In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (∼10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.

Objective To observe the value of transabdominal bowel ultrasound for monitoring therapeutic efficacy of vedolizumab in patients with moderate-to-severe ulcerative colitis.Methods Totally 47 ulcerative colitis patients with Mayo endoscopic score(MES)≥2 and treated with vedolizumab were retrospectively included.Transabdominal bowel ultrasound examinations were performed at baseline,at the end of induction therapy,also 3 and 6 months after maintenance therapy,while colonoscopy was performed at baseline and 6 months after maintenance therapy.According to colonoscopy results 6 months after maintenance therapy,the patients were divided into improved group(MES≤1 or MES reduction≥1,n=25)and non-improved group(n=22),and ultrasonic findings of sigmoid colon were compared between and within groups.Results At baseline,no significant difference of ultrasonic findings of sigmoid colon was observed between groups(all P＞0.05),whereas differences of bowel wall thickness at the end of induction therapy,of Limberg grade and abnormal perienteric lymph nodes 3 months after maintenance therapy,as well as bowel wall stratification 6 months after maintenance therapy were noticed between groups(all P＜0.05).Within improved group,compared with those in baseline,bowel wall thickness improved at all time points after the beginning of treatment,Limberg grade improved 3 and 6 months after maintenance therapy,while bowel wall stratification,abnormal perienteric lymph node and perienteric fat edema improved 6 months after maintenance therapy(all P＜0.05).Meanwhile,no significant change of ultrasonic findings of sigmoid colon was observed in non-improved group during the above periods(all P＞0.05).Conclusion Transabdominal bowel ultrasound could be used to accurately monitor the therapeutic efficacy of vedolizumab in patients with moderate-to-severe ulcerative colitis.

Objective:To establish a method for the rapid detection of varicella-zoster virus (VZV) by recombinase-aid amplification (RAA) combined with Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system.Methods:Clinical samples of suspected herpes zoster in Shandong province and Shanghai from 2023 to 2024 were collected, nucleic acids of positive samples were extracted, RAA-specific primers and crRNA (CRISPR RNA, crRNA) were designed for the conserved region of VZV, and the fluorescence intensity generated by Cas12a non-specific cleavage of single-stranded fluorescent probes was used to screen highly sensitive crRNAs and optimize the concentrations of crRNA, Cas12a and ssDNA probes. The sensitivity and reproducibility of the RAA-CRISPR/Cas12a detection method were evaluated by using synthesized plasmids and clinical samples, and the specificity of the method was evaluated by using other viral nucleic acids. The method was used to detect clinical samples by using the method and quantitative real-time PCR (qPCR) method, and the detection rate and consistency of the two method were compared.Results:The highly sensitive crRNA-4 was screened from the four crRNAs designed, and a VZV detection method for RAA-CRISPR/CAS12a based on fluorescence intensity measurement was established, which could be detected at 37℃ in 45 min, and the sensitivity of the detection could reach 10 copies/μL, a minimum clinical sample with a Ct value of 38.980 can be detected. It has high specificity and no cross-reactivity with Adenovirus 7, Herpes simplex virus type I, Herpes simplex virus type II, Coxsackieviruses A16, Cytomegalovirus, Epstein-Barr virus, Measles virus, Mumps virus, Enterovirus 71, Japanese encephalitis virus genotype 5. It has good stability, and can be successfully detected in low, medium and high concentrations of viral positive plasmids with good consistency. The detection rate of the clinically positive samples was 100%, which was completely consistent with the qPCR test result.Conclusions:RAA isothermal amplification technology combined with CRISPR-CAS12a technology was used to establish an accurate method for the detection of VZV virus, which was highly sensitive, specific, and had low requirements for experimental conditions, and could be completed within 45 min, which could provide strong technical support for the early detection of VZV.

Objective:To explore the value of nomogram model based on multimodal ultrasound features for predicting the malignant risk of micro lesions in breast areola region.Methods:The case data of Beijing Tiantan Hospital affiliated to Capital Medical University from May 2020 to July 2024 were retrospectively analyzed. A total of 50 patients with benign intraductal papilloma（bIDP group）and 54 patients with malignant risk breast tumor（mrBT group）were found to have micro lesions in breast areola region and confirmed by puncture or surgical pathology. Clinical data，conventional ultrasound and contrast-enhanced ultrasound features were compared between the two groups. Multivariate Logistic regression analysis and Lasso regression analysis were performed on statistically significant factors to screen out influencing factors. ROC curves were plotted to evaluate diagnostic efficacy，nomogram model and clinical decision curves were constructed to evaluate clinical benefits.Results:The differences of age，nipple discharge presentation，conventional ultrasound features（including boundary，morphology，aspect ratio，internal echo，internal microcalcification，far-field echo，peripheral irregular hyperechoic ring，dilate of peripheral ducts），and contrast-enhanced ultrasound features（including wash-in time，enhancement intensity，enhancement mode，enhancement scope，blood perfusion defect，crab foot sign，penetrating vessels）were statistically significant between the bIDP group and mrBTgroup（all P<0.05）. Regression analysis showed that age，uniformity of internal echo within the lesion，dilation of surrounding ducts，and enhanced crab foot sign were the affect factors for the diagnosis of mrBT（all P<0.05）. Based on these factors，a nomogram model was constructed with an area under ROC curve（AUC）of 0.907（95% CI=0.851-0.963），a sensitivity of 0.907，and a specificity of 0.780. The decision curve analysis showed that the collective model had good predictive performance. Conclusions:The nomogram model based on multimodal ultrasound features has good value in predicting malignant risk micro breast tumor of areola region.

Objective:To establish a model based on the characteristics of breast cancer ultrasound images through deep learning methods to predict the risk of axillary lymph node metastasis（ALNM）in patients with breast cancer（maximum diameter ≤2.5 cm）before surgery.Methods:A total of 419 patients（3 433 breast tumor ultrasound images）with breast cancer（maximum diameter ≤2.5 cm）who underwent axillary lymph node dissection at Beijing Tiantan Hospital，Capital Medical University from January 2019 to December 2024 were retrospectively included. According to the pathological results of axillary lymph nodes，they were divided into 220 cases in the ALNM occurrence group（positive group）and 199 cases in the non-ALNM occurrence group（negative group）. The breast cancer ultrasound images of the two groups of cases were randomly classified into the training set（2 404 images），the validation set（687 images）and the test set（342 images）according to a ratio of 7∶2∶1. YOLOv8 was used as the basic model of You Only Look Once（YOLO）and optimized. The optimized model was applied to locate and capture the potential ultrasound features of breast cancer cases in the training set. A prediction model was constructed based on the captured ultrasound features. The model was adjusted and optimized through the validation set，and then matched with the case images in the test set. The confusion classification matrix graph and the curve graph for measuring the model performance were used to evaluate the model prediction performance and interpret the model，and the efficacy of this model in identifying breast cancer patients at risk of ALNM was analyzed.Results:There were statistically significant differences between the positive and negative groups in terms of the pathological maximum diameter of breast tumors，pathological T staging，the differentiation degree，the presence of distant metastasis，the maximum diameter measured by ultrasound，the quadrant of breast tumor occurrence，the Breast Imaging - Reporting and Data System（BI-RADS）classification of breast tumors，and the presence of abnormal ultrasound features of lymph node（all P<0.05）. The established deep learning model could automatically perform bounding box localization for the breast cancer of patients.The breast tumors in the positive group had potential ultrasound features that could be captured by the model compared with those in the negative group. The mean average precision（mAP）50 was 0.883，mAP 50-95 was 0.636，PR-AUC was 0.884 5，strict PR-AUC was 0.636 4，the sensitivity was 90.5%，and the specificity was 91.2%，and it had a good predictive efficacy. Conclusions:This prediction model based on the ultrasound characteristics of breast cancer through deep learning can effectively predict breast cancer（maximum diameter ≤ 2.5 cm）with the risk of ALNM，providing an effective basis for the clinical management of axillary lymph nodes in breast cancer patients.

BACKGROUND:The repair process of myocardial injury involves complex cellular and molecular mechanisms,especially mitochondrial calcium homeostasis,macrophage autophagy and pyroptosis pathways.Traditional Chinese medicine(TCM)has shown significant clinical efficacy in improving myocardial injury,but its mechanism of action needs to be thoroughly investigated. OBJECTIVE:To investigate the role of mitochondrial calcium homeostasis-mediated macrophage autophagy and pyroptosis pathways in myocardial injury,and to summarize the progress of TCM in this field. METHODS:A computerized search was performed for relevant literature from the database inception to March 2024 in the Web of Science,PubMed and CNKI.The search terms were"mitochondrial calcium homeostasis,macrophage autophagy,macrophage pyroptosis,traditional Chinese medicine,myocardial injury,myocardial injury reperfusion"in Chinese and English.Through literature review,we analyzed the relationship between mitochondrial calcium homeostasis and macrophage autophagy and pyroptosis,explored the mechanism of their roles in myocardial injury,and summarized the pathways of multi-targeted,multi-pathway effects of TCM. RESULTS AND CONCLUSION:The maintenance of mitochondrial calcium homeostasis has been found to be closely related to the normal function of cardiomyocytes.Macrophages can participate in the repair process of myocardial injury through autophagy and pyroptosis pathways.Autophagy contributes to cell clearance and regulation of inflammatory response,while pyroptosis affects myocardial repair by releasing inflammatory factors.TCM regulates mitochondrial calcium homeostasis and macrophage function through multiple mechanisms.For example,astragalosid regulates calcium homeostasis by lowering mitochondrial membrane potential and inhibiting cytochrome C,and epimedium glycoside plays a role in reducing β-amyloid deposition.In addition,herbal compounds and single drugs promote myocardial repair by activating or inhibiting specific signaling pathways,such as PI3K/AKT and nuclear factor-κB signaling pathways.Future studies should focus on the interactions between mitochondrial calcium homeostasis,autophagy and pyroptosis pathways,as well as how TCM can exert therapeutic effects through these pathways to provide new strategies and drugs for the treatment of myocardial injury.

Objective: To explore the current status and influencing factors of eating behaviors in adolescents, so as to provide a theoretical foundation for health promotion education among adolescents. Methods: Based on the database from Survey of Chinese Family Health Index (2021), by a random number table method, 1 065 teenagers were selected from the provincial capitals of 22 provinces and 5 autonomous regions in China, as well as 4 municipalities directly under the central government. A general characteristic questionnaire, Patient Health Questionnaire-9 (PHQ-9), Short Form of the Family Health Scale (FHS-SF), 10-item Short Version of the Big Five Personality(BFP-10), Content-based Media Exposure Scale (CM-E) and Sakata Eating Behavior Scale Short Form(EBS-SF) were used to collect information. Multivariate stepwise linear regression analysis was employed to identify and analyze related factors of eating behaviors among adolescents. Receiver operating characteristic was used to validate the predictive ability of the EBS-SF score for overweight and obesity among adolescents. Results: The average scores of BFI-10,C-ME, FHS-SF, PHQ-9 and EBS-SF were (33.08±4.64)(19.20±4.55)(38.48±6.65)(6.09±5.63)(16.75±4.36), respectively. Multivariate linear regression showed that family type (other types), agreeableness, conscientiousness, family health and depression were the main related factors of EBS-SF scores among adolescents( B =2.61,-0.42,0.20,-0.11,0.23, P <0.05).The analysis of receiver operating characteristic curve showed that the EBS-SF scores had a good ability in predicting obesity among male adolescents ( AUC= 0.73, P <0.01). Conclusions Family type, big five personality, family health,depression are the related factors of eating behaviors among adolescents. EBS-SF scores are predictive of obesity in adolescents, which would provide a new perspective for promoting healthy eating habits among adolescents.

Objective To explore the relationship between peripheral blood mitochondrial DNA(mtDNA)copy number and urinary microalbumin(MAlb)in patients with type 2 diabetes mellitus(T2DM).Methods 87 patients with T2DM from the Endocrinology Department of East Hospital of Tongji University were selected based on inclusion criteria.According to urinary MAlb levels,patients were divided into T2DM group(MAlb＜30 mg/L)and MAlb group(MAlb＞30 mg/L).General patient information was collected,and clinical indicators such as blood glucose,lipid profile,glycated hemoglobin and insulin were measured.Peripheral blood mtDNA was extracted and the copy number was detected using real-time quantitative polymerase chain reaction(RT-PCR).Logistic regression analysis was used to identify the risk factors for albuminuria.Results Compared with T2DM group,DM duration,serum creatinine,serum uric acid and copy number of mtDNA in MAlb group increased(P＜0.05),while high density lipoprotein cholesterol decreased(P＜0.05).Logistic analysis showed that the copy number of mtDNA was the influencing factor of MAlb in T2DM patients.Conclusions The peripheral blood mtDNA copy number in T2DM patients is positively correlated with urinary microalbumin,thus providing a potential target for early detection of DKD.

Objective To explore the relationship between peripheral blood mitochondrial DNA(mtDNA)copy number and urinary microalbumin(MAlb)in patients with type 2 diabetes mellitus(T2DM).Methods 87 patients with T2DM from the Endocrinology Department of East Hospital of Tongji University were selected based on inclusion criteria.According to urinary MAlb levels,patients were divided into T2DM group(MAlb＜30 mg/L)and MAlb group(MAlb＞30 mg/L).General patient information was collected,and clinical indicators such as blood glucose,lipid profile,glycated hemoglobin and insulin were measured.Peripheral blood mtDNA was extracted and the copy number was detected using real-time quantitative polymerase chain reaction(RT-PCR).Logistic regression analysis was used to identify the risk factors for albuminuria.Results Compared with T2DM group,DM duration,serum creatinine,serum uric acid and copy number of mtDNA in MAlb group increased(P＜0.05),while high density lipoprotein cholesterol decreased(P＜0.05).Logistic analysis showed that the copy number of mtDNA was the influencing factor of MAlb in T2DM patients.Conclusions The peripheral blood mtDNA copy number in T2DM patients is positively correlated with urinary microalbumin,thus providing a potential target for early detection of DKD.

Objective To observe the value of transabdominal bowel ultrasound for monitoring therapeutic efficacy of vedolizumab in patients with moderate-to-severe ulcerative colitis.Methods Totally 47 ulcerative colitis patients with Mayo endoscopic score(MES)≥2 and treated with vedolizumab were retrospectively included.Transabdominal bowel ultrasound examinations were performed at baseline,at the end of induction therapy,also 3 and 6 months after maintenance therapy,while colonoscopy was performed at baseline and 6 months after maintenance therapy.According to colonoscopy results 6 months after maintenance therapy,the patients were divided into improved group(MES≤1 or MES reduction≥1,n=25)and non-improved group(n=22),and ultrasonic findings of sigmoid colon were compared between and within groups.Results At baseline,no significant difference of ultrasonic findings of sigmoid colon was observed between groups(all P＞0.05),whereas differences of bowel wall thickness at the end of induction therapy,of Limberg grade and abnormal perienteric lymph nodes 3 months after maintenance therapy,as well as bowel wall stratification 6 months after maintenance therapy were noticed between groups(all P＜0.05).Within improved group,compared with those in baseline,bowel wall thickness improved at all time points after the beginning of treatment,Limberg grade improved 3 and 6 months after maintenance therapy,while bowel wall stratification,abnormal perienteric lymph node and perienteric fat edema improved 6 months after maintenance therapy(all P＜0.05).Meanwhile,no significant change of ultrasonic findings of sigmoid colon was observed in non-improved group during the above periods(all P＞0.05).Conclusion Transabdominal bowel ultrasound could be used to accurately monitor the therapeutic efficacy of vedolizumab in patients with moderate-to-severe ulcerative colitis.