1.A virtual simulation system-based teaching method for the experimental course of oral local nerve block anesthesia
Yubin CAO ; Chao YANG ; Yi MEN ; Peng WANG ; Wei ZENG ; Guiquan ZHU ; Chaohong XIA ; Lei LIU ; Huixu XIE
Chinese Journal of Medical Education Research 2024;23(1):74-77
Objective:To investigate the effect of the virtual simulation system-based teaching method for the experimental course of oral local nerve block anesthesia in improving the effect of traditional teaching methods.Methods:One hundred and eighteen undergraduate dental students were randomly divided into two groups, the experimental group was taught using a virtual simulation-based system, and the control group was taught using traditional teaching. The results of the teaching were comprehensively evaluated through course feedback questionnaires, analysis of theoretical test scores, evaluations of the trainees administering and receiving anesthesia on the current anesthesia, and faculty evaluations of the success of the anesthesia, and t-tests and chi-square tests were performed using SPSS 23.0.Results:There was no significant difference in baseline level between the two groups. The students in the experimental group thought that the learning was more vivid ( t=4.24, P=0.005) and had more self-confidence in local anesthesia ( t=4.99, P<0.001). The students in the experimental group felt less needle tip jitter during injection ( t=2.22, P=0.048) and better contact with the medial surface of the mandible ( t=2.22, P=0.020). The students who received anesthesia reported less pain during injection ( t=1.99, P=0.029) and better anesthesia of the inferior alveolar nerve ( t=3.36, P=0.039) in the experimental group. Teacher assessment revealed that the experimental group had a significantly lower failure rate of inferior alveolar nerve block than the control group ( χ2=4.40, P=0.036). Conclusions:The virtual simulation system can optimize the experimental teaching of oral local nerve block anesthesia and can achieve a satisfactory teaching effect.
2.The effect of Ba Duan Jin on the balance of community-dwelling older adults: a cluster randomized control trial
Leilei DUAN ; Yubin ZHAO ; Yuliang ER ; Pengpeng YE ; Wei WANG ; Xin GAO ; Xiao DENG ; Ye JIN ; Yuan WANG ; Cuirong JI ; Xinyan MA ; Cong GAO ; Yuhong ZHAO ; Suqiu ZHU ; Shuzhen SU ; Xin'e GUO ; Juanjuan PENG ; Yan YU ; Chen YANG ; Yaya SU ; Ming ZHAO ; Lihua GUO ; Yiping WU ; Yangnu LUO ; Ruilin MENG ; Haofeng XU ; Huazhang LIU ; Huihong RUAN ; Bo XIE ; Huimin ZHANG ; Yuhua LIAO ; Yan CHEN ; Linhong WANG
Chinese Journal of Epidemiology 2024;45(2):250-256
Objective:To assess the effectiveness of a 6-month Ba Duan Jin exercise program in improving the balance of community-dwelling older adults.Methods:A two arms, parallel-group, cluster randomized controlled trial was conducted in 1 028 community residents aged 60-80 years in 40 communities in 5 provinces of China. Participants in the intervention group (20 communities, 523 people) received Ba Duan Jin exercise 5 days/week, 1 hour/day for 6 months, and three times of falls prevention health education, and the control group (20 communities, 505 people) received falls prevention health education same as the intervention group. The Berg balance scale (BBS) score was the leading outcome indicator, and the secondary outcome indicators included the length of time of standing on one foot (with eyes open and closed), standing in a tandem stance (with eyes open and closed), the closed circle test, and the timed up to test.Results:A total of 1 028 participants were included in the final analysis, including 731 women (71.11%) and 297 men (28.89%), and the age was (69.87±5.67) years. After the 3-month intervention, compared with the baseline data, the BBS score of the intervention group was significantly higher than the control group by 3.05 (95% CI: 2.23-3.88) points ( P<0.001). After the 6-month intervention, compared with the baseline data, the BBS score of the intervention group was significantly higher than the control group by 4.70 (95% CI: 4.03-5.37) points ( P<0.001). Ba Duan Jin showed significant improvement ( P<0.05) in all secondary outcomes after 6 months of exercise in the intervention group compared with the control group. Conclusions:This study showed that Ba Duan Jin exercise can improve balance in community-dwelling older adults aged 60-80. The longer the exercise time, the better the improvement.
3.Evaluation of efficacy and safety of tislelizumab combined with chemotherapy in neoadjuvant treatment for resectable esophageal cancer
Qin WU ; Dong WU ; Jianlong XIE ; Qinhui LUO ; Liangling LAO ; Yubin ZENG ; Liyao LIN
Journal of International Oncology 2024;51(10):620-626
Objective:To analyze the short-term efficacy and safety of tislelizumab combined with neoadjuvant chemotherapy in the treatment of resectable esophageal squamous cell carcinoma (ESCC) .Methods:The clinical data of 56 patients with ESCC who received neoadjuvant therapy combined with surgical resection in the Department of Thoracic Surgery, Affiliated Hospital of Guangdong Medical University from April 2021 to October 2023 were collected. According to the different preoperative neoadjuvant therapy methods, the patients were divided into neoadjuvant chemotherapy combined with immunotherapy group (chemoimmunization group, n=24) and neoadjuvant chemotherapy group (chemotherapy group, n=32). The postoperative tumor regression grade, objective response rate (ORR), disease control rate (DCR), pathological complete response (pCR) rate, major pathological remssion (MPR) rate, R0 resection rate, perioperative indicators, and security were compared between the two groups. Results:In chemoimmunization group, the tumor regression grade was better than that in chemotherapy group, with a statistically significant difference ( Z=9.39, P=0.025). The ORR and the DCR were 75.00% (18/24) and 91.67% (22/24) in chemoimmunization group, and 46.88% (15/32) and 65.62% (21/32) in chemotherapy group, with statistically significant differences ( χ2=4.48, P=0.034; χ2=5.21, P=0.022). The R0 resection rate was 87.50% (21/24) in chemoimmunization group, which was higher than that of the chemotherapy group [59.38% (19/32) ], with a statistically significant difference ( χ2=5.31, P=0.021). The pCR rate and MPR rate were 29.17% (7/24) and 54.17% (13/24) in chemoimmunization group, and 6.25% (2/32) and 28.12% (9/32) in chemotherapy group, there was no statistically significant difference in pCR rate ( χ2=3.78, P=0.052), but there was a statistically significant difference in MPR rate ( χ2=3.89, P=0.048). The interval between the end of neoadjuvant treatment and the start of surgery was (42.71±8.29) days in chemoimmunization group, and (42.25±8.03) days in chemotherapy group. The intraoperative blood loss of patients was (215.54±57.85) ml in chemoimmunization group, and (229.65±57.74) ml in chemotherapy group. The operation time of patients was (293.52±37.50) minutes in chemoimmunization group, and (295.31±37.66) minutes in chemotherapy group. The postoperative hospitalization time of patients was (17.90±3.49) days in chemoimmunization group, and (18.42±3.82) days in chemotherapy group, all with no statistically significant differences ( t=0.21, P=0.835; t=0.90, P=0.370; t=0.18, P=0.861; t=0.52, P=0.603). In terms of postoperative complications, there was no statistically significant difference in the total incidence of postoperative complications between the two groups [62.50% (15/24) vs. 84.38% (27/32), χ2=0.59, P=0.440]. The main adverse drug reactions in the two groups included decreased white blood cell count, nausea and vomiting, liver dysfunction, pruritus, hypothyroidism, etc. Most of them were grade 1-2, 3 cases were grade 3, and no grade 4 adverse reactions occurred. The total incidence of adverse reactions was 62.50% (15/24) in chemoimmunization group, and 65.62% (21/32) in chemotherapy group, with no statistically significant difference ( χ2=0.06, P=0.809) . Conclusion:For the preoperative neoadjuvant therapy of resectable ESCC, the combination of tislelizumab and chemotherapy has better short-term efficacy and better safety than the single chemotherapy scheme, which can improve the surgical efficacy.
4.Advances in the structure and function of chitosanase.
Jie XIE ; Yubin LI ; Jingwei LIU ; Yan GOU ; Ganggang WANG
Chinese Journal of Biotechnology 2023;39(3):912-929
Chitosanases represent a class of glycoside hydrolases with high catalytic activity on chitosan but nearly no activity on chitin. Chitosanases can convert high molecular weight chitosan into functional chitooligosaccharides with low molecular weight. In recent years, remarkable progress has been made in the research on chitosanases. This review summarizes and discusses its biochemical properties, crystal structures, catalytic mechanisms, and protein engineering, highlighting the preparation of pure chitooligosaccharides by enzymatic hydrolysis. This review may advance the understandings on the mechanism of chitosanases and promote its industrial applications.
Chitosan/chemistry*
;
Chitin
;
Glycoside Hydrolases/genetics*
;
Protein Engineering
;
Oligosaccharides/chemistry*
;
Hydrolysis
5.Use of the target territory hepatic artery dye-injection method in anatomical hepatectomy
Yan SONG ; Ting SHI ; Bing ZHOU ; Yubin XU ; Yu XIE ; Guofeng CHEN
Chinese Journal of Hepatobiliary Surgery 2022;28(9):695-697
The clinical data of patients with hepatocellular carcinoma who underwent anatomical hepatectomy at the Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University from June 2021 to January 2022 were retrospectively analyzed. Of 4 patients, there were 3 males and 1 female, aged (52.0±3.7) years. These patient underwent anatomical hepatectomy using the " target territory hepatic artery dye-injection" method. There were 2 patients with right hemi liver tumors with portal vein tumor thrombus, and 1 patient with a right anterior section tumor which involved the ventral segment of right anterior branch of portal vein. One patient had a left hemi liver tumor with portal vein tumor thrombus. The surgical operations were right hemihepatectomy combined with thrombectomy of portal vein in 2 patients, right anterior sectionectomy in 1 patient, and left hemihepatectomy combined with thrombectomy of portal vein in 1 patient. There were no postoperative complications including bile fistula or bleeding. The "Target territory hepatic artery dye-injection" method could be used in appropriate by selected patients.
6.Study on the gene frequency and polymorphism of 11 RBC blood group systems in RhD negtive population in Hunan, China
Binbin ZOU ; Yubin XIE ; Zhifen YANG ; Qing WANG ; Yonghe YAN
Chinese Journal of Blood Transfusion 2022;35(2):144-148
【Objective】 To investigate the gene frequency and polymorphism of RBC blood group systems in RhD negtive population in Hunan, so as to lay a foundation for clinical blood transfusion and construction of multiple rare blood group database. 【Methods】 Blood samples were taken from 300 RhD negative blood donors, confirmed by serological method, from June 2019 to June 2020,. RHD genotyping was performed by SSP-PCR. For blood donors with typing results as RhD negative plus RHD gene deletion, antigens genotyping of MNS, Duffy, Kell, Domrock, Diego, Kidd, Sciawnna, Colton, Lutheran and Yt RBC blood group systems were performed by SSP-PCR and analyzed by the chi square test of SPSS 20 statistical software. 【Results】 RHD gene deletions accounted for 58.67% (176 / 300) of serological D negative blood donors. The gene frequencies were as follows: MNS: GYPB*S=0.045 5(8/176), GYPB*s=0.954 5(168/176), GYP*Dane=0.039 8(7/176); Duffy: FY*A =0.965 6(170/176), FY*B=0.034 1(6/176); Dombrock: DO*A=0.082 4(14.5/176), DO*B=0.917 6(161.5/176); Diego: DI*A=0.025 6(4.5/176), DI*B =0.974 4(171.5/176); Kidd: JK*A=0.485 8(85.5/176), JK*B=0.514 2(90.5/176); Kell: KP*A=0.005 7(1/176), KP*B=0.994 3(175/176); Lutheran: LU*A=0.005 7(1/176), LU*B=0.994 3(175/176); Yt: YT*A=0.002 8(0.5/176), YT*B=0.997 2(175.5/176). The genotypes of Kell(K+ /k+ ), Scianna and Colton blood groups were KEL*02 /KEL*02, SC*01 /SC*01 and CO*A /CO*B, respectively. The expected frequencies of the combination of type O, RhD negative and other blood group systems were between 1/100 000 to 1/10 000. 【Conclusion】 Among RhD negative blood donors in Hunan, the gene profiles of MNS, Duffy, Domrock, Diego, Kidd, Kell and Lutheran blood group system were polymorphic, and Kell (K+ /k+ ), Colton and Scianna were homozygous. The data of other RBC blood group systems from RhD negative blood donors is of great significance to establish local database of rare blood groups.
7.Clinical value of muscle index changing value during neoadjuvant chemotherapy in predicting the prognosis of gastric cancer after radical gastrectomy
Yihui TANG ; Yubin MA ; Desiderio JACOPO ; Jianxian LIN ; Yinan LIU ; Ping LI ; Jianwei XIE ; Jiabin WANG ; Jun LU ; Qiyue CHEN ; Longlong CAO ; Chaohui ZHENG ; Amilcare PARISI ; Changming HUANG
Chinese Journal of Digestive Surgery 2021;20(9):955-966
Objective:To investigate the clinical value of muscle index changing value during neoadjuvant chemotherapy in predicting the prognosis of gastric cancer after radical gastrec-tomy.Methods:The retrospective cohort study was conducted. The clinicopathological data of 362 gastric cancer patients undergoing neoadjuvant chemotherapy combined with radical gastrectomy in 3 medical centers, including 163 cases in Fujian Medical University Union Hospital, 141 cases in the Affiliated Hospital of Qinghai University and 58 cases in St. Mary′s Hospital, from January 2010 to December 2017 were collected. There were 270 males and 92 females, aged from 26 to 79 years, with a median age of 61 years. Of 362 patients, 304 cases in Fujian Medical University Union Hospital and the Affiliated Hospital of Qinghai University were allocated into modeling group and 58 cases in St. Mary′s Hospital were allocated into validation group. Observation indicators: (1) changes of indicators including body composition parameters, tumor markers and stress status indicators in patients in modeling group during neoadjuvant chemotherapy; (2) follow-up and survival of patients; (3) analysis of risk factor affecting prognosis of patients in modeling group; (4) construc-tion and comparison of prognostic prediction models; (5) evaluation of prognostic prediction models. Follow-up was conducted using outpatient examination, telephone interview and mail communication to detect postoperative survival of patients up to April 2021. Measurement data with normal distribution were represented as Mean± SD. Measurement data with skewed distribution were represented as M(range). Count data were described as absolute numbers. Univariate and multivariate analysis were performed using the COX proportional hazard model. The Kaplan-Meier method was used to calculate survival rates and draw survival curves. The Log-rank test was used for survival analysis. Results:(1) Changes of indicators including body composition parameters, tumor markers and stress status indicators in patients in modeling group during neoadjuvant chemotherapy: the subcutaneous adipose index, visceral adipose index, muscle index, carcinoem-bryonic antigen, CA19-9, body mass index, prognostic nutritional index and modified systemic inflammation score of 304 gastric cancer patients in the modeling group before neoadjuvant chemotherapy were 31.2 cm 2/m 2(range, 0.6?96.0 cm 2/m 2), 25.1 cm 2/m 2(range, 0.1?86.3 cm 2/m 2), 47.1 cm 2/m 2(range, 27.6?76.6 cm 2/m 2), 43.2 μg/L(range, 0.2?1 000.0 μg/L), 108.7(range, 0.6? 1 000.0)U/mL, 21.9 kg/m 2(range, 15.6?29.7 kg/m 2), 46.8(range, 28.6?69.0), 1.0±0.8, respectively. The above indicators of 304 gastric cancer patients in the modeling group before radical gastrec-tomy were 32.5 cm 2/m 2(range, 5.1?112.0 cm 2/m 2), 25.4 cm 2/m 2(range, 0.2?89.0 cm 2/m 2), 47.0 cm 2/m 2(range, 16.8?67.0 cm 2/m 2), 17.0 μg/L(range, 0.2?1 000.0 μg/L), 43.9 U/mL(range, 0.6?1 000.0 U/mL), 21.6 kg/m 2(range, 31.1?29.0 kg/m 2), 47.7(range, 30.0?84.0), 1.0±0.8, respectively. The changing value of above indicators of 304 gastric cancer patients in the modeling group during neoadjuvant chemotherapy were 1.4 cm 2/m 2(range, ?31.0?35.1 cm 2/m 2), 0.2 cm 2/m 2(range, ?23.5?32.6 cm 2/m 2), ?0.1 cm 2/m 2(range, ?18.2?15.9 cm 2/m 2), ?26.2 μg/L(range, ?933.5?89.9 μg/L), ?64.9 U/mL(range, ?992.1?178.6 U/mL), ?0.3 kg/m 2(range, ?9.7?7.1 kg/m 2), 0.9(range, ?27.1?38.2), 0.0±0.8, respec-tively. (2) Follow-up and survival of patients: 284 of 304 patients in the modeling group were followed up for 3 to 130 months, with a median follow-up time of 36 months. During follow-up, 130 cases died of tumor recurrence and metastasis and 9 cases died of non-tumor causes. The 5-year overall survival rate was 54.6%. Fifty-two of 58 patients in the validation group were followed up for 2 to 91 months, with a median follow-up time of 29 months. During follow-up, 21 cases died with the 5-year overall survival rate of 63.8%. (3) Analysis of risk factor affecting prognosis of patients in modeling group: results of univariate analysis showed that the postoperative pathological type and postoperative pathological staging were related factors affecting 5-year overall survival rate [ hazard ratio=1.685, 2.619, 95% confidence interval(CI): 1.139?2.493, 1.941?3.533, P<0.05] and 5-year progression free rate survival of 304 gastric cancer patients in the modeling group after radical gastrectomy ( hazard ratio=1.468, 2.577, 95% CI: 1.000?2.154, 1.919?3.461, P<0.05). Results of multivariate analysis showed that the postoperative pathological type and postoperative pathological staging were independent influencing factors for 5-year overall survival rate of 304 gastric cancer patients in the modeling group after radical gastrectomy ( hazard ratio=1.508, 2.287, 95% CI: 1.013?2.245, 1.691?3.093, P<0.05) and the postoperative patholo-gical staging was an independent influencing factor for 5-year progression free survival rate of 304 gastric cancer patients in the modeling group after radical gastrectomy ( hazard ratio= 2.317,95% CI: 1.719?3.123, P<0.05). (4) Construction and comparison of prognostic prediction models: the area under curve (AUC) of prognostic prediction model of subcutaneous adipose index changing value, visceral adipose index changing value, carcinoembryonic antigen changing value, CA19-9 changing value, body mass index changing value, prognostic nutritional index changing value, modified systemic inflammation score changing value for 304 gastric cancer patients in the modeling group were 0.549(95% CI: 0.504?0.593), 0.501(95% CI: 0.456?0.546), 0.566(95% CI: 0.521?0.610), 0.519(95% CI: 0.474?0.563), 0.588(95% CI: 0.545?0.632), 0.553(95% CI: 0.509?0.597), 0.539(95% CI: 0.495?0.584). The AUC of prognostic prediction model of muscle index changing value was 0.661(95% CI: 0.623?0.705) with significant differences to the AUC of prognostic predic-tion model of subcutaneous adipose index changing value, visceral adipose index changing value, carcinoembryonic antigen changing value, CA19-9 changing value, body mass index changing value, prognostic nutritional index changing value, modified systemic inflammation score changing value, respectively ( Z=3.960, 5.326, 3.353, 4.786, 2.455, 3.448, 3.987, P<0.05). The optimum cut-off value was 0.7 cm 2/m 2 for prognostic prediction model of muscle index changing. Kaplan-Meier survival curve showed there were significant differences of overall survival and progression free survival for gastric cancer patients with subcutaneous adipose index changing value <0.7 cm 2/m 2 and ≥0.7 cm 2/m 2 in the modeling group ( χ2 =27.510, 21.830, P<0.05). The nomogram prognostic prediction model was cons-tructed based on 3 prognostic indicators including muscle index change value combined with postoperative pathological type and postoperative pathological staging and the AUC of nomogram prognostic prediction model were 0.762(95% CI: 0.708?0.815) and 0.788(95% CI: 0.661?0.885) for the modeling group and the validation group, respectively. The AUC of postoperative pathological staging prognostic prediction model were 0.706(95% CI: 0.648?0.765) and 0.727(95% CI: 0.594?0.835)for the modeling group and the validation group, respectively. There were significant differences of the AUC between the nomogram prognostic prediction model of muscle index change value combined with postoperative pathological type and postoperative pathological staging and the postoperative pathological staging prognostic prediction model in the modeling group and the validation group, respectively ( Z=3.522, 1.830, P<0.05). (5) Evaluation of prognostic prediction models: the nomogram prognostic prediction model of muscle index change value combined with postoperative pathological type and postoperative pathological staging showed that patients with score of 0-6 were classified in the low risk group, patients with score of >6 and ≤10 were classified in the moderate-low risk group, patients with score of >10 and ≤13 were classified in the moderate-high risk group and patients with score of >13 were classified in the high risk group. Kaplan-Meier survival curve showed there were significant differences of the overall survival between the low risk group, moderate-low risk group, moderate-high risk group and high risk group patients in the modeling group and the validation group, respectively ( χ2 =75.276, 14.989, P<0.05). Results of decision making curve showed the nomogram prognostic prediction model of muscle index change value combined with postoperative pathological type and postoperative pathological staging had better clinical utility than the postoperative pathological staging prognostic prediction model in the modeling group and the validation group. Conclusions:The muscle index changing value of gastric cancer patient during neoadjuvant chemotherapy can be used as a prognostic indicator for gastric cancer patient prognosis after radical gastrectomy. The risk score of the nomogram prognostic prediction model of muscle index change value combined with postoperative pathological type and postoperative pathological staging can be used to evaluate the survival and prognosis of gastric cancer patients after radical gastrectomy.
8.Complaints of blood quality: from 2014 to 2019 in Changsha
Qiao PENG ; Min TANG ; Qing LI ; Yubin XIE ; Huiping ZHANG
Chinese Journal of Blood Transfusion 2021;34(12):1347-1351
【Objective】 To investigate the complaints of blood quality in Changsha, in order to continuously improve blood quality management. 【Methods】 The Handling Forms of Blood Quality Complaints of our center during 2014~2019, and the blood units issued, corresponded to the occurrence period of complaints, were collected from the SHINOW 9.0 system, and the overall blood supply and complaints of blood quality, including various components, were classified and analyzed by SPSS19.0. 【Results】 1 865 466 bags of blood were delivered from 2014 to 2019 in Changsha, coming down 435 complaints with 435 bags of blood involved, and the total ratio of blood quality complaints rated at 0.23‰(435/1 865 466), of which red blood cell complaint accounted for 45.06%(196/435), with a rise from 30.23%(26/86) in 2014 to 49.49%(49/99) in 2019. Meanwhile, the cryoprecipitate complaint increased from 10.47%(9/86) to 20.20%(20/99). The complaints were mainly broken blood bags 29.89%(130/435), positive serological testing results(irregular antibody screening+ or direct anti globulin test+ ) 34.48%(150/435), floccule or precipitates 18.39%(80/435), clot 5.52%(24/435), lipemia 3.45%(15/435), and blood type variant(ABO subgroups and variants of RhD) 2.07%(9/435). The complaints were different in blood components, each with a particular tilt as follows: positive serological testing results in red blood cell [72.45%(142/186)], broken blood bags in plasma [83.74%(103/123)], floccule or precipitates in platelet [54.17%(13/24)] and cryoprecipitate [64.13%(59/92)] . 【Conclusion】 Broken blood bags of plasma, floccule or precipitates of cryoprecipitate, and positive serological testing results of red blood cell were the main complaints of blood quality in Changsha. Blood banks should strengthen quality control, handle quality complains cautiously and strengthen community with hospitals before transfusion to improve blood satisfaction in clinical, and save blood resources.
9.Approaches against the interference of autoantibodies with pre-transfusion compatibility testing
Fengxia LIU ; Rong HUANG ; Yongjun WANG ; Ming ZHOU ; Rong GUI ; Yubin XIE ; Jiongcai LAN ; Wei SHEN
Chinese Journal of Blood Transfusion 2021;34(8):803-808
Pre-transfusion compatibility testing is complicated in autoimmune hemolytic anemia (AIHA) patients due to the presence of autoantibodies. Delays in blood transfusion or even life-threatening would occur if blood type, isoantibodies/ autoantibodies of these patients could not be correctly identified to choose the appropriate blood components. Knowing the detection and treatment countermeasures against blood transfusion compatibility in AIHA patients is of great significance to ensure the timeliness and safety of blood transfusion. Based on the research progress at home and abroad, this article summarizes the serological characteristics, autoantibody types, blood group identification methods, antibody screening and antibody identification methods, and blood transfusion strategies about AIHA patients, in order to eliminate the interference of autoantibodies and provide transfusion guidance for the staff of Blood Transfusion Department.
10.DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning.
Yubin XIE ; Xiaotong LUO ; Yupeng LI ; Li CHEN ; Wenbin MA ; Junjiu HUANG ; Jun CUI ; Yong ZHAO ; Yu XUE ; Zhixiang ZUO ; Jian REN
Genomics, Proteomics & Bioinformatics 2018;16(4):294-306
Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases. Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively, demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%-42% improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http://deepnitro.renlab.org.
Amino Acid Sequence
;
Amino Acids
;
metabolism
;
Deep Learning
;
Humans
;
Internet
;
Neural Networks (Computer)
;
Nitrosation
;
Proteins
;
chemistry
;
metabolism
;
Reproducibility of Results
;
Software

Result Analysis
Print
Save
E-mail