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):101260-101260
The identification and optimization of mutations in nanobodies are crucial for enhancing their therapeutic 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 workflow, 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 mutations to predict their impact on binding affinity to the targets. The results showed that multiple mutations 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.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.
3.Construction and evaluation of a training program for health management specialist nurses
Xiaotao XU ; Hua GUAN ; Li XIAO ; Lili TU ; Xiaojuan YANG ; Qing WEN ; Xiaoqian LI
Chinese Journal of Health Management 2025;19(2):119-126
Objective:To construct and evaluate a training program for health management specialist nurses.Methods:Mainly qualitative analysis, The training system of health management specialist nurses was preliminarily drawn up based on literature review and semi-structured interview. The Delphi expert consultation method was used to conduct a two-round expert letter inquiry with 17 experts in the professions such as health management medicine, health management nursing, nursing management, and nursing education; and the analytic hierarchy process was applied to determine the weights of the indicators.Results:The effective recall rates of the questionnaires for the 2 rounds of expert consultation was 94.44%(17/18) and 100%(17/17), with expert authority coefficients of 0.90 and 0.92 and Kendall harmony coefficients of 0.207 and 0.249, respectively (all P<0.001). The training system of health management specialist nurses included 4 parts: training objective, training content, training management, training assessment and evaluation. There were 8 indicators in the training objective part. There were 5 first-level indicators, 15 second-level and 67 third-level indicators in the training content part. There were 5 first-level indicators, 12 second-level indicators in the training management part. There were 3 first-level indicators, 10 second-level indicators in the training assessment and evaluation part. Conclusion:The training program for specialized nurses in health management developed in this study demonstrates high levels of expert enthusiasm, authority, and consensus, indicating its feasibility.
4.Impact factors and reference range upper limit of thyroid volume in children aged 8-10 years old in Huangpu District, Shanghai
Weihua CHEN ; Chengdi SHAN ; Lili SONG ; Lifang MA ; Yun CAO ; Youshun QIAN ; Aina HE ; Jun XIAO
Journal of Environmental and Occupational Medicine 2025;42(2):205-210
Background As one of the key populations in the prevention and treatment of iodine deficiency disorders, it is important to continuously monitor the iodine nutritional level of school-age children. The current reference interval for thyroid volume in China is based on age only, without taking into account differences in individual developmental levels, and the distribution of thyroid volume may vary regionally due to economic, demographic, and environmental factors. The current reference cut-off points for thyroid volume proposed by the World Health Organization are not based on the Chinese population. Objective To understand the iodine nutritional status and distribution of thyroid volume (Tvol) among children aged 8-10 years in Huangpu District, Shanghai, China, to identify impact factors of Tvol, and to propose a reference range upper limit for local thyroid health surveillance, so as to provide a basis for goiter control and prevention. Methods Six hundred children aged 8-10 years in Huangpu District were recruited in 2017, 2020, and 2023, and body height, weight, thyroid volume, urinary iodine, and iodine content of household edible salt were determined. A multilevel model was constructed using population density and area as regional variables, and age, body surface area (BSA), and body mass index (BMI) as potential impact factors for at the individual level, to assess their effects on thyroid volume. Quantile regression of thyroid volume was performed, and the 98th percentile (P98) of thyroid volume was predicted based on age and BSA. Results The iodized salt coverage in the households of surveyed children in 2017, 2020, and 2023 was 72.0%, 57.0%, and 48.0%, respectively, and the iodized salt coverage decreased by year (χ2=24.31, P<0.001). The urinary iodine level of children in 2017 was higher than that in 2020 and 2023 (χ2=18.77, P<0.001). The Tvol medians of children in 2017, 2020, and 2023 were 2.29, 2.49, and 2.97 mL, respectively, and the Tvol increased by year (χ2=60.04, P<0.001). The proportion of goiter was higher in children in 2023 than in 2017 and 2020 (χ2=6.57, P<0.05). Sex differences were not statistically significant for urinary iodine levels, thyroid volume, and goiter. The median Tvol was 2.26, 2.58, and 2.76 mL in children of 8, 9, and 10 years old respectively, and the Tvol increased with age (χ2=49.02, P <0.001). Tvol was positively correlated with age, BSA, and BMI with correlation coefficients of
5.Growth and Development of Atractylodes chinensis and Microecological Response of Cultivated Soil Mediated by Two Microbial Fertilizers
Xuewei LIU ; Chunping XIAO ; Lili WENG ; Zhaoyang LI ; Xinxing HU ; Bo LIU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(18):157-165
ObjectiveThe effects of two microbial fertilizers (Bacillus subtilis fertilizer and Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer) on the growth and development, the accumulation of active ingredients, and the microbial community diversity of rhizosphere soil of Atractylodes chinensis were investigated. MethodsA field experiment was carried out with two-year-old Atractylodes chinensis as the test material. Plant samples were collected during the wilt stage (September 26, 2023) to determine the general agronomic traits of Atractylodes chinensis. High-performance liquid chromatography (HPLC) was utilized to evaluate the effects of microbial fertilizers on the synthesis and accumulation of four active ingredients (atractylodin, atractylon, β-eudesmol, and atractylenolide Ⅰ) in Atractylodes chinensi. PacBio Sequel sequencing technology was used to explore the differences in bacterial community structures and diversity in the rhizosphere soil of Atractylodes chinensis treated with different microbial fertilizers. ResultsThe two microbial fertilizers had significant growth-promoting effects on Atractylodes chinensis. Compared with those of the CK group, the stem diameter, stem and leaf dry and fresh weight, and rhizome dry and fresh weight of Atractylodes chinensis significantly increased by 0.47-1.07 times (P<0.05) after the application of the Bacillus subtilis fertilizer (16 kg/667 m2), and those significantly increased by 0.62-0.96 times (P<0.05) after the application of the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer (1.5 kg/667 m2). The effect on plant height was not significant. The application of two microbial fertilizers was beneficial to the accumulation of atractylodin, atractylon, β-eudesmol, and atractylenolide Ⅰ (P<0.01), and the effect of the Bacillus subtilis fertilizer on the accumulation of active ingredients of Atractylodes chinensis was better than that of the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer. The results of high-throughput sequencing showed that compared with the CK group, the Bacillus subtilis fertilizer (8 kg/667 m2) could significantly increase the diversity of rhizosphere bacterial species by regulating the Simpson index and Shannon index (P<0.05), and the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer significantly reduced the bacterial diversity (P<0.05). The relative abundance of dominant bacteria was compared at the phylum and genus levels. The relative abundance of Proteobacteria (45.73%) and Burkholderia_Caballeronia_Paraburkholderia (9.98%) significantly increased after the application of the Bacillus subtilis fertilizer (P<0.01), and the relative abundance of Acidobacteriota (20.53%) and Sphingomonas (3.63%) increased significantly (P<0.01) after the application of the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer. The relative abundance of beneficial bacteria in the Bacillus subtilis fertilizer was slightly higher than that in the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer. Pearson correlation analysis showed that Burkholderia_Caballeronia_Paraburkholderia and Sphingomonas were positively correlated with the content of atractylodin, atractylon, β-eudesmol, and atractylenolide Ⅰ (P<0.05). ConclusionThe application of the Bacillus subtilis fertilizer and Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer can increase the yield of medicinal materials and promote the synthesis and accumulation of active ingredients by regulating the rhizosphere microecological diversity of Atractylodes chinensis, and the application effect of the Bacillus subtilis fertilizer is better than that of the Trichoderma harzianum-Purpureocillium lilacinum compound fertilizer.
6.Epidemiological characteristics of positive nucleic acid test results of the discharged re-positive cases infected with SARS-CoV-2 in Pudong New Area, Shanghai
Yanxin XIE ; Songqing GUO ; Lili FENG ; Chuchu YE ; Shaotan XIAO ; Lipeng HAO ; Dan LIU
Shanghai Journal of Preventive Medicine 2025;37(3):222-226
ObjectiveTo obtain the epidemiological characteristics of re-positive cases infected with SARS-CoV-2 in Pudong New Area from March to July 2022, including clinical manifestations, duration of a negative nucleic acid conversion after tested for re-positive, and length of time from the discharge of the initial infection to the most recent re-positivity, so as to provide a scientific basis for the prevention and control of COVID-19. MethodsA questionnaire survey was conducted among the re-positive cases infected with SARS-CoV-2 after discharged from hospital/quarantine facility in Pudong New Area, and descriptive epidemiological methods were used for characteristics analysis. ResultsA total of 2 422 re-positive cases met the inclusive and exclusive criteria, with males accounting for 61.02%. The age distribution mainly fell between 18 and <60 years old, accounting for 62.39%. Clinical manifestations were predominantly asymptomatic (72.15%), followed by cough (12.03%) and sore throat (6.58%). Among the stratified randomized sample of 416 individuals, there were statistically significant differences in symptoms (χ²=262.667, P<0.001), clinical typing (χ²=12.996, P=0.001), and duration of a negative nucleic acid conversion (χ²=142.578, P<0.001) between the initial positive and re-positive instances. Besides, statistically significant differences in symptoms (χ²=13.696, P=0.016) and self-perception of the severity of re-infection (χ²=7.923, P=0.048) between the initial and re-positive cases were observed by different genders. ConclusionAmong re-positive cases, males experienced milder symptoms compared to females, and the self-perception of symptoms during re-positivity is milder than that in the initial positive infection. The length of time for negative nucleic acid conversion during the initial positive period is shorter than that during the re-positive period.
7.An assessment model for efficacy of autologous CD19 chimeric antigen receptor T-cell therapy and relapse or refractory diffuse large B-cell lymphoma risk.
Bin XUE ; Yifan LIU ; Min ZHANG ; Gangfeng XIAO ; Xiu LUO ; Lili ZHOU ; Shiguang YE ; Yan LU ; Wenbin QIAN ; Li WANG ; Ping LI ; Aibin LIANG
Chinese Medical Journal 2025;138(1):108-110
8.Association between elevated blood pressure and increased pulse wave velocity in adolescents
ZHANG Xiao, WANG Yuedong, ZHAO Min, YANG Lili, XI Bo
Chinese Journal of School Health 2025;46(11):1653-1657
Objective:
To explore the association between blood pressure levels and brachial-ankle pulse wave velocity (baPWV) in adolescents, so as to provide a scientific basis for early prevention and control of cardiovascular disease.
Methods:
The study utilized data from the October to December 2023 survey conducted by of the Huantai Child Cardiovascular Health Cohort, which included 1 197 adolescents aged 12-17 years. According to the Reference of Screening for Elevated Blood Pressure among Children and Adolescents aged 7-18 years, participants were classified into normal, high normal, and elevated blood pressure groups. The baPWV elevation was defined as a baPWV value greater than or equal to the 90th percentile of the sex and age specific baPWV values in the study population. The association between elevated blood pressure and increased baPWV was assessed by binary Logistic regression models. Restricted cubic spline model was applied to evaluate the dose response curve of the relationship between blood pressure Z scores and increased baPWV.
Results:
Among adolescents, the prevalence of high normal and elevated blood pressure were 22.6% and 14.1%, respectively. The mean baPWV values were 918, 978 and 1 030 cm/s in the normal, high normal, and elevated blood pressure groups, respectively. The prevalence rates of elevated baPWV were 7.3%, 9.6% and 27.2% in these three groups correspondingly. Logistic regression analysis showed that, after adjusting for covariates, both high normal and elevated blood pressure were significantly associated with higher odds of increased baPWV[ OR(95%CI )=1.87(1.08-3.20) and 8.24(4.73-14.50), both P < 0.05]. Linear dose response associations were identified between systolic and diastolic blood pressure Z scores and increased baPWV ( P non linearity>0.05).
Conclusions
Elevated blood pressure in adolescents is positively associated with high baPWV. Greater emphasis should therefore be placed on blood pressure monitoring and health management during adolescence.
9.Therapeutic effect of compound kushen injection combined with fentanyl transdermal patch in the treatment of carcinoma pain
Jingjing ZHANG ; Lili XIAO ; Xinjie ZHANG
Tianjin Medical Journal 2025;53(3):317-320
Objective To observe the clinical efficacy of compound kushen injection combined with fentanyl transdermal patch for the treatment of final stage cancer pain.Methods A total of 100 patients with cancer pain were divided into 2 groups of 50 patients each according to the randomized numerical table method.The control group was treated with fentanyl transdermal patch only,and the observation group was treated with fentanyl transdermal patch combined with compound kushen injection.The KPS score,NRS score,pain relief rate after treatment,incidence of adverse reactions and effect on levels of inflammatory factors IL-6,IL-8 and CRP were compared between the two groups.Results The pain relief rate of the observation group was significantly better than that of the control group(P<0.05).After treatment,the KPS score of the observation group was higher than that of the control group(P<0.05),and the incidence of NRS score,IL-6,IL-8,CRP levels and gastrointestinal reactions were lower than those of the control group(P<0.05).There were no significant differences in the incidence of hepatic and renal damage,dizziness and somnolence between the two groups(P>0.05).Conclusion Compound kushen injection combined with fentanyl transdermal patch can effectively improve cancer pain,reduce the release of inflammatory factors,improve the patient quality of life,and the incidence of adverse reactions is low.
10.Antimicrobial resistance surveillance in the bacterial strains isolated from pediatric intensive care units in China:results from 2020 to 2022
Jing LIU ; Huiyuan YAN ; Gangfeng YAN ; Guoping LU ; Pan FU ; Chuanqing WANG ; Danqun JIN ; Wenjia TONG ; Chenyu ZHANG ; Jianli CHEN ; Yi LIN ; Jia LEI ; Yibing CHENG ; Qunqun ZHANG ; Kaijie GAO ; Yuanyuan CHEN ; Shufang XIAO ; Juan HE ; Li JIANG ; Huimin XU ; Yuxia LI ; Hanghai DING ; Hehe CHEN ; Yao ZHENG ; Qunying CHEN ; Ying WANG ; Hong REN ; Chenmei ZHANG ; Zhenjie CHEN ; Mingming ZHOU ; Yucai ZHANG ; Yiping ZHOU ; Zhenjiang BAI ; Saihu HUANG ; Lili HUANG ; Weiguo YANG ; Weike MA ; Qing MENG ; Pengwei ZHU ; Yong LI ; Yan XU ; Yi WANG ; Yanqiang DU ; Huijun CAI ; Bizhen ZHU ; Huixuan SHI ; Shaoxian HONG ; Yukun HUANG ; Meilian HUANG
Chinese Journal of Infection and Chemotherapy 2025;25(3):303-311
Objective This study aimed to investigate the antimicrobial resistance profiles of bacterial strains isolated from pediatric intensive care units(PICU)in China for better antimicrobial therapy.Methods Clinical isolates were collected from 17 institutions,including tertiary care children's hospitals and pediatric department of tertiary general hospitals in China from January 1,2020 to December 31,2022.Antimicrobial susceptibility testing was carried out according to a unified protocol using Kirby-Bauer method or automated systems.Results were interpreted according to the breakpoints released by the Clinical and Laboratory Standards Institute(CLSI)in 2020.Results A total of 10 688 isolates were collected,including gram-positive organisms(39.2%)and gram-negative organisms(60.8%).The top three organisms were S.aureus(13.6%,1 453/10 688),A.baumannii(10.0%,1 067/10 688),and coagulase-negative Staphylococcus(9.9%,1 058/10 688).Multi-drug resistant organisms(MDROs)were very common in children.The prevalence of methicillin-resistant Staphylococcus aureus(MRSA),carbapenem-resistant Enterobacterales(CRE),carbapenem-resistant E.coli,carbapenem-resistant K.pneumoniae(CRKP),carbapenem-resistant A.baumannii(CRAB),and carbapenem-resistant P.aeruginosa(CRPA)was 41.1%,19.4%,8.8%,30.9%,67.4%,and 28.8%,respectively.Overall,more than 50%of Enterobacteriales isolates were resistant to cephalosporins,while nearly 25%of Enterobacteriales isolates were resistant to carbapenems.MDROs were highly resistant to commonly used antibiotics.More than 80%of CRE and CRAB strains were resistant to all beta-lactam antibiotics.CRE and CRAB showed low resistance rates to tigecycline and polymyxin.CRPA showed lower resistance rates to piperacillin,beta-lactamase inhibitor combinations than the resistance rates to third and fourth generation cephalosporins.All of the Staphylococcus and Enterococcus isolates were susceptible to vancomycin and tigecycline.None of PRSP strains isolated from meningitis and nonmeningitis samples were resistant to rifampicin,vancomycin,or linezolid.The prevalence of β-lactamase-negative ampicillin-resistant(BLNAR)strains was 43.3%in Haemophilus influenzae.Conclusions MDROs were prevalent in PICU.It is necessary to establish an effective multidisciplinary team(MDT)to control the antimicrobial resistance.


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