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.Application of cochlear microphonics combined with otoacoustic emission in early differential and localization diagnosis of auditory neuropathy
Yuhan CHEN ; Hongyang WANG ; Danyang LI ; Ziyi CHEN ; Tao SHI ; Wei SHI ; Lan LAN ; Qiuju WANG
Chinese Journal of Otorhinolaryngology Head and Neck Surgery 2025;60(9):1163-1171
Objective:The purpose of this study was to investigate the diagnostic value and clinical significance of cochlear microphonics (CM) combined with otoacoustic emission (OAE) in patients with auditory neuropathy (AN).Methods:The study included patients who were diagnosed with bilateral AN and had CM originating from both sides. The CM amplitude, latency, duration and intensity-amplitude (I/O) function curve were recorded by CM test. According to whether the distortion product otoacoustic emissions (DPOAE) passed through, the patients were divided into three groups: bilateral OAE passed group (OAE PP Group), bilateral OAE failed group (OAE RR Group), and unilateral OAE passed through one side failed group (OAE PR Group). OAE was elicited by four or more frequencies of 750-8 000 Hz. The characteristics of CM and its related influencing factors were analyzed, and data were processed and analyzed by SPSS 26.0 software. Results:(1) A total of 256 patients (512 ears) with AN were enrolled, including 161 patients (322 ears) in OAE PP group, 32 patients (64 ears) in OAE PR group and 63 patients (126 ears) in OAE RR group. OAE failed in 30.9% of patients with AN. (2) When the stimulation intensity was 100 dB nHL, the CM amplitude of OAE passing ear (OAE P+CM P group) in AN patients aged 3 years was 0.43±0.17μV, which was significantly higher than that of OAE not passing ear (OAE R+CM P group) (0.29±0.15) μV ( t=4.876, P<0.001). The CM duration of the OAE P+CM P group was (5.18±1.04) ms, which was longer than that of the OAE R+CM P group at 4.60±1.12 ms ( P=0.005). The I/O function curve of OAE P+CM P group showed a nonlinear trend, while, that of OAE R+CM P group showed a linear trend. (3) In the OAE P+CM P group of AN patients, the amplitude of CM was negatively correlated with the onset age, test age, disease course, PTA, and ASSR threshold ( P<0.001), with correlation coefficients of r=-0.475, r=-0.519, r=-0.367, r=-0.374, and r=-0.494, respectively. In the OAE R+CM P group of AN patients, the amplitude of CM was negatively correlated with the onset age, test age, and ASSR threshold ( P<0.05), with correlation coefficients of r=-0.271, r=-0.240, and r=-0.287, respectively. Conclusions:Excluding patients with high-frequency steeply sloping hearing loss, when ABR is absent or abnormal and OAE is absent, CM detection can reduce the rate of missed diagnosis of AN. The analysis of CM amplitude and I/O function curve is helpful to determine the lesion site of AN patients, which is convenient for early diagnosis and effective intervention.
3.Feasibility and efficacy of lingual mucosal replacement ureteral stricture repair and plasty for the treatment of polyps in long ureteral segments
Luyi WANG ; Jiawei WU ; Xiaoran LI ; Enguang YANG ; Danyang WANG ; Junsheng BAO
Chinese Journal of Urology 2025;46(2):114-118
Objective:To explore the feasibility and and clinical efficacy of lingual mucosa replacement ureteral stenosis repair and plasty for the treatment of long segment ureteral polyps.Methods:Clinical data of 3 patients (4 sides) with long-segment ureteral polyps admitted to the Second Hospital of Lanzhou University from October 2017 to October 2019 were retrospectively analyzed. Two cases were male and one case was female. The ages were22, 16, and 45 years old. Preoperative urologic ultrasound, CT urography and ureteroscopy were performed. The lesions were located on the left side in 3 cases and on the right side in 1 case; the stenosis was located in the middle and upper ureter; the length of the ureteral stenosis was 6, 7, 6, and 6 cm, respectively; and the preoperative blood creatinine was 72, 85, and 70 μmol/L, respectively. Three cases underwent ureteral stenosis repair and plasty with tongue mucosal substitution. During the operation, the ureter was fully exposed and longitudinally incised, polyps were removed, and 7.0-10.0 cm long and 1.5-2.0 cm wide lingual mucosa was harvested according to the length of the stenosis, and then the lingual mucosa was transplanted to the muscular layer and the inner surface of the sheath in the stenosed ureter, fixed with 6-0 thread until the muscular layer was rolled into shape and wrapped with a large omentum. All of them left one double-J tube in the ureter on the affected side. Perioperative results and complications were recorded. The patients' blood creatinine and anterior and posterior renal pelvic diameters were compared before and after treatment.Results:In our study, all three 4-sided surgeries were successfully completed without any serious intraoperative or postoperative complications (Clavien-Dindo score ≥ grade Ⅲ). Mean surgical. Time was (240.0±49.0) min, intraoperative bleeding was 50 ml, postoperative drain retention time was (6.3±2.5) d, and median postoperative hospitalization time was 6.5(3, 9)d. The double J-tube was removed at 3 months postoperatively, and renal function and imaging tests were reviewed. Because the postoperative follow-up results of patient 1 were missing, the mean value of blood creatinine in the other 2 patients was 73.0 μmol/L at 3 months postoperatively, which was significantly improved compared with the preoperative value of 58.2 μmol/L, and the difference was statistically significant ( P < 0.05). And the average value of anterior and posterior renal pelvic separation diameters of the other 2 patients after surgery was <5 mm, which was significantly improved compared with the preoperative value of 17.9 mm, but the difference was not statistically significant ( P>0.05).There was no restenosis in all 2 patients after surgery, and the intravenous urography showed that the ureter was patent after the surgery, and the degree of urinary obstruction did not aggravate. The group was followed up for 3 to 8 months (mean 4.7 months), and no recent complications have occurred so far. Conclusions:Lingual mucosa replacement ureteral stenosis repair and plasty for the treatment of ureteral polyps in the long segment has a high success rate and precise efficacy, and its operation is feasible.
4.Construction and validation of nomogram model for prolonged length of stay in patients with acute cerebral infarction based on total cerebral small vessel disease burden scores
Erli ZHANG ; Lanlan HE ; Danyang LI ; Li SHEN ; Zhonghua WU ; Jun ZHANG ; Yongqiang YE
China Modern Doctor 2025;63(8):9-13
Objective To construct a nomogram model for prolonged length of stay in patients with acute cerebral infarction(ACI)based on total cerebral small vessel disease(CSVD)burden scores,and validate its effectiveness.Methods A total of 462 ACI patients admitted to the Department of Neurology of South Taihu Hospital Affiliated To Huzhou College from January 2021 to December 2023 were selected as the study subjects.According to the ratio of 7:3,patients were divided into training group of 323 cases and validation group of 139 cases.Lasso-Logistic regression was used to analyze the risk factors for prolonged length of stay in ACI patients,construct a nomogram model and validate the model using validation data.Receiver operating characteristic(ROC)curve were used to evaluate the predictive performance of the model.Results Based on the training group data,Lasso regression screened four non-zero coefficient indicators,including baseline National Institutes of Health stroke scale(NIHSS)score,age-adjusted Charlson comorbidity index(aCCI)score,neutrophil to lymphocyte ratio(NLR)and total CSVD burden score.Multivariate Logistic regression analysis showed that baseline NIHSS score,aCCI score,NLR and total CSVD burden score were independent risk factors for prolonged length of stay in ACI patients(P<0.05).Based on the above four indicators,a nomogram model was constructed.The results showed that the ROC curve area of the model predicted prolonged length of stay between training group and validation group were 0.812(95%CI:0.756-0.868)and 0.820(95%CI:0.730-0.909).Conclusion The nomogram model for prolonged length of stay in ACI patients based on total CSVD burden score has good predictive performance and can be used as a screening tool for evaluating the prolonged length of stay in ACI patients.
5.Role of cancer-associated fibroblasts autophagy in papillary thyroid cancer
Xuemei ZHANG ; Danyang SUN ; Ning LI ; Qicheng ZHANG ; Ke XU ; Wei ZHENG ; Qiang JIA ; Jian TAN ; Zhaowei MENG
Chinese Journal of Endocrinology and Metabolism 2025;41(2):135-144
Objective:To investigate the inpact of thyroid cancer-derived cancer-associated fibroblasts(CAF) autophagy on papillary thyroid cancer(PTC).Methods:CAF and normal fibroblasts were isolated from cancerous and adjacent normal thyroid tissues from four PTC patients. Expressions of fibroblast activation protein(FAP) and α-smooth muscle actin in cells were assessed. Conditioned medium of CAF and normal fibroblasts were prepared and used to culture PTC cells. The effects of CAF and normal fibroblasts on survival, proliferation, migration, invasion and iodine uptake of PTC cells were evaluated through cell proliferation assay, cell scratch assay, cell invasion assay, and cell iodine uptake assay. The autophagy level of CAF was also evaluated. Autophagy inhibition and activation were used to regulate the autophagy of CAF, and then their effects on PTC cell proliferation, migration and invasion were further evaluated. The in vivo effect of CAF autophagy on PTC xenograft tumor growth was evaluated.Results:CAF exhibited higher FAP expression and basal autophagy levels. PTC cells co-cultured with CAF-conditioned media showed enhanced proliferation, migration, invasion, and reduced iodine uptake. Autophagy inhibition reduced these effects, while autophagy activation further promoted them. In vivo, inhibiting CAF autophagy suppressed tumor growth.Conclusions:CAF promotes PTC cell malignancy through autophagy activation, enhancing proliferation, migration, and invasion while reducing iodine uptake.
6.Effects of pulse indicated continuous cardiac output monitoring on outcomes of intensive care unit patients with shock: a propensity score matching analysis
World Journal of Emergency Medicine 2025;16(5):469-474
BACKGROUND: Pulse indicated continuous cardiac output (PiCCO) has largely replaced Swan-Ganz catheterization in shock patients. However, whether PiCCO monitoring can improve outcomes of shock patients, such as mortality, length of hospital stay, duration of mechanical ventilation, or laboratory parameters, remains unknown.
METHODS: This retrospective cohort study included patients with shock in the intensive care unit (ICU) from January 2013 to January 2020. Patients were divided into PiCCO group and non-PiCCO group based on treatment with PiCCO monitoring or not. Demographic characteristics, Acute Physiology and Chronic Health Evaluation (APACHE) II scores, quick Sequential Organ Failure Assessment (qSOFA) scores, 14-day mortality, and N-terminal pro-B-type natriuretic peptide (NT-proBNP) levels at 0, 1, 3 and 7 days after onset of shock, duration of mechanical ventilation, length of hospital stay and hospitalization costs were compiled and analyzed using propensity score matching (PSM).
RESULTS: Real-world analysis of 1,583 ICU patients suffering shock after propensity score matching revealed that 14-day mortality did not differ between PiCCO and non-PiCCO groups (36.2% vs. 32.6%, P=0.343). Duration of mechanical ventilation, hospital stay, and hospitalization costs were also similar between the two groups (P>0.05). No differences in changes of NT-proBNP levels on days 0, 1, 3, and 7 as compared to baseline were noted between the two groups (P>0.05).
CONCLUSIONS: The results of our real-world indicate that PiCCO monitoring may not shorten the duration of mechanical ventilation, length of hospital stay, or reduce hospitalization costs, nor will it bring survival benefits to ICU patients suffering shock.
7.Application and research advance of poly-ether-ether-ketone(PEEK)in removable partial dentures
Danyang LI ; Hao DING ; Jie WU ; Hongjun XIE
STOMATOLOGY 2025;45(7):546-549,555
As a commonly used material for removable partial dentures,cobalt-chromium alloy frameworks offer excellent corrosion resistance,processability and stability.However,they also have drawbacks,including a high modulus of elasticity and poor aesthetics.Titanium,known for its lighter weight and superior corrosion resistance,also has disadvantages such as insufficient ductility and higher cost.Thus,exploring materials with improved performance for removable partial dentures has been a hot topic in the field of oral resto-ration.In recent years,poly-ether-ether-ketone(PEEK)has attracted attention for its outstanding mechanical properties,wear resist-ance,and biocompatibility,and has been gradually applied in the oral medicine fields of bone defect repair,implantation,restoration,and orthodontics.This paper provides an overview of the application and research progress of PEEK in the repair of removable partial dentures,and offers a perspective on its future application prospects and development directions in this area.
8.Analysis of domestic research on noise-induced hearing loss in recent 30 years
Yang CAO ; Hongyang WANG ; Danyang LI ; Jin LI ; Jing GUAN ; Dayong WANG ; Qiuju WANG
Journal of Audiology and Speech Pathology 2025;33(3):265-269
Objective To investigate the research hotspot and development trend of noise-induced hearing loss(NIHL)in the past 30 years.Methods The CNKI(China national knowledge infrastructure)database,Wanfang Medical network and VIP database.NoteExpress were used for literature screening.CiteSpace 6.1.R6 software were used for bibliometric analysis and data visualization.Results A total of 3 823 articles were included for analy-sis.The top 3 keywords were:"noise","hearing loss",and"noise-induced deafness".A total of 358 literatures were published on the pathogenesis of NIHL.The pathogenesis included oxidative stress,genetic susceptibility,mechanical damage,microcirculation disturbance,calcium overload,etc.Conclusion The number of papers pub-lished in the field of NIHL has increased year by year,and the overall development can be divided into three stages:exploration of the influence of noise,research on etiology,and prevention and assessment of occupational noise-in-duced hearing loss.In terms of pathogenesis,the oxidative stress mechanism has been widely recognized by schol-ars,and genetic susceptibility has become a research hotspot.
9.Shugan Jianpi Granules (疏肝健脾颗粒) Combined with Chushi Zhiyang Oinement (除湿止痒软膏) for Atopic Dermatitis with Sleep Disturbance of Liver Constraint and Spleen Deficiency Syndrome: A Randomized Controlled Trial
Danyang LI ; Qiang YIN ; Zebing ZHU ; Xingwu DUAN ; Jiuli ZHAO
Journal of Traditional Chinese Medicine 2025;66(11):1133-1139
ObjectiveTo explore the effectiveness and potential mechanism of Shugan Jianpi Granules (疏肝健脾颗粒) combined with Chushi Zhiyang Ointment (除湿止痒软膏) in the treatment of atopic dermatitis with sleep disturbance of liver constraint and spleen deficiency syndrome. MethodsSixty-six patients with atopic dermatitis combined with sleep disturbance of liver constraint and spleen deficiency syndrome were randomly divided into 33 cases each in the treatment group and the control group. Both groups were treated with Chushi Zhiyang Ointment for external use. The treatment group additionally received Shugan Jianpi Granules orally, one dose per day; and the control group received cetirizine hydrochloride tablets orally, 10mg per day, taken before bedtime. Both groups were under the treatment for 4 weeks. Clinical effectiveness was evaluated after treatment, and the SCORing Atopic Dermatitis (SCORAD) index, pruritus visual analog scale (VAS) score, Insomnia Severity Index (ISI) score, and Pittsburgh Sleep Quality Index (PSQI) score were recorded before and after treatment, and serum levels of melatonin (MLT), interleukin-4 (IL-4), interleukin-6 (IL-6), interleukin-13 (IL-13), and tumor necrosis factor-α (TNF-α) were measured. The patients were also tested for blood routine, liver function and kidney function before and after treatment, and the occurrence of adverse events was also observed. ResultsThe total effective rate in the treatment group (90.63%, 29/32) was significantly higher than that in the control group (66.67%, 20/30, P<0.05). After the interventions, the scores for SCORAD, VAS, ISI, and PSQI, as well as the levels of IL-4, IL-6, IL-13, and TNF-α, were significantly reduced in both groups. In contrast, the MLT levels in treatment group significantly elevated compared to that before treatment (P<0.05). Comparing between the two groups after treatment, the scores of SCORAD, ISI, PSQI, and VAS, as well as the levels of serum IL-4 and IL-13 in the treatment group were significantly lower than those in the control group, while the MLT levels were markedly higher than that in the control group (P<0.05 or P<0.01). There was no obvious abnormality in blood routine, liver function and kidney function in both groups when compared before and after treatment. The incidence rate of adverse reactions was 9.38% (3/32) in the treatment group and 13.33% (4/30) in the control group, and the difference between groups showed no statistical difference (P>0.05). ConclusionOn the basis of topical application of Chushi Zhiyang Ointment, the combined application of Shugan Jianpi Granules can significantly alleviate the degree of skin lesions and itching, and improve the quality of sleep in atopic dermatitis patients with sleep disturbance of liver constraint and spleen deficiency syndrome, and its mechanism may be related to regulating the immune balance, reducing the secretion of inflammatory factors, and elevating the level of MLT.
10.SRSF7 promotes pulmonary fibrosis through regulating PKM alternative splicing in lung fibroblasts.
Tongzhu JIN ; Huiying GAO ; Yuquan WANG ; Zhiwei NING ; Danyang BING ; Yan WANG ; Yi CHEN ; Xiaomu TIAN ; Qiudi LIU ; Zhihui NIU ; Jiayu GUO ; Jian SUN ; Ruoxuan YANG ; Qianqian WANG ; Shifen LI ; Tianyu LI ; Yuhong ZHOU ; Wenxin HE ; Yanjie LU ; Yunyan GU ; Haihai LIANG
Acta Pharmaceutica Sinica B 2025;15(6):3041-3058
Idiopathic pulmonary fibrosis (IPF), a chronic interstitial lung disease, is characterized by aberrant wound healing, excessive scarring and the formation of myofibroblastic foci. Although the role of alternative splicing (AS) in the pathogenesis of organ fibrosis has garnered increasing attention, its specific contribution to pulmonary fibrosis remains incompletely understood. In this study, we identified an up-regulation of serine/arginine-rich splicing factor 7 (SRSF7) in lung fibroblasts derived from IPF patients and a bleomycin (BLM)-induced mouse model, and further characterized its functional role in both human fetal lung fibroblasts and mice. We demonstrated that enhanced expression of Srsf7 in mice spontaneously induced alveolar collagen accumulation. Mechanistically, we investigated alternative splicing events and revealed that SRSF7 modulates the alternative splicing of pyruvate kinase (PKM), leading to metabolic dysregulation and fibroblast activation. In vivo studies showed that fibroblast-specific knockout of Srsf7 in conditional knockout mice conferred resistance to bleomycin-induced pulmonary fibrosis. Importantly, through drug screening, we identified lomitapide as a novel modulator of SRSF7, which effectively mitigated experimental pulmonary fibrosis. Collectively, our findings elucidate a molecular pathway by which SRSF7 drives fibroblast metabolic dysregulation and propose a potential therapeutic strategy for pulmonary fibrosis.


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