1.Weighted gene co-expression network analysis and machine learning identification of key genes in rheumatoid arthritis synovium
Yingkai WU ; Gaolong SHI ; Zonggang XIE
Chinese Journal of Tissue Engineering Research 2025;29(2):294-301
BACKGROUND:Rheumatoid arthritis is a condition that affects the entire immune system in the body and is known for causing inflammatory hyperplasia in the joints and destruction of articular cartilage.The pathogenesis of rheumatoid arthritis is still unclear;therefore,there is an urgent need to discover new highly sensitive and specific diagnostic biomarkers. OBJECTIVE:To identify and screen key genes in the synovium of rheumatoid arthritis patients using bioinformatics techniques and machine learning algorithms and to construct and validate a rheumatoid arthritis prediction model. METHODS:Three datasets containing synovial tissue samples from rheumatoid arthritis patients(GSE77298,GSE55235,GSE55457)were downloaded from the Gene Expression Omnibus(GEO)database.GSE77298 and GSE55235 were used as the training set,while GSE55457 served as the test set,with a total of 66 samples,including 39 samples from rheumatoid arthritis patients and 27 normal synovial samples.Differentially expressed genes in the training set were selected using R language,and then the weighted gene co-expression network analysis was used to modularize the genes in the training set.The most relevant module was selected,and feature genes within this module were identified.Differentially expressed genes and the feature genes from the module were intersected for the subsequent machine learning analysis.Three machine learning methods,namely the least absolute shrinkage and selection operator algorithm,support vector machine with recursive feature elimination,and random forest algorithm,were employed to further analyze the intersected genes and identify the hub genes.The hub genes obtained from these three machine learning algorithms were intersected again to obtain the key genes in the synovium of rheumatoid arthritis.A predictive rheumatoid arthritis model was constructed using these key genes as variables,and the risk of developing rheumatoid arthritis in patients was inferred based on the model.The receiver operating characteristic curve was used to determine the diagnostic value of the rheumatoid arthritis prediction model and its key genes. RESULTS AND CONCLUSION:Through the differential analysis,a total of 730 differentially expressed genes were identified in the training set,and 185 feature genes were identified in the weighted gene co-expression network analysis feature modules.There were 159 intersected genes obtained.There were 4 hub genes identified by the least absolute shrinkage and selection operator algorithm,11 hub genes by the support vector machine with recursive feature elimination algorithm,and 5 hub genes by the random forest algorithm.After intersection,2 key genes(TNS3 and SDC1)were obtained.Based on the two key genes,a nomogram model was constructed in the training and test sets,with good fit between the calibration prediction curve and the standard curve,and good clinical efficacy in predicting the onset of rheumatoid arthritis.These findings indicate that TNS3 and SDC1,obtained based on bioinformatics and machine learning algorithms,may become key targets for the diagnosis and treatment of rheumatoid arthritis.
2.Safety of high-carbohydrate fluid diet 2 h versus overnight fasting before non-emergency endoscopic retrograde cholangiopancreatography: A single-blind, multicenter, randomized controlled trial
Wenbo MENG ; W. Joseph LEUNG ; Zhenyu WANG ; Qiyong LI ; Leida ZHANG ; Kai ZHANG ; Xuefeng WANG ; Meng WANG ; Qi WANG ; Yingmei SHAO ; Jijun ZHANG ; Ping YUE ; Lei ZHANG ; Kexiang ZHU ; Xiaoliang ZHU ; Hui ZHANG ; Senlin HOU ; Kailin CAI ; Hao SUN ; Ping XUE ; Wei LIU ; Haiping WANG ; Li ZHANG ; Songming DING ; Zhiqing YANG ; Ming ZHANG ; Hao WENG ; Qingyuan WU ; Bendong CHEN ; Tiemin JIANG ; Yingkai WANG ; Lichao ZHANG ; Ke WU ; Xue YANG ; Zilong WEN ; Chun LIU ; Long MIAO ; Zhengfeng WANG ; Jiajia LI ; Xiaowen YAN ; Fangzhao WANG ; Lingen ZHANG ; Mingzhen BAI ; Ningning MI ; Xianzhuo ZHANG ; Wence ZHOU ; Jinqiu YUAN ; Azumi SUZUKI ; Kiyohito TANAKA ; Jiankang LIU ; Ula NUR ; Elisabete WEIDERPASS ; Xun LI
Chinese Medical Journal 2024;137(12):1437-1446
Background::Although overnight fasting is recommended prior to endoscopic retrograde cholangiopancreatography (ERCP), the benefits and safety of high-carbohydrate fluid diet (CFD) intake 2 h before ERCP remain unclear. This study aimed to analyze whether high-CFD intake 2 h before ERCP can be safe and accelerate patients’ recovery.Methods::This prospective, multicenter, randomized controlled trial involved 15 tertiary ERCP centers. A total of 1330 patients were randomized into CFD group ( n = 665) and fasting group ( n = 665). The CFD group received 400 mL of maltodextrin orally 2 h before ERCP, while the control group abstained from food/water overnight (>6 h) before ERCP. All ERCP procedures were performed using deep sedation with intravenous propofol. The investigators were blinded but not the patients. The primary outcomes included postoperative fatigue and abdominal pain score, and the secondary outcomes included complications and changes in metabolic indicators. The outcomes were analyzed according to a modified intention-to-treat principle. Results::The post-ERCP fatigue scores were significantly lower at 4 h (4.1 ± 2.6 vs. 4.8 ± 2.8, t = 4.23, P <0.001) and 20 h (2.4 ± 2.1 vs. 3.4 ± 2.4, t= 7.94, P <0.001) in the CFD group, with least-squares mean differences of 0.48 (95% confidence interval [CI]: 0.26–0.71, P <0.001) and 0.76 (95% CI: 0.57–0.95, P <0.001), respectively. The 4-h pain scores (2.1 ± 1.7 vs. 2.2 ± 1.7, t = 2.60, P = 0.009, with a least-squares mean difference of 0.21 [95% CI: 0.05–0.37]) and positive urine ketone levels (7.7% [39/509] vs. 15.4% [82/533], χ2 = 15.13, P <0.001) were lower in the CFD group. The CFD group had significantly less cholangitis (2.1% [13/634] vs. 4.0% [26/658], χ2 = 3.99, P = 0.046) but not pancreatitis (5.5% [35/634] vs. 6.5% [43/658], χ2 = 0.59, P = 0.444). Subgroup analysis revealed that CFD reduced the incidence of complications in patients with native papilla (odds ratio [OR]: 0.61, 95% CI: 0.39–0.95, P = 0.028) in the multivariable models. Conclusion::Ingesting 400 mL of CFD 2 h before ERCP is safe, with a reduction in post-ERCP fatigue, abdominal pain, and cholangitis during recovery.Trail Registration::ClinicalTrials.gov, No. NCT03075280.
3.Distribution and drug resistance of wound pathogenic microorganisms in outpatients of wound healing center
Lifang HUANG ; Yiwen NIU ; Jun XIANG ; Xian MA ; Yutian KANG ; Jiaoyun DONG ; Jingqi ZHOU ; Fangyi WU ; Xiaozan CAO ; Fei SONG ; Wei DONG ; Jiajun TANG ; Yingkai LIU ; Xu LUO ; Xiaoyun JI ; Shuliang LU
Chinese Journal of Trauma 2021;37(2):141-145
Objective:To analyze the distribution and drug resistance of wound pathogenic microorganisms in outpatients of wound healing center so as to provide a basis for the standardized construction of wound healing centers.Methods:A retrospective case series study was used to analyzed the data of 365 outpatients treated at Ruijin Hospital, Shanghai Jiaotong University School of Medicine from December 2017 to October 2019. There were 220 males and 145 females, aged (58.8±18.9)years (range, 18-98 years). The patients included 92 first-visit patients and 273 re-visit patients. The culture results (positive rate of pathogenic microorganisms, bacterial species, bacterial distribution) and drug sensitivity results of the wound secretions were compared and analyzed.Results:(1) Among 365 samples of wound secretions, 198 patients were positive for pathogenic microorganisms with a positive rate of 54.3%. A total of 107 strains (51.0%) of Gram-positive bacteria were detected, mainly Staphylococcus aureus (70 strains, 33.3%); 95 strains (45.2%) of Gram-negative bacteria were detected, mainly Escherichia coli (20 strains, 9.5%), followed by Pseudomonas aeruginosa (17 strains, 8.1%); 8 strains (3.8%) of fungi were detected. (2) A total of 26 (28.3%) first-visit patients were positive for pathogenic microorganisms, and 172 (63.0%) re-visit patients were positive for pathogenic microorganisms. The rate of positive microorganism detection had significant differences between first-visit and re-visit patients ( P<0.05). (3) A total of 29 strains were detected in first-visit patients, including 16 strains (55.2%) of Gram-positive bacteria, 11 strains (37.9%) of Gram-negative bacteria and 2 strains (6.9%) of fungi. A total of 181 strains were detected in re-visit patients, including 91 strains (50.3%) of Gram-positive bacteria, 84 strains (46.4%) of Gram-negative bacteria and 6 strains (3.3%) of fungi. The microbial distribution was significantly different between first-visit and re-visit patients ( P<0.05). (4) Compared with first-visit patients, the resistance of Staphylococcus aureus isolated from the re-visit patients to spenicillin, oxacillin, ciprofloxacin, tetracycline, clindamycin, moxifloxacin, erythromycin, and levofloxacin were increased variably. No vancomycin-resistant Staphylococcus aureus was detected, indicating that the staphylococcus aureus presented in the wound was highly sensitive to vancomycin. Conclusions:Staphylococcus aureus is the most common microorganism in wound secretions in outpatients of wound healing center. The rate of positive pathogenic microorganisms in wound secretions of re-visit patients is significantly higher than that of first-visit patients, and the distribution of pathogenic microorganisms of first-visited and revisited patients differs significantly. The Staphylococcus aureus detected in re-visit patients has a higher resistance to common antibiotics compared with first-visit patients. It is suggested that timely detection of pathogenic microorganisms in outpatients and effective control and supervision of outpatient infections are important contents that cannot be ignored in the construction of wound healing center.
4.Advice on the rationalized layout of outpatient clinics in a wound repair department
Ming ZHOU ; Chunlan WANG ; Jiajun TANG ; Yiwen NIU ; Yingkai LIU ; Yechen LU ; Lifang HUANG ; Jingqi ZHOU ; Fangyi WU ; Xian MA
Chinese Journal of Burns 2021;37(7):666-667
According to a document issued by the General Office of National Health Commission, "one person, one diagnosis, and one room" is required in the process of outpatient consultation. However, the patient will need to go to another room for dressing change after the doctor checks the wound if sticking to the conventional layout of current wound repair specialist outpatient clinic in hospitals and following the regulation of "separation of diagnosis and treatment". To allow a patient walking back and forth with the exposed wounds to different clinics or going to another clinic for dressing change with the original dressing reapplied to the wound is against the regulation of nosocomial infection control and the principle of sterility. To ensure that the layout of the outpatient clinic in the wound repair outpatient department not only conforms to the principle of "one person, one diagnosis, and one room", but also meets the characteristics of the diagnosis and treatment process of chronic wounds, this paper proposes the layout of "large space and small partition" in the wound repair clinic.
5.Application value of flexible endoscopy and rigid endoscopy in the clinical examination of chronic sinus tract wounds with different shapes
Guilu TAO ; Yingkai LIU ; Jiajun TANG ; Xian MA ; Lifang HUANG ; Jingqi ZHOU ; Fangyi WU ; Aobuliaximu YAKUPU ; Hanqi WANG ; Haonan GUAN ; Jiaoyun DONG ; Shuliang LU
Chinese Journal of Burns 2021;37(8):747-751
Objective:To explore the application value of flexible endoscopy and rigid endoscopy in the clinical examination of chronic sinus tract wounds with different shapes.Methods:A retrospective observational study was conducted. From January 1 to December 23, 2019, a total of 46 patients with chronic sinus tract wounds, who met the inclusion criteria were admitted to the Wound Healing Center of Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, including 23 males and 23 females, aged 18-81 (48±21) years. On admission, computer tomography (CT) imaging and three-dimensional reconstruction were performed to examine the shapes of wound sinus tract and classify the wounds, with the lengths of wound sinus tract by CT imaging examination (hereinafter referred to as reference lengths) recorded. The lengths of wound sinus tract were examined and measured by rigid endoscopy and flexible endoscopy. The wounds with and without obviously curved sinus tract were classified into curve group and linear group respectively, and the deviation rates between the lengths of wound sinus tract measured by flexible endoscopy or rigid endoscopy and the reference lengths (hereinafter referred to as deviation rates of lengths) in each group were calculated. The difference between the deviation rates of lengths examined by flexible endoscopy and rigid endoscopy and the differences between the above two and the deviation rate of reference lengths (0) in each group were compared. Data were statistically analyzed with paired sample t test and Wilcoxon signed rank sum test. Results:CT imaging and three-dimensional reconstruction showed that there were 4 types of wound sinus tract, including tubular (36/46), lamellar (4/46), club-mallet (4/46), and irregular (2/46) shape. Tubular wounds were further divided into type I (23/36), type L (4/36), and type Y (9/36). Wounds with type I tubular, lamellar, and club-mallet sinus tract were classified into linear group (31/46), while those with type Y tubular, type L tubular, and irregular sinus tract were classified into curve group (15/46). In linear group, the deviation rates of lengths examined and measured by rigid endoscopy and flexible endoscopy were 0. In curve group, the deviation rate of lengths examined and measured by flexible endoscopy was 0 (0, 0.58%), which was significantly lower than 41.18% (31.68%, 48.41%) examined and measured by rigid endoscopy, Z=-3.408, P<0.01; the deviation rate of lengths examined and measured by rigid endoscopy (40±19)% was significantly higher than the deviation rate of reference lengths ( t=8.343, P<0.01), while the deviation rate of the lengths examined and measured by flexible endoscopy was similar to the deviation rate of reference lengths ( Z=-1.342, P>0.05). Conclusions:Compared with rigid endoscopy, flexible endoscopy can observe the internal characteristics of chronic sinus tract wounds in a wider range in the clinical examination of this kind of wound, especially for the exploration of curved chronic sinus tract wounds. The promotion of this method will be conducive to the diagnosis and treatment of chronic sinus tract wounds.
6. Attention should be paid to the exposure risk of patients with chronic wounds on the way to hospital during corona virus disease 2019 epidemic prevention and control
Jingqi ZHOU ; Wei DONG ; Honglian XU ; Yunmin CAI ; Donghai SHENG ; Fangyi WU ; Yingkai LIU ; Jiajun TANG ; Weidong LIN ; Lifang HUANG ; Shuliang LU
Chinese Journal of Burns 2020;36(0):E003-E003
Statistics show that 76.74% (4 688) of 6 109 patients with chronic wounds are those over 50 years of age; the proportion of patients with underlying diseases in all age groups above 50 years ranges from 78.25% to 100.00%; among the underlying diseases of chronic wound patients, the top four diseases are diabetes mellitus , cardiovascular and cerebrovascular diseases, hypertension, and respiratory diseases. The above underlying diseases and ages of patients are the susceptibility factors of corona virus disease 2019 released by National Health Commission of China. It is an unavoidable fact that patients with chronic wounds have to go to the hospital for treatment prescribed by the physician. At the same time, we found that there were not a few patients who go far afield because of various reasons when go to the hospital for treatment. During the period of epidemic prevention and control, this kind of "go far afield" style of seeking medical treatment may increase the exposure risk during transportation. Accordingly, we convened 36 wound care clinics in different regions in Shanghai to implement the "Five Measures" to encourage patients with chronic wounds to seek medical treatment proximately. The principle of this operation is that when seeking medical treatment, trying our best to reduce as much as possible the transportation distance for patients with chronic wounds to minimize the exposure risk during the epidemic period and eventually support the epidemic prevention and control campaign.
7. Diagnosis and treatment standard for treatment with endoscopy technique in chronic wounds with sinus tract (trial version)
Xian MA ; Jiajun TANG ; Minjie WU ; Yingkai LIU ; Wei DONG ; Yakupu AOBULIAXIMU ; Yong LU ; Lifang HUANG ; Jingqi ZHOU ; Jiaoyun DONG ; Shuliang LU
Chinese Journal of Burns 2019;35(12):833-838
The " exploration of treatment technology of chronic wound with sinus tract supported by endoscope and related auxiliary methods" study had been conducted by Wound Healing Center of Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. The feasibility and effectiveness of this technique have been confirmed, and good clinic results have been achieved. In order to further promote the new technology and its related research, the theoretical knowledge and technical experience accumulated in the early stage are summarized as
8. Study on the clinical benefits of endoscopy combined with contrast fistulography in the diagnosis and treatment of chronic wound with sinus tract adjacent to body cavity
Xian MA ; Guilu TAO ; Yakupu AOBULIAXIMU ; Minfei JIANG ; Minjie WU ; Jiajun TANG ; Yingkai LIU ; Yong LU ; Hanqi WANG ; Jing SUN ; Lifang HUANG ; Shuliang LU
Chinese Journal of Burns 2019;35(6):441-445
Objective:
To explore the advantages of endoscopy combined with contrast fistulography in the clinical diagnosis and treatment of chronic wound with sinus tract adjacent to body cavity.
Methods:
Thirty-two patients (14 males and 18 females, aged 17 to 87 years) of chronic wounds with sinus tracts adjacent to body cavity, who underwent endoscopy combined with contrast fistulography (CT or magnetic resonance imaging) for the diagnosis and treatment in the Outpatient Department of Wound Healing Center of our hospital from October 2017 to March 2019, were enrolled in the study. Their diagnosis and treatment results were retrospectively analyzed. The following data were calculated. (1) The incidence rates of sinus wound involving body cavity or fistula. (2) The detection rates of sinus wound involving body cavity detected by routine examination and by endoscopy combined with contrast fistulography. (3) The detection rate of pathological features at deep part of wound by routine examination and by endoscopy combined with contrast fistulography. (4) The proportion of patients who benefited from routine examination and from endoscopy combined with contrast fistulography. Data were processed with paired chi-square test and Fisher′s exact probability test.
Results:
(1) The incidence rate of sinus wound involving body cavity was 43.75% (14/32); the incidence rate of fistula was 0. (2) The detection rate of sinus wound involving body cavity detected by endoscopy combined with contrast fistulography was 43.75% (14/32), which was obviously higher than that by routine examination [12.50% (4/32),
9.Clinical implication of changes of circulating endotheliao microparticles in burned patients
Jiajun TANG ; Minjie WU ; Yingkai LIU ; Lifang HUANG
Chinese Journal of Trauma 2018;34(5):441-448
Objective To evaluate the clinical implication of circulating endothelial microparticles in severe burned patients in burn shock resuscitation period and in patients with severe infection.Methods A retrospective case control study was conducted on 90 burned patients from January 2009 to December 2015.The patients were divided into burn shock group (n =57) and infection group (n =33).The infection group was further divided into sepsis group (n =18) and non sepsis group (n=15).There were 17 healthy controls.The numbers of CD31 +,CD51 +,CD144 +,CD54 +,and CD62E + EMPs in plasma were measured by flow cytometry immediately thereafter.The numbers and ratios of EMPs in plasma of the 16 patients from burn shock group were compared before and after fluid resuscitation.The numbers and ratios of EMPs in plasma were compared among groups.Sequential Organ Failure Assessment (SOFA) scores were used to assess the burn severity in patients at enrollment.The numbers and ratios of EMPs in plasma were compared between sepsis and non sepsis group.The correlations of SOFA with the numbers of EMPs and with the burn size were analyzed.Results Compared with control group,the numbers of CD31 +,CD51 +,CD144 +,CD54 +,and CD62E + EMPs were increased significantly in both burn shock group and infection group (P <0.05 or <0.01);the ratios of CD31 + EMPs,CD51 + EMPs,and CD54 + EMPs in plasma were significantly higher in burn shock group (P<O.05 or <0.01);the ratios of CD31 + EMPs and CD54 + EMPs were significantly higher in infection group (P < 0.05 or < 0.01).The number of CD62E + EMPs,the ratios of CD144 + EMPs and CD62E + EMPs were higher in burn shock group than those in infection group (P <0.05 or <0.01).The ratio of CD31 + EMPs in plasma was significantly higher before resuscitation than that after resuscitation in burn shock period patients (8.8 ± 1.7 vs.5.2 ±0.9) (P <0.05).The ratios of CD31 + EMPs and CD54 + EMPs were significantly higher in sepsis group than those in non-sepsis group (8.0± 1.3 vs.4.5 ± 1.0;18.3 ± 2.2 vs.8.9 ± 1.4) (P < 0.05 or < 0.O1).The number of antigen-positive EMPs correlated significantly with SOFA score (P <0.05 or <0.01).The ratio of CD54 + EMPs correlated significantly with SOFA score (P <0.01).The number and the ratio of CD54 + EMPs as well as the ratio of CD144 + EMPs was correlated with bum size (P < 0.05).SOFA score was positively correlated with the burn size (P < 0.01).Conclusions Expressions of CD31,CD54,CD144,CD62E antigens EMPs might play a role in burn pathological damage and serve as an indicator of endothelium function change after bums.Expression of CD54 of EMPs plays a role in assessing the function and severity of burned organs.
10. Application value of endoscope in probing chronic wound with sinus tract in clinic
Jiajun TANG ; Shuliang LU ; Xian MA ; Minjie WU ; Yingkai LIU ; Yong LU ; Hanqi WANG ; Chunlan WANG ; Lifang HUANG ; Jiaoyun DONG ; Xiaozan CAO ; Fei SONG ; Xiaoyun JI
Chinese Journal of Burns 2018;34(6):365-369
Objective:
To explore the application value of endoscope in probing the chronic wound with sinus tract in clinic.
Methods:
Twenty-eight chronic wounds with sinus tracts from 27 patients conforming to the inclusion criteria admitted to Outpatient Department of Wound Healing Center of Ruijin Hospital from December 2017 to March 2018 were investigated in a prospective and self-controlled trial. After being cleaned, the diameter of the opening of sinus tract was measured with a rule. A probe was used to measure the depth of a sinus tract according to the touch from the probe extremity in operation, and to measure the depth of a sinus tract that could be observed with naked eyes with the help of a pair of hemostatic forceps. Five minutes later, a probe was inserted deeply into the sinus tract to measure the depth under the endoscopic view combined with touch from the probe extremity in operation. Afterwards, the sinus tract was observed with endoscope, and the depth of the tract which could be observed under the endoscopic view was measured using a probe inserted deeply into the sinus tract. After completion of the above exploration, the sinus tract was infused with contrast agent Omnipaque 350 and scanned by computed tomography (CT) later to obtain its depth. The following indicators were calculated: the ratio of the depth of the sinus tract measured by CT to the diameter of the opening of the sinus tract (hereinafter referred to as the depth/diameter ratio of the sinus tract), the deviation rate comparing the depth of the sinus tract measured by conventional method (measured by probe only) and by endoscope (measured by probe under the endoscope view) with the depth of the sinus tract measured by CT (hereinafter referred to as the deviation rate of the measured depth of the sinus tract), the deviation rate comparing the depth of the sinus tract that could be observed measured by conventional method and by endoscope with the depth of the sinus tract measured by CT (hereinafter referred to as the deviation rate of the depth of the sinus tract that could be observed). Data were processed with paired

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