective tool for the rapid optimization of nanobodies and facilitates the application of PLMs in the biomedical field.
2.Relationship of miR-155,miR-92a and miR-126 with restenosis after interventional surgery in elderly CHD patients
Jianhua LIU ; Shixun LI ; Weiqiang ZHANG ; Shuhan YANG
Chinese Journal of Geriatric Heart Brain and Vessel Diseases 2025;27(7):885-889
Objective To explore the relationship of microRNA(miR)-155,miR-92a and miR-126 with in-stent restenosis(ISR)after percutaneous coronary intervention(PCI)in elderly patients with coronary heart disease(CHD).Methods A total of 118 elderly CHD patients receiving PCI in our hospital from January 2021 to June 2023 were enrolled,and according to whether ISR occurred by coronary angiography(CAG)at 1 year after surgery,they were divided into a stenosis group(45 cases)and a non-stenosis group(73 cases).Their baseline data,number of stent,stent diameter,medication,coronary artery lesion score,and serum expression levels of miR-155,miR-92a and miR-126 were compared between the two groups.The correlation of expression levels of the three miRNAs and clinical indicators was analyzed.Multivariate logistic regression analysis was performed to identify the risk factors of ISR in elderly CHD patients.ROC curve was adopted to analyze the diagnostic value of the three miRNAs for ISR in the elderly patients.Results Signifi-cantly higher BMI,SBP and DBP,and larger proportions of stent count ≥3 and stent diameter<3 mm were observed in the stenosis group than the non-stenosis group(P<0.05,P<0.01).The expression levels of miR-155 and miR-126 were obviously lower,while that of miR-92a was nota-bly higher in the stenosis group than the non-stenosis group(P<0.01).Pearson correlation analy-sis showed that miR-155 and miR-126 were negatively correlated with BMI,SBP,DBP,and stent count,and positively correlated with stent diameter(P<0.01);miR-92a was positively correlated with BMI,SBP,DBP,and stent count,and negatively with stent diameter(P<0.01).Multivariate logistic regression analysis suggested that stent count,stent diameter and miR-92a were risk fac-tors for ISR in elderly CHD patients after PCI,and miR-155 and miR-126 were protective factors(P<0.05,P<0.01).ROC curve analysis revealed that the AUC value of miR-155,miR-92a,and miR-126 alone and combined together was 0.742,0.778,0.751 and 0.853,respectively,with a sen-sitivity of 86.67%,71.11%,73.33%and 93.33%respectively,and the combined detection showed better diagnostic value for ISR than the single detection(P<0.01).Conclusion Down-regulation of miR-155 and miR-126 and up-regulation of miR-92a may be involved in the occurrence of ISR in elderly CHD patients after PCI.Monitoring the three miRNAs is beneficial to auxiliary clinical prediction for ISR after PCI.
3.Effect of Lianpu Yin on Improvement of Duodenal Microinflammation in FD Rats and Its Mechanism via NLRP3 Activation
Yang ZHANG ; Wenliang LYU ; Shuhan ZHOU ; Ningfeng MAO ; Jiawei HE ; Yi ZHAO ; Zixuan XU ; Linlin LIU ; Xueyan WANG
World Science and Technology-Modernization of Traditional Chinese Medicine 2025;27(6):1693-1698
Objective To investigate the effect of Lianpu Yin on duodenal microinflammation in rats with functional dyspepsia(FD)by regulating NLRP3 activation.Methods Wistar rats were randomly divided into blank group and model group.FD rats were reconstructed by iodoacetamide method(2%sucrose solution containing 0.1%iodoacetamide),and the model was verified.FD model rats were randomly divided into model group,Lianpu Yin group and Moxapride group by random number expression method.After a period of two weeks of administration,measurements were taken to determine the body mass,three-hour food consumption,as well as the rates of gastric emptying and intestinal propulsion.The pathological structure of duodenal tissue was observed by HE staining.The serum levels of IL-1β and IL-18 were quantified using the enzyme-linked immunosorbent assay(ELISA)method.The expression levels of NLRP3 and Caspase-1 in each group were detected by Western blot.Expression levels of NLRP3 and Caspase-1 proteins were detected by immunofluorescence.Results Compared with the blank group,body weight,food intake at 3 h,gastric emptyand intestinal propulsion rate in model group were significantly decreased(P<0.01),and inflammatory infiltration of duodenum tissue appeared in the model group.Meanwhile,the expressions of NLRP3 and Caspase-1 proteins,as well as the levels of IL-1β and IL-18 in the duodenal tissue of the model group,showed significant increasing(P<0.05).Compared with the model group,rats in the Lianpu Yin and Moxapride groups displayed significant increasing in body weight,gastric emptying rate,and intestinal propulsion rate(P<0.01).Additionally,inflammatory infiltration of duodenum tissue reduced in these groups.Furthermore,NLRP3 and Caspase-1 protein expressions,as well as IL-1β and IL-18 levels,significantly decreased in the Lianpu Yin and Moxapride groups compared to the model group(P<0.05).Conclusion Lianpu Yin can treat FD rats by inhibiting duodenal microinflammation and then restoring gastrointestinal motility,which may be related to the abnormal activation of NLRP3 inflammasome.
4.Risk factors for recurrent intracerebral hemorrhage
Xinyue YANG ; Shuhan LIU ; Shaojun WANG
International Journal of Cerebrovascular Diseases 2025;33(1):52-58
Spontaneous intracerebral hemorrhage (ICH) is the second common subtype of stroke, characterized by high incidence, high mortality and high disability rates. The recurrent ICH not only brings physical pain to patients, but also increases the burden on families and society. In recent years, researches on the risk factors for recurrent ICH have been increasing day by day. This article reviews the risk factors for recurrent ICH from the perspectives of clinical features, biomarkers, and imaging characteristics, in order to provide a basis for the secondary prevention of ICH.
5.Cerebral autoregulation in cerebral small vessel disease
Furong LI ; Ya'nan ZHANG ; Shuhan LIU ; Weiwei DONG ; Xiaowen SUI ; Xin PAN ; Hongling ZHAO
International Journal of Cerebrovascular Diseases 2025;33(5):383-386
Cerebral blood flow directly affects the metabolism of substances and neural activity in the brain, and is closely associated with the occurrence and development of cerebral small vessel disease (CSVD). Multiple studies have revealed that various imaging biomarkers in patients with CSVD, such as lacunar infarction, enlarged perivascular spaces, cerebral microbleeds, cerebral atrophy, and white matter hyperintensities, are closely associated with cerebral autoregulation (CA) function. Therefore, understanding the regulatory mechanism of CA in patients with CSVD is of great significance for delaying the further development of CSVD, improving cerebral ischemia and cognitive impairment. This article reviews the correlation and mechanism between CA and CSVD.
6.Design and application of a pressure ulcer prevention nursing device for critically ill patients
Jing LI ; Yan YUE ; Shuhan TU ; Mengling XIANG ; Min DENG ; Jing LIU ; Guojin XIAO
Chinese Journal of Integrated Traditional and Western Medicine in Intensive and Critical Care 2025;32(3):361-363
Pressure ulcer is a common complication of long-term bed rest in intensive care unit(ICU)patients,which can increase the risk of infection and prolong ICU hospitalization.They are an important indicator of patient safety and nursing quality in medical institutions.Early prevention of pressure ulcer is an important means of controlling their development.At present,the prevention of pressure ulcer mainly involves timed flipping and the use of pressure reducing devices.However,during the flipping process,it often requires two or more nursing staff to complete,which increases the workload and also exacerbates the occurrence of occupational lower back pain among nursing staff.In addition,existing pressure reducing devices still have certain limitations in use,and their functions are single,often requiring the combination of multiple tools to increase material and financial resources.Based on this,the research team from the department of critical care medicine of Hospital of Chengdu University of Traditional Chinese Medicine,has designed a nursing device for preventing pressure ulcer in critically ill patients,and has obtained a National Utility Model Patent of China(Patent Number:ZL 202320609787.6).It has several inflation components and connecting structures.The inflation components are equipped with a connected air inlet,a connected air outlet,and a discharge port on the side;the inflatable components are fitted together and can be detachably connected through a connecting structure.The connected air inlet of one inflatable component corresponds to the connected air outlet of adjacent inflatable components.This device is connected by multiple inflation components,which lower or raise the height of the airbag through inflation and deflation,adjust the pressure on various parts of the patient's body,and solve the problem of labor-intensive and heavy workload in nursing work;In addition,multiple inflatable components can be detachably connected to form an inflatable mattress.When in use,the number of inflatable component connections can be selected according to the specific needs of different patients or nursing areas.The device is easy to operate,flexible in combination,and suitable for timed flipping pressure reduction regulation in pressure ulcer high-risk areas under various postures.It has good clinical application value.
7.Expert consensus on visualized tele-round and quality control management based on the improvement of clinical practice ability
Wanhong YIN ; Xiaoting WANG ; Ran ZHOU ; Dawei LIU ; Yan KANG ; Yaoqing TANG ; Xiaochun MA ; Jianguo LI ; Zhenjie HU ; Haitao ZHANG ; Wei HE ; Lixia LIU ; Wenjin CHEN ; Ran ZHU ; Jun WU ; Hongmin ZHANG ; Lina ZHANG ; Wenzhao CHAI ; Shihong ZHU ; Wangbin XU ; Rongqing SUN ; Xiangyou YU ; Tianjiao SONG ; Ying ZHU ; Hong REN ; Ai SHANMU ; Qing ZHANG ; Wei FANG ; Xiuling SHANG ; Liwen LYU ; Shuhan CAI ; Xin DING ; Heng ZHANG ; Guang FENG ; Lipeng ZHANG ; Bo HU ; Dong ZHANG ; Weidong WU ; Feng SHEN ; Xiaojun YANG ; Zhenguo ZENG ; Qibing HUANG ; Xueying ZENG ; Tongjuan ZOU ; Milin PENG ; Yulong YAO ; Mingming CHEN ; Hui LIAN ; Jingmei WANG ; Yong LI ; Feng QU ; Gang YE ; Rongli YANG ; Xiukai CHEN ; Suwei LI ; Juxiang WANG ; Yangong CHAO
Chinese Journal of Internal Medicine 2025;64(2):101-109
Turning to critical illness is a common stage of various diseases and injuries before death. Patients usually have complex health conditions, while the treatment process involves a wide range of content, along with high requirements for doctor′s professionalism and multi-specialty teamwork, as well as a great demand for time-sensitive treatments. However, this is not matched with critical care professionals and the current state of medical care in China. Telemedicine, which shortens the distance of medical professionals and the gap of disease diagnosis and treatments in various regions through electronic information, can effectively solve the current problem. Therefore, there is an urgent need to develop a standardized, high-quality visualization telemedicine round system .Therefore, experts have been organized to search domestic and foreign literature on telemedicine round for critically ill patients and to form this consensus based on clinical experiences so as to further improve the level of critical care treatments in regions.
8.Sputum metabolomics study in patients with occupational coal workers′ pneumoconiosis
Yiming ZHANG ; Qiufang QU ; Qingnan ZHOU ; Shuhan GUO ; Le LIU ; Yuke WANG ; Zhenlin HE ; Sanqiao YAO
China Occupational Medicine 2025;52(3):241-248
Objective To investigate the sputum metabolic profiles of patients with occupational coal workers' pneumoconiosis (CWP) by an untargeted metabolomics method, and to identify relevant differential metabolic pathways and potential biomarkers. Methods A total of 12 male patients with stage Ⅰ CWP were selected as the CWP group, and 16 healthy male individuals were selected as the control group, using a judgmental sampling method. Sputum metabolites of individuals in both groups were detected to perform non-targeted metabolomic analysis using the ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Differential metabolites (DMs) and their pathways were screened using principal component analysis, partial least squares discriminant analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Potential biomarkers were analyzed and identified via the receiver operating characteristic curve (ROC). Results There were apparent metabolic alterations observed in sputum of CWP patients compared with healthy controls. In the positive ion mode, a total of 42 DMs were identified in sputum from CWP patients, including 19 downregulated and 23 upregulated metabolites. In the negative ion mode, a total of 25 DMs were identified in sputum from CWP patients, including 16 downregulated and 9 upregulated metabolites. KEGG enrichment analysis of sputum from CWP patients showed that seven DMs pathways were enriched in ABC transporters, histidine metabolism, phenylalanine metabolism, arachidonic acid metabolism, linoleic acid metabolism, purine metabolism, and oxidative phosphorylation, involving 26 DMs. ROC analysis indicated that 16(R)-hydroxyarachidonic acid, pyrophosphate, and 2-hydroxyphenylacetate of these 26 DMs may serve as potential biomarkers for CWP. Conclusion Sputum metabolomic profiles were altered in CWP patients compared with healthy controls. The potential biomarkers of CWP prevention and treatment are 16(R)-hydroxyarachidonic acid, pyrophosphate, and 2-hydroxyphenylacetate.
9.The role and mechanism of calcium-binding protein S100A9 in acute lung injury induced by hepatic ischemia-reperfusion in mice
Yingli CAO ; Mingwei SHENG ; Chen ZHANG ; Shuhan HUO ; Wenna LIU ; Hongyin DU ; Wenli YU
Chinese Journal of Organ Transplantation 2025;46(5):382-388
Objective:To investigate the role of calcium-binding protein S100A9 in acute lung injury induced by hepatic ischemia-reperfusion (HIR) in mice, and to explore its relationship with nuclear factor erythroid 2-related factor 2 (Nrf2).Methods:A total of 12 specific pathogen-free (SPF) male wild-type (WT) and 12 S100A9 knockout (S100A9 KO) C57BL/6J mice aged 6~8 weeks and weighing 20-25 g were randomly divided into four groups using a random number table: WT+Sham group, S100A9 KO+Sham group, WT+HIR group, and S100A9 KO+HIR group ( n=6 per group). The HIR model was established by clamping the portal vein and hepatic artery of the left and median liver lobes for 60 minutes followed by reperfusion. At 6 hours post-reperfusion, mice were anesthetized again, and blood samples were collected from the inferior vena cava. Both lungs were harvested. The lung wet-to-dry (W/D) weight ratio was measured. Hematoxylin and eosin (HE) staining was used to assess histopathological changes and calculate lung injury scores. The levels of inflammatory markers—S100A9, tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) —as well as oxidative stress indicators including myeloperoxidase (MPO), reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD) in serum and lung tissue were measured. Western blotting was used to assess the expression levels of nuclear and cytoplasmic Nrf2, and cytoplasmic HO-1. Results:Compared with the WT+Sham group, both the WT+HIR and S100A9 KO+HIR groups showed significantly increased lung injury scores, W/D ratio, TNF-α, IL-6, ROS, MPO, and MDA levels (all P<0.05). Compared with the WT+HIR group, the S100A9 KO+HIR group exhibited significantly reduced levels of these indicators (all P<0.05). Moreover, the S100A9 KO+HIR group showed elevated nuclear Nrf2 expression and decreased cytoplasmic Nrf2 expression, accompanied by increased expression of HO-1, Gclm, Gclc, and Nqo1 (all P<0.05). Conclusion:Upregulation of S100A9 is involved in the development of HIR-induced acute lung injury, possibly through inhibition of Nrf2 nuclear translocation.
10.Analysis of medium-term efficacy of single anastomosis sleeve ileal bypass for gastroesophageal reflux after laparoscopic sleeve gastrectomy
Xiaohan WEI ; Zhen REN ; Shuhan WANG ; Hu LIU ; Chen PAN ; Lisheng WU
Chinese Journal of General Surgery 2025;40(6):451-456
Objective:To evaluate the mid-term efficacy of sleeve gastrectomy combined with single anastomosis gastric-ileal bypass (SASI) for treating gastroesophageal reflux disease (GERD) after laparoscopic sleeve gastrectomy (LSG).Methods:Clinical data of 10 patients with post-LSG GERD undergoing SASI at the Department of Hernia and Bariatric Surgery, the First Affiliated Hospital of University of Science and Technology of China between Jan 2022 and Oct 2024 was retrospectively analyzed. Surgical safety and mid-term outcomes were evaluated.Results:The mean follow-up period was (25.40±17.33) months. The GerdQ score significantly decreased from (14.00±2.05) preoperatively to (5.70±1.49) postoperatively ( t=10.330, P<0.001), with a GERD remission rate of 90 % (9/10). Postoperative body weight and body mass index (BMI) both showed statistically significant reductions compared to preoperative values. Weight dropped from (110.29±22.92) kg to (84.95±15.89) kg ( t=5.889, P<0.001), and BMI decreased from (38.98±7.16) kg/m2 to (30.02±4.88) kg/m2 ( t=6.086, P<0.001). The percentage of excess weight loss was 65.88%±32.85%, and the percentage of total weight loss was 22.43%±9.65%. Only one patient experienced transient postoperative diarrhea, which resolved spontaneously, and no severe malnutrition cases were observed. Conclusion:SASI effectively improves GERD symptoms after LSG with favorable safety, serving as a suitable revisional surgical option for those patients.

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