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.

Animal experiments are crucial in evaluating the preclinical safety and efficacy of new dental materials, drugs, instruments, and equipment by identifying and eliminating potential health risks to humans. An international team of several dental experts formulated a guideline named Preferred Reporting Items for Animal Studiesin Endodontology (PRIASE) 2021. Consisting of 11 domains, 43 individual items, and a flowchart. PRIASE provides guidance for animal experiments in dentistry and improves the quality of experiment design and reporting. This work introduces the process and basic content of the guideline and interprets the key items of its checklist with specific examples to provide reference for the reporting of animal experiment in dentistry in China.
Animals ; Animal Experimentation/standards* ; Checklist ; China ; Endodontics ; Guidelines as Topic ; Research Design

[摘 要] 目的：探讨CXCL5/CXCR2/VEGF通路在HBV相关肝癌血管生成过程中的作用及其机制。方法：收集2022年10月至2022年12月间在广西中医药大学附属瑞康医院入院的10例HBV-DNA阳性患者的外周血标本[其中5例肝细胞癌（HCC）和5例肝硬化（LC）]，用高通量RNA测序技术检测并筛选差异表达mRNA，用GO富集和KEGG通路分析这些差异表达基因的生物学功能和相关信号通路。常规培养HCC细胞HepG2，用转染试剂将C-X-C基序趋化因子配体5（CXCL5）过表达质粒和对照质粒转染至HepG2细胞中，分为对照组，空载组，250 ng/mL和520 ng/mL CXCL5过表达质粒组。用CCK-8法、ELISA、血管生成实验、qPCR法、WB法和免疫荧光染色技术分别检测过表达CXCL5对HepG2细胞增殖能力、VEGF分泌、成管能力、CXCL5、CXCR2、VEGF mRNA及其蛋白表达，以及VEGF表达的影响。结果：RNA测序结果显示，HCC和LC患者外周血中 mRNA表达存在显著差异。GO富集分析发现，这些差异mRNA的相关基因主要参与细胞发育过程的调控、G蛋白偶联受体活性、细胞外区域的组成和信号受体结合。KEGG通路分析发现，这些异表达基因可能参与细胞因子与受体相互作用通路、cAMP信号通路等与癌症作用机制相关的通路、神经活性配体与受体相关作用的通路、钙相关信号通路。过表达CXCL5可明显促进HepG2细胞的增殖能力（P < 0.05）、VEGF的分泌（P < 0.05）、人脐静脉内皮细胞（HUVEC）的成管能力（P < 0.05）、CXCL5、CXCR2和VEGF mRNA和蛋白的表达（P < 0.05或P < 0.01），以及增强HepG2细胞中VEGF的表达。结论：CXCL5可能通过CXCL5/CXCR2/VEGF轴促进HepG2细胞的增殖和HUVEC的成管能力。

Objective:To analyze the relationship between body mass index (BMI) and fat mass percentage (FMP) in children aged 3-17 years in China.Methods:The BMI and FMP data of children aged 3-17 years from the National Nutrition and Health Systematic Survey in 0-18 years old children in China was analyzed. BMI- Z score/BMI and FMP were used to classify the subjects, respectively. Spearman correlation was used to analyze the correlation between BMI and FMP. The consistency between BMI- Z score/BMI and FMP in classifying the subjects was measured using Kappa coefficient. Results:The FMP of malnutrition, normal and overweight/obesity in boys was higher in age group 10-13-year than in other age groups (all P<0.001). The FMP of all nutritional status in girls increased with age (all P<0.05). The BMI of boys in all the FMP levels increased with age (all P<0.05). When the FMP of girls was 25%- or ≥30%, BMI increased with age (all P<0.001). The relationship between BMI and FMP was strong ( r=0.705, P<0.001), with r of 0.618 in boys and 0.884 in girls. The consistency between BMI- Z score/BMI and FMP in classifying the subjects was found to be moderate (Kappa=0.574, P<0.001). Conclusions:There was a strong relationship between BMI and FMP. The consistency between BMI- Z score/BMI and FMP in classifying the subjects was moderate.

Objective To analyze the expression of SPAG5 in gastric cancer tissues and its regulatory roles in gastric cancer cell growth.Methods TCGA analysis,immunohistochemistry,and immunofluorescence staining were used to analyze the expression patterns of SPAG5 and MKi67 in gastric cancer and adjacent tissues.In gastric cancer AGS and MGC803 cells,the effects of lentivirus-mediated SPAG5 knockdown on cell growth and apoptosis were evaluated using Celigo,MTT,clone formation assays and flow cytometry.Results Proteinatlas and TCGA database analysis suggested that SPAG5 was highly expressed in gastric cancer,and Kaplan-Meier analysis and GEPIA analysis showed high expressions of SPAG 5 in lung adenocarcinoma,breast cancer,hepatocellular carcinoma,pancreatic carcinoma,cervical cancer and bladder carcinoma.Immunohistochemistry revealed that SPAG5 was highly expressed in gastric cancer tissues(P<0.001),and immunofluorescence colocalization analysis demonstrated a significant correlation between SPAG5 and MKI67(R=0.393,P<0.001).RT-qPCR and Western blotting showed that SPAG5 was highly expressed in MKN74,BGC823,MGC803,SGC7901 and AGS cells.In AGS and MGC803 cells,SPAG5 knockdown significantly inhibited proliferation and promoted apoptosis.Conclusions The expressions of SPAG5 and MKi67 are correlated in gastric cancer tissues,and SPAG5 knockdown inhibits the proliferation of gastric cancer cells.SPAG5 is associated with the prognosis of gastric cancer patients and may serve as a promising biomarker for gastric cancer.

Objective To analyze the expression of SPAG5 in gastric cancer tissues and its regulatory roles in gastric cancer cell growth.Methods TCGA analysis,immunohistochemistry,and immunofluorescence staining were used to analyze the expression patterns of SPAG5 and MKi67 in gastric cancer and adjacent tissues.In gastric cancer AGS and MGC803 cells,the effects of lentivirus-mediated SPAG5 knockdown on cell growth and apoptosis were evaluated using Celigo,MTT,clone formation assays and flow cytometry.Results Proteinatlas and TCGA database analysis suggested that SPAG5 was highly expressed in gastric cancer,and Kaplan-Meier analysis and GEPIA analysis showed high expressions of SPAG 5 in lung adenocarcinoma,breast cancer,hepatocellular carcinoma,pancreatic carcinoma,cervical cancer and bladder carcinoma.Immunohistochemistry revealed that SPAG5 was highly expressed in gastric cancer tissues(P<0.001),and immunofluorescence colocalization analysis demonstrated a significant correlation between SPAG5 and MKI67(R=0.393,P<0.001).RT-qPCR and Western blotting showed that SPAG5 was highly expressed in MKN74,BGC823,MGC803,SGC7901 and AGS cells.In AGS and MGC803 cells,SPAG5 knockdown significantly inhibited proliferation and promoted apoptosis.Conclusions The expressions of SPAG5 and MKi67 are correlated in gastric cancer tissues,and SPAG5 knockdown inhibits the proliferation of gastric cancer cells.SPAG5 is associated with the prognosis of gastric cancer patients and may serve as a promising biomarker for gastric cancer.

Objective:To explore the effects of the intervention of ginger baixiao moxibustion combined with probiotics on immune function, liver and kidney function of colorectal cancer patients after surgery, so as to provide a theoretical basis for clinical intervention methods to promote postoperative rehabilitation of patients.Methods:This study was a randomized controlled trial, and 180 patients with colorectal cancer radical resection from the Cancer Hospital of Guangxi Medical University were randomly divided into 4 groups, namely control group, probiotic group, ginger baixiao moxibustion group, and combination group, with 45 cases in each group. The control group was given routine nursing before and after surgery. In the probiotic group, probiotics were used for 3 d in routine preoperative care and 4 d from the first day after surgery. The preoperative routine care of the ginger baixiao moxibustion group was supplemented by ginger baixiao moxibustion for 3 d, and the intervention was carried out on the first day after surgery for 4 d. The combined group was treated with probiotics before and after surgery, and the specific intervention methods were the same as those of the probiotics group and the ginger baixiao moxibustion group. The differences in postoperative immune function, liver and kidney function and and other indexes among the four groups were compared.Results:Forty-five cases were ultimately selected from each of the 4 groups. There were 31 males and 14 females, aged (56.67 ± 10.13) years old in the control group. There were 27 males and 18 females, aged (55.33 ± 13.02) years old in the probiotic group. There were 20 males and 25 females, aged (57.87 ± 12.43) years old in the ginger baixiao moxibustion group. There were 26 males and 19 females, aged (57.67 ± 11.63) years old in the combination group. The IgA at 5 d after the operation in the control group, the probiotic group, the ginger baixiao moxibustion group and the combined group were (1.46 ± 0.42), (1.71 ± 0.49), (1.72 ± 0.58), (1.97 ± 0.72) g/L, and the IgM were (0.96 ± 0.20), (1.13 ± 0.33), (1.11 ± 0.35), (1.18 ± 0.52) g/L, and the IgG were (8.45 ± 1.68), (9.57 ± 1.71), (9.41 ± 2.14), (10.40 ± 2.16) g/L, and the differences among the four groups were statistically significant ( F=6.20, 10.64, 7.69, all P<0.05). The CD3 + values at 5 d after the operation in the control group, the probiotic group, the ginger baixiao moxibustion group and the combined group were 0.616 ± 0.094, 0.671 ± 0.101, 0.653 ± 0.119, 0.723 ± 0.091, and CD4 + were 0.408 ± 0.060, 0.444 ± 0.063, 0.441 ± 0.103, 0.483 ± 0.069, and CD4 +/CD8 + were 2.173 ± 0.715, 2.367 ± 0.963, 2.204 ± 1.137, 2.803 ± 1.064, and the differences among the four groups were statistically significant ( F=8.58, 7.43, 3.93, all P<0.05). The alanine aminotransferases at 5 d after the operation in the control group, the probiotic group, the ginger baixiao moxibustion group and the combined group were (16.22 ± 11.56), (15.87 ± 10.69), (12.91 ± 7.45), (11.31 ± 8.31) U/L, and the aspartate aminotransferases were (26.13 ± 7.97), (25.84 ± 7.89), (25.67 ± 10.85), (21.84 ± 5.51) U/L, and the differences among the four groups were statistically significant ( F=2.71, 2.70, both P<0.05). Conclusions:The combination of ginger baixiao moxibustion and probiotics intervention can effectively improve the immune function of colorectal cancer patients after surgery, and improve the liver function and other indexes of patients to a certain extent, so as to benefit patients.

Objective:To introduce a surgical method involving the indwelling of double-J tubes(DJT)in the seminal vesicles after transurethral seminal vesiculoscopy(TSV)in order to reduce the recurrence of refractory ejaculatory duct obstruction(EDO).Methods:This randomized controlled trial included 67 EDO patients undergoing TSV in our hospitals,27 with(the trial group)and 29 without postoperative indwelling of DJTs in the seminal vesicles(the control group).We collected the general information on the pa-tients and TSV-related parameters,including age,body mass index(BMI),preoperative use of antibiotics,history of urinary tract dis-ease,operation time,hospital stay and intra-and postoperative complications,and performed comparative analyses particularly on the surgical effect,complications,recurrence rate and time to recurrence in the two groups of patients.Results:The patients in the trial and control groups were followed up for(40.5±10.6)and(32.5±14.8)months,respectively.There were no statistically signifi-cant differences in the baseline data,intra-and postoperative complications,and postoperative hospital days between the two groups(P＞0.05).Compared with the controls,the patients in the trial group showed a significantly shorter operation time([62.8±6.1]vs[49.5±7.7]min,P＜0.05)and a lower recurrence rate than the controls(18.5％vs 44.8％,P＜0.05),but with no statisti-cally significant difference in the median time to recurrence(21.0 mo vs 22.0 mo,P＞0.05).Conclusion:The novel technique of indwelling double-J tubes in the seminal vesicles after TSV can significantly reduce the recurrence rate of refractory EDO.

Objective To investigate the relationship among circulating soluble major histocompatibility complex class Ⅰ-related chain A(sMICA),soluble major histocompatibility complex class Ⅰ-related chain B(sMICB),the activity of systemic lupus erythematosus(SLE)and autoantibodies.Methods A total of 156 SLE patients(SLE group)and 103 healthy volunteers(control group)who underwent physical examination in outpatient physical examination center were selected from the Qianjiang Hospital Affiliated to Chongqing University from January 2020 to January 2023.According to SLE disease activity score(SLEDAI),these SLE patients were divided into mild activity group(n=43),moderate activity group(n=69),and severe activity group(n=44).Serum levels of sMICA and sMICB,and the proportion of autoantibodies and peripheral blood NK cells were detected.Spearman or Pearson method was used to analyze the correlation among sMICA,sMICB,score,autoantibodies and peripheral blood NK cells proportion.Receiver operating characteristics(ROC)curve was used to evaluate the value of sMICA and sMICB in the diagnosis of SLE activity.Results Serum sMICA(173.65±23.92 pg/ml)and sMICB(96.35±15.74 pg/ml)levels in SLE group were higher than those in control group(32.51±6.27 pg/ml,12.03±2.47 pg/ml),while the proportion of CD3-CD56+NK cells(12.02％±2.65％)in peripheral blood was lower than that in control group(18.35％±3.71％),and the differences were statistically significant(t=58.498,53.897,-16.010,all P＜0.05).Serum sMICA and sMICB levels in severe active group were higher than those in moderately active group and mildly active group(t=8.192,12.352;19.652,23.742,all P＜0.05),and the proportion of CD3-CD56+NK cells in peripheral blood was lower than that in moderate and mild active groups(t=8.154,10.658,P＜0.05).The differences in positive rates of anti-dsDNA antibody,anti-nuclear antibody,anti-nucleosome antibody and anti-histone antibody in SLE patients with different disease activities were significant(x2=8.795,7.216,7.539,8.946,all P＜0.05).Serum sMICA and sMICB levels in SLE patients were positively correlated with SLED AI score,anti-dsDNA antibody,anti-nuclear antibody,anti-nucleosome antibody and anti-histone antibody(r=0.206～0.402,all P＜0.05),and negatively correlated with the proportion of CD3-CD56+NK cells in peripheral blood(r=-0.563,-0.427,all P＜0.05).The areas under the curve of SLE in severe active group diagnosed by sMICA and sMICB alone were 0.652 and 0.704,respectively.The area under the curve of SLE in severe active group diagnosed by sMICA and sMICB combined with SLE was 0.812,which was higher than that by the single diagnosis(Z=3.050,2.346,all P＜0.05).Conclusion The increased serum sMICA and sMICB levels in SLE patients were associated with the increased positive rate of SLE autoantibodies,the decreased proportion of NK cells in peripheral blood and the enhanced disease activity,which could be used as potential markers of SLE.

Aim To investigate the impact of Cinobu-facini on the proliferation,invasion,and apoptosis of HepG2 cells and the underlying mechanism.Methods The proliferation of HepG2 cells was assessed using the CCK-8 method following treatment with Cinobufaci-ni.The invasion capability of HepG2 cells was evalua-ted through Transwell assay after exposure to Cinobufa-cini.The apoptosis rates of HepG2 cells post Cinobufa-cini intervention were measured using flow cytometry,and the expression levels of VEGF in the culture medi-um of HepG2 cells were determined using enzyme-linked immunoassay.Furthermore,qRT-PCR and Western blot analyses were conducted to assess the im-pact of Cinobufacini on mRNA and protein expression levels related to the CXCL5/FOXD1/VEGF pathway.The interaction between CXCL5 and FOXD1 was inves-tigated via co-immunoprecipitation.Results Cinobufa-cini treatment led to a gradual decrease in HepG2 cell viability in a dose-dependent manner compared to the control group(P＜0.05).Moreover,Cinobufacini sig-nificantly suppressed HepG2 cell invasion(P＜0.05)while enhancing cell apoptosis(P＜0.05).Notably,Cinobufacini exhibited inhibitory effects on the CX-CL5/FOXD1/VEGF pathway,as evidenced by re-duced expression of related mRNA and proteins(P＜0.05).FOXD1 was identified as the binding site of CXCL5.Overexpression of CXCL5 resulted in in-creased proliferation and VEGF secretion by HepG2 cells(P＜0.05),and increased expression of FOXD1 and VEGF(P＜0.05).However,Cinobufacini inter-vention effectively inhibited liver cancer cell prolifera-tion and invasion(P＜0.05),promoted apoptosis(P＜0.05),reduced VEGF secretion by HepG2 cells(P＜0.05),and downregulated the expression of CXCL5 and FOXD1 in HepG2 cells(P＜0.05);but com-pared with the unexpressed group of Cinobufacini,its ability to inhibit cell activity was weakened(P＜0.05),and its ability to inhibit the expression of CX-CL5,FOXD1,and VEGF was weakened(P＜0.05).Conclusion Cinobufacini may inhibit HepG2 cell pro-liferation and invasion and promote HepG2 cell apopto-sis by regulating the CXCL5/FOXD1/VEGF pathway.