In recent years, the application of artificial intelligence (AI) in the field of biology has witnessed remarkable advancements. Among these, the most notable achievements have emerged in the domain of protein structure prediction and design, with AlphaFold and related innovations earning the 2024 Nobel Prize in Chemistry. These breakthroughs have transformed our ability to understand protein folding and molecular interactions, marking a pivotal milestone in computational biology. Looking ahead, it is foreseeable that the accurate prediction of various physicochemical properties of proteins—beyond static structure—will become the next critical frontier in this rapidly evolving field. One of the most important protein properties is thermodynamic stability, which refers to a protein’s ability to maintain its native conformation under physiological or stress conditions. Accurate prediction of protein stability, especially upon single-point mutations, plays a vital role in numerous scientific and industrial domains. These include understanding the molecular basis of disease, rational drug design, development of therapeutic proteins, design of more robust industrial enzymes, and engineering of biosensors. Consequently, the ability to reliably forecast the stability changes caused by mutations has broad and transformative implications across biomedical and biotechnological applications. Historically, protein stability was assessed via experimental methods such as differential scanning calorimetry (DSC) and circular dichroism (CD), which, while precise, are time-consuming and resource-intensive. This prompted the development of computational approaches, including empirical energy functions and physics-based simulations. However, these traditional models often fall short in capturing the complex, high-dimensional nature of protein conformational landscapes and mutational effects. Recent advances in machine learning (ML) have significantly improved predictive performance in this area. Early ML models used handcrafted features derived from sequence and structure, whereas modern deep learning models leverage massive datasets and learn representations directly from data. Deep neural networks (DNNs), graph neural networks (GNNs), and attention-based architectures such as transformers have shown particular promise. GNNs, in particular, excel at modeling spatial and topological relationships in molecular structures, making them well-suited for protein modeling tasks. Furthermore, attention mechanisms enable models to dynamically weigh the contribution of specific residues or regions, capturing long-range interactions and allosteric effects. Nevertheless, several key challenges remain. These include the imbalance and scarcity of high-quality experimental datasets, particularly for rare or functionally significant mutations, which can lead to biased or overfitted models. Additionally, the inherently dynamic nature of proteins—their conformational flexibility and context-dependent behavior—is difficult to encode in static structural representations. Current models often rely on a single structure or average conformation, which may overlook important aspects of stability modulation. Efforts are ongoing to incorporate multi-conformational ensembles, molecular dynamics simulations, and physics-informed learning frameworks into predictive models. This paper presents a comprehensive review of the evolution of protein thermodynamic stability prediction techniques, with emphasis on the recent progress enabled by machine learning. It highlights representative datasets, modeling strategies, evaluation benchmarks, and the integration of structural and biochemical features. The aim is to provide researchers with a structured and up-to-date reference, guiding the development of more robust, generalizable, and interpretable models for predicting protein stability changes upon mutation. As the field moves forward, the synergy between data-driven AI methods and domain-specific biological knowledge will be key to unlocking deeper understanding and broader applications of protein engineering.

OBJECTIVE: To investigate the impact of bone mass and volume of low-density zones beneath the tibial plateau on the maximum von Mises stresses experienced by the cartilage and meniscus in the knee joint. METHODS: The study included one healthy adult volunteer, from whom CT scans were obtained, and one patient diagnosed with knee osteoarthrisis (KOA), for whom X-ray films were acquired. A static model of the knee joint featuring a low-density zone was established based on a normal knee model. In the finite element analysis, axial loads of 1 000 N and 1 800 N were applied to the weight-bearing region of the upper surface of the femoral head for model validation and subsequent finite element studies, respectively. The maximum von Mises stresses in the femoral cartilage, as well as the medial and lateral tibial cartilage and menisci, were observed, and the stress percentage of the medial and lateral components were concurrently analyzed. Additionally, HE staining, as well as alkaline magenta staining, were performed on the pathological specimens of patients with KOA in various low-density regions. RESULTS: The results of model validation indicated that the model was consistent with normal anatomical structures and correlated with previous calculations documented in the literature. Static analysis revealed that the maximum von Mises stress in the medial component of the normal knee was the lowest and increased with the advancement of the hypointensity zone. In contrast, the lateral component exhibited an opposing trend, with the maximum von Mises stress in the lateral component being the highest and decreasing as the hypointensity zone progressed. Additionally, the medial component experienced an increasing proportion of stress within the overall knee joint. HE staining demonstrated that the chondrocyte layer progressively deteriorated and may even disappear as the hypointensity zone expanded. Furthermore, alkaline magenta staining indicated that the severity of microfractures in the trabecular bone increased concurrently with the expansion of the hypointensity zone. CONCLUSION The presence of subtalar plateau low-density zone may aggravate joint degeneration. In clinical practice, it is necessary to pay attention to the changes in the subtalar plateau low-density zone and actively take effective measures to strengthen the bone status of the subtalar plateau low-density zone and restore the complete biomechanical function of the knee joint, in order to slow down or reverse the progression of osteoarthritis.
Humans ; Finite Element Analysis ; Knee Joint/physiology* ; Tibia/anatomy & histology* ; Cartilage, Articular/physiology* ; Menisci, Tibial/physiopathology* ; Tomography, X-Ray Computed ; Osteoarthritis, Knee/diagnostic imaging* ; Weight-Bearing ; Bone Density ; Adult ; Stress, Mechanical ; Male ; Middle Aged ; Biomechanical Phenomena ; Female

OBJECTIVES: To investigate the genomic characteristics and prognostic factors of juvenile myelomonocytic leukemia (JMML) with RAS mutations. METHODS: A retrospective analysis was conducted on the clinical data of JMML children with RAS mutations treated at the Hematology Hospital of Chinese Academy of Medical Sciences, from January 2008 to November 2022. RESULTS: A total of 34 children were included, with 17 cases (50%) having isolated NRAS mutations, 9 cases (27%) having isolated KRAS mutations, and 8 cases (24%) having compound mutations. Compared to children with isolated NRAS mutations, those with NRAS compound mutations showed statistically significant differences in age at onset, platelet count, and fetal hemoglobin proportion (P<0.05). Cox proportional hazards regression model analysis revealed that hematopoietic stem cell transplantation (HSCT) and hepatomegaly (≥2 cm below the costal margin) were factors affecting the survival rate of JMML children with RAS mutations (P<0.05); hepatomegaly was a factor affecting survival in the non-HSCT group (P<0.05). CONCLUSIONS Children with NRAS compound mutations have a later onset age compared to those with isolated NRAS mutations. At initial diagnosis, children with NRAS compound mutations have poorer peripheral platelet and fetal hemoglobin levels than those with isolated NRAS mutations. Liver size at initial diagnosis is related to the prognosis of JMML children with RAS mutations. HSCT can improve the prognosis of JMML children with RAS mutations.
Humans ; Leukemia, Myelomonocytic, Juvenile/therapy* ; Mutation ; Male ; Female ; Child, Preschool ; Retrospective Studies ; Child ; Infant ; GTP Phosphohydrolases/genetics* ; Membrane Proteins/genetics* ; Adolescent ; Hematopoietic Stem Cell Transplantation ; Proportional Hazards Models ; Proto-Oncogene Proteins p21(ras)/genetics* ; Prognosis

OBJECTIVE To design and synthesize rifamycin S derivatives and load them into milk exosomes to evaluate their in vitro antimicrobial activity.METHODS Rifamycin S derivatives were synthe-sized and characterized by mass spectrometry and NMR.Using the dilution assay method,the inhibitory activity of each rifamycin S derivatives molecule against Staphylococcus aureus and Pseudomonas aerugi-nosa was determined,and the IC50 was calculated.Derivatives molecules with excellent antimicrobial activity were selected and loaded into milk exosomes using the ultrasonication method,resulting in the preparation of milk exosome-loaded rifamycin S derivatives.The antimicrobial activity against Staphylo-coccus aureus was determined using the dilution assay method.The inhibitory effect of the exosome-loaded rifamycin S derivatives on Staphylococcus aureus residing within macrophages was detected using the plate colony counting method.RESULTS Three rifamycin S derivatives were successfully designed and synthesized,which demonstrated superior antimicrobial activity against Staphylococcus aureus(the parent compound's antimicrobial activity is merely from 1/20 to 1/80 of that of the three rifamycin S derivatives)and Pseudomonas aeruginosa(the parent compound's antimicrobial activity is only 1/14 and 1/9 of that of compound 1 and compound 3)compared to the parent compound.The loading of milk exosomes with the rifamycin S derivatives compound 3 was successfully achieved,with a loading efficiency of 10.9％.The antimicrobial activity of the compound after exosome loading was significantly enhanced against Staphylococcus aureus in vitro and against Staphylococcus aureus residing within macrophages(P＜0.01).CONCLUSION The designed and synthesized derivatives of rifamycin S possess stronger anti-microbial activity,and their antibacterial efficacy against both extracellular and intracellular bacteria can be further enhanced after loading into exosomes.

Objective To evaluate the safety and efficacy of valve-in-valve transcatheter mitral valve replacement(ViV-TMVR)in patients with bioprosthetic valve degeneration who are at high surgical risk.Methods This study is a multi-center,retrospective cohort analysis of 20 consecutive patients who underwent transseptal ViV-TMVR using the Edwards SAPIEN 3 transcatheter heart valve(THV).The primary endpoints include technical success and procedural success,both defined according to the Mitral Valve Academic Research Consortium(MVARC)criteria,as well as mortality and functional change assessed based on New York Heart Association(NYHA)classification at 30-days and six months post-procedure.Clinical follow-up assessments are conducted at 30-days and six months.Results From February 2021 to October 2022,a total of 20 patients with symptoms of bioprosthetic valve degeneration were enrolled across nine sites in China.The patients had a mean age of(73.5±5.5)years,with 85.0％being females and 70.0％classified as NYHA class Ⅲ/Ⅳ.The study achieved a 100.0％technical success rate and a 90.0％procedural success rate finally.All patients remained alive during the 30-day follow-up period.However,six months post-intervention,two patients(10.0％)were re-hospitalized due to heart failure,and sadly,one of them(5.0％)died.None of the patients reported any adverse events related to ViV-TMVR during the follow-up period.Notably,there was a significant improvement in NYHA class compared to baseline(P=0.0004)at six-month follow-ups.Conclusions The transseptal ViV-TMVR technique proved to be highly successful and was associated with significant improvement in NYHA class function.These findings strongly suggest that it serves as a safe and efficient treatment alternative for high-risk patients suffering from bioprosthetic valve degeneration.

BACKGROUND:Existing studies have made significant progress in PIWI-interacting RNAs(piRNAs)against osteoporosis,but the specific targets and related mechanisms by which piRNAs exert their functions remain to be explored.OBJECTIVE:To investigate the effects and downstream mechanisms of piR-7472 on the differentiation of mouse osteoblasts(MC3T3-E1 cells).METHODS:(1)Twelve C57/BL6J mice were randomly divided into a sham-operated and an ovariectomized group,with six mice in each group.Changes in bone mass and the expression of piR-7472 were detected using Micro-CT and RT-qPCR,respectively,at 8 weeks after surgery.(2)MC3T3-E1 cells were divided into NC mimics group,piR-7472 mimics group,NC inhibitor group,and piR-7472 inhibitor group.The mRNA expression of piR-7472,osteopontin,type I collagen,Runt-related transcription factor 2,and potassium voltage-gated channel modifier subfamily F member 1 were detected by RT-qPCR after 7 days of osteogenic induction.The protein expression of osteopontin,Runt-related transcription factor 2,bone morphogenetic protein 2,and potassium voltage-gated channel modifier subfamily F member 1(KCNF1)was detected using western blot assay.The expression of alkaline phosphatase was detected by alkaline phosphatase staining after 14 days of osteogenic induction,and the number of mineralized nodules was detected by alizarin red staining after 21 days of induction.Whether piR-7472 could bind to KCNF1 was observed by the dual luciferase reporter gene assay.RESULTS AND CONCLUSION:(1)Bone mineral density,bone volume fraction,bone trabecular thickness,bone trabecular number were significantly decreased and bone trabecular separation was significantly increased in ovariectomized mice,and piR-7472 in bone tissue was significantly down-regulated in osteoporotic mice.(2)Compared with the NC group,the mRNA expression of osteopontin,type I collagen,and Runt-related transcription factor 2 were significantly increased,the protein expression of osteopontin,Runt-related transcription factor 2,and bone morphogenetic protein 2 were significantly elevated,and the levels of mineralized deposition and alkaline phosphatase were increased in the piR-7472 mimics group.Compared with the NC inhibitor group,the mRNA expression of osteopontin,type I collagen,and Runt-related transcription factor 2 was significantly downregulated,the protein expression of osteopontin,Runt-related transcription factor 2,and bone morphogenetic protein 2 were significantly decreased,and the levels of mineralized deposition and alkaline phosphatase were reduced in the piR-7472 inhibitor group.(3)piR-7472 was found to interact with the potassium voltage-gated channel modifier subfamily F member 1 as predicted by the miRanda database.The dual luciferase reporter gene assay revealed that piR-7472 mimics could bind to and promote the expression of KCNF1.To conclude,piR-7472 can promote osteogenic differentiation of osteogenic precursor cells MC3T3-E1,and its mechanism of action may be achieved by promoting the expression of KCNF1.

Objective To analyze the effect of graded exercise rehabilitation in patients with acute exacerbation of chronic obstructive pulmonary disease,and to provide references for clinical nursing practice.Methods A total of 70 patients with acute exacerbation of chronic obstructive pulmonary disease who met the criteria in the Department of Respiratory Medicine of a tertiary hospital in Zunyi City from September to December 2023 were randomly divided into an experimental group and a control group(with 35 cases in each group).The experimental group implemented graded exercise rehabilitation based on the Global Chronic Obstructive Pulmonary Initiative guidelines,and the control group implemented routine exercise rehabilitation.After intervention,the lung function,blood gas analysis,oxygenation index,6 min walking test and the incidence of complications related to non-invasive mechanical ventilation were compared between the 2 groups.Results Finally,34 cases were included in the experimental group and 35 cases in the control group.After intervention,the forced expiratory volume in the first second of the experimental group was improved compared with the control group(P＜0.05).The 6-minute walking test of the experimental group was higher than that of the control group(P＜0.05).The total incidence of non-invasive mechanical ventilation-related complications in the experimental group was lower than that in the control group(P＜0.05).There was no significant difference in blood gas analysis and oxygenation index between the 2 groups(P＜0.05).Conclusion The implementation of graded exercise rehabilitation based on the Global Chronic Obstructive Pulmonary Initiative guidelines can help patients with acute exacerbation of chronic obstructive pulmonary disease improve their respiratory function,improve their exercise endurance,and reduce non-invasive mechanical ventilation-related complications.

Objective:To investigate the anti-leukemic effects and resistance mechanisms of venetoclax in acute myeloid leukemia (AML). Genomic, transcriptomic, and clinical data from AML patients who underwent venetoclax drug sensitivity testing were downloaded from the Beat AML database. Correlation analysis was performed between these data and venetoclax sensitivity outcomes. Differentially expressed genes (DEGs) associated with venetoclax sensitivity were identified from transcriptomic data and subsequently validated using GEO database transcriptomic results and in vitro experiments (including Western blot). Functional enrichment analyses (KEGG and GSEA), transcription factor enrichment analysis (KnockTF), and data from public databases were employed to further investigate key genes and pathways influencing drug sensitivity.Results:After filtering the Beat AML cohort, data from 52 patient samples with available in vitro venetoclax sensitivity results were included for analysis. Patients with FLT3 mutations exhibited greater sensitivity to venetoclax compared to those with FLT3 wild-type. Correlation analysis between clinical information and drug sensitivity data indicated that higher peripheral blood tumor burden was associated with increased sensitivity to venetoclax. Transcriptomic analysis and in vitro experiments confirmed that venetoclax inhibits the FLT3-related signaling pathway, including downregulation of FLT3 expression and reduced phosphorylation of its downstream targets AKT and STAT5. KEGG pathway and KnockTF transcription factor enrichment analyses indicated that venetoclax resistance was associated with increased transcriptional activity of FOXM1 and STAT3. Moreover, high expression of FOXM1 and STAT3 correlated with shorter overall survival in patients.Conclusion:Venetoclax can inhibit the activation of FLT3-related signaling pathways. The activation of STAT3 and FOXM1 transcription factors is a potential key mechanism contributing to venetoclax resistance in AML.

Objective:To investigate the effect of human epidermal growth factor receptor 2 (HER2) on bladder cancer by regulating phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt) signaling pathway via tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon peptide (YWHAE) and to examine its mechanism.Methods:The gene expression profiling interactive analysis (GEPIA) database was used to analyze HER2 expression in 408 bladder cancer tissues and 19 adjacent normal tissues. HER2 expression was then compared between 215 tumor protein 53 ( TP53) mutant and 193 TP53 non-mutant bladder cancer tissues. Tissue samples were obtained from patients who underwent surgical resection for bladder cancer in Tianjin Medical University General Hospital between June 2010 and March 2015. Immunohistochemistry and Western blotting were performed to validate HER2 and p53 protein expression, as well as analyze their correlation. Bladder cancer T24 cells were transfected with short hairpin RNA targeting HER2 (shHER2) control (shCon) or shHER2, designated as shCon and shHER2 groups. Bladder cancer UMUC3 cells were transfected with overexpression control (oeCon), HER2 overexpression (oeHER2), oeYWHAE, or short hairpin RNA targeting murine double minute 2 (MDM2) (shMDM2), and were designated as the oeCon, oeHER2, oeYWHAE and shMDM2 groups, respectively. UMUC3 cells were then treated with either 0.1% dimethyl sulfoxide or 100 mmol/L dihydrotestosterone and designated as the solvent control and dihydrotestosterone groups, respectively. Additionally, oeCon and oeYWHAE UMUC3 cells were treated with the PI3K inhibitor LY294002 (25 μmol/L), designated as the LY294002 and LY294002+oeYWHAE groups. On this basis, shHER2 was transfected into the oeCon and oeYWHAE groups, which were then designated as the shHER2-2 and shHER2-2+oeYWHAE groups. The relative expression levels of HER2, YWHAE mRNA, and HER2, p53, YWHAE, MDM2, phosphorylated Akt (p-Akt), and Akt proteins were determined using quantitative reverse transcription PCR and Western blotting. Cell Counting Kit-8, Transwell, and wound-healing assays were performed to evaluate the impact of HER2 on the proliferation, invasion, and migration of bladder cancer cells. Mass spectrometry and co-immunoprecipitation assays were performed to confirm the interaction between YWHAE and HER2, and immunofluorescence was used to detect p53 expression. BALB/c nude mice were subcutaneously injected with 5×10 6 UMUC3 cells in the scapular region. According to the random number table method, they were divided into negative the control group and the transfection group, with 3 mice in each group, and transfected with oeCon and oeHER2, respectively. Tumor volume and weight were measured and calculated, and HER2 and p53 protein expression in bladder cancer tissues was validated by immunohistochemistry and Western blotting. Independent sample t test or Mann-Whitney U test was used to compare the two groups. One-way analysis of variance or Kruskal-Wallis test was used for comparison of multiple groups. Results:GEPIA database analysis demonstrated significantly higher levels of HER2 expression in bladder cancer tissues and in TP53 mutant bladder cancers compared with adjacent normal tissues (both P<0.01). HER2 expression was inversely correlated with p53 expression ( r=?0.6). Immunohistochemistry and Western blotting confirmed that p53 expression level in the bladder cancer tissues (5.32±0.11) was higher than that in the adjacent normal tissues (2.00±0.01), while HER2 expression level in the bladder cancer tissues (1.13±0.02) was lower than that in the adjacent normal tissues (6.20±0.06) (both P<0.01). HER2 mRNA and protein expression, absorbance at 450 nm wavelength ( A450) values, and cell invasion number and cell migration distance in the shHER2 group were all lower than those in the shCon group [0.25±0.01 vs 1.00±0.05, 1.00± 0.01 vs 3.26±0.09, 1.36±0.04 vs 1.65±0.06, (107.00±5.51) vs (202.70±11.61) cells, and (298.70±6.94) vs (454.30±7.84) μm] ( P<0.05, 0.01). HER2 mRNA and protein expression, absorbance ( A450) values, and cell invasion number and cell migration distance in the oeHER2 group were all higher than those in the oeCon group [0.78±0.02 vs 0.46±0.01, 2.05±0.02 vs 1.00±0.00, 1.23±0.06 vs 0.78±0.03, (136.30±5.24) vs (59.00±5.51) cells, and (153.70±7.27) vs (66.33±33.84) μm] ( P<0.05, 0.01). HER2 protein expression level in the dihydrotestosterone group was higher than that in the solvent control (1.83±0.19 vs 1.00±0.00), while p53 protein expression level in the dihydrotestosterone group was lower than that in the solvent control group (1.10±0.10 vs 1.53±0.15) (both P<0.01). The differentially expressed protein between the dihydrotestosterone group and solvent control group was YWHAE. The expression levels of YWHAE mRNA and protein in the dihydrotestosterone group (1.10±0.12 and 3.05±0.03) were higher than those in the solvent control group (0.30±0.12 and 1.00±0.00) (both P<0.01). YWHAE protein expression level in the oeHER2 group was higher than that in the oeCon group (1.37±0.08 vs 1.00±0.00) ( P<0.01) and YWHAE expression level in the bladder cancer tissues was higher than that in the adjacent normal tissues ( P<0.01). YWHAE expression positively correlated with HER2 expression ( r=0.4). Co-immunoprecipitation confirmed direct binding between HER2 and YWHAE. Overexpression of YWHAE significantly reduced p53 expression. The relative expression level of MDM2 protein in the oeYWHAE group (2.73±0.09) was lower than that in the oeCon group (3.43±0.12) ( P<0.01). The relative expression level of MDM2 protein in the shMDM2 group (1.00±0.00) was lower than that in the oeYWHAE group, and the relative expression level of p53 protein (2.00±0.00) was higher than that in the oeYWHAE group (1.07±0.07) (both P<0.01). The relative expression levels of YWHAE and p-Akt protein in the oeYWHAE group (1.23±0.09, 3.00±0.06) were higher than those in the oeCon group (1.00±0.00, 1.13±0.03) ( P<0.05, 0.01). The relative expression level of p-Akt protein in LY294002 group (2.20±0.06) was lower than that in the oeCon group (3.30±0.10), and the relative expression level of p53 protein (2.10±0.06) was higher than that in the oeCon group (1.00±0.00) (both P<0.01). The relative expression level of p-Akt protein in LY294002+oeYWHAE group (2.00±0.06) was lower than that in the oeYWHAE group (3.53±0.14), and the relative expression level of p53 protein (2.10±0.06) was higher than that in the oeYWHAE group (1.00±0.06) (both P<0.01). The relative expression levels levels of YWHAE, p-Akt and MDM2 protein in the shHER2-2 group (1.60±0.15, 1.70±0.06, 0.80±0.06) were lower than those in the oeCon group (2.30±0.06, 2.30±0.06, 1.13±0.09), and the relative expression level of p53 protein (1.83±0.12) was higher than that in the oeCon group (1.00±0.00) ( P<0.05, 0.01). The relative expression level of YWHAE protein in the shHER2-2+oeYWHAE group (2.00±0.06) was lower than that in the oeCon group ( P<0.01), and the relative expression levels of MDM2 and p53 protein (2.63±0.15, 1.13±0.03) were higher than those in the oeCon group ( P<0.05, 0.01). The tumor volume, tumor weight, and relative expression levels of HER2, YWHAE, p-Akt, and MDM2 proteins on day 28 in the transfection group [(5 133.0±185.6) mm 3, (0.65±0.12) g, 2.23±0.02, 4.00±0.12, 3.33±0.06 and 2.24±0.02] were higher than those in the negative control group [(2 633.0±88.2) mm 3, (0.33±0.07) g, 0.98±0.02, 1.27±0.03, 1.29±0.02 and 1.46±0.06] (all P<0.01). The relative expression level of p53 protein (1.21±0.04) was lower than that in the negative control group (3.29±0.04) ( P<0.01). Conclusions:HER2 may promote the malignant progression of bladder cancer by regulating the PI3K-Akt pathway via YWHAE, thereby facilitating MDM2 nuclear translocation and p53 degradation. This ultimately enhances the proliferative, migratory, and invasive capacities of bladder cancer cells.