1.High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome.
Yifei SHEN ; Qinghong QIAN ; Liguo DING ; Wenxin QU ; Tianyu ZHANG ; Mengdi SONG ; Yingjuan HUANG ; Mengting WANG ; Ziye XU ; Jiaye CHEN ; Ling DONG ; Hongyu CHEN ; Enhui SHEN ; Shufa ZHENG ; Yu CHEN ; Jiong LIU ; Longjiang FAN ; Yongcheng WANG
Protein & Cell 2025;16(3):211-226
Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
Humans
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Gastrointestinal Microbiome/genetics*
;
Bacteriophages/physiology*
;
High-Throughput Nucleotide Sequencing
;
Sequence Analysis, RNA/methods*
;
Bacteria/virology*
2.Nano-Bacillus Calmette-Guérin immunotherapies for improved bladder cancer treatment
ZENG SHENG ; XING SHAOQIANG ; ZHANG YIFEI ; WANG HAIFENG ; LIU QIAN
Journal of Zhejiang University. Science. B 2024;25(7):557-567
Cancer immunotherapy has rapidly become the fourth mainstream treatment alternative after surgery,radiotherapy,and chemotherapy,with some promising results.It aims to kill tumor cells by mobilizing or stimulating cytotoxic immune cells.However,the clinical applications of tumor immunotherapies are limited owing to a lack of adequate delivery pathways and high toxicity.Recently,nanomaterials and genetic engineering have shown great potential in overcoming these limitations by protecting the delivery of antigens,activating targeted T cells,modulating the immunosuppressive tumor microenvironment,and improving the treatment efficacy.Bacillus Calmette-Guérin(BCG)is a live attenuated Mycobacterium bovis vaccine used to prevent tuberculosis,which was first reported to have antitumor activity in 1927.BCG therapy can activate the immune system by inducing various cytokines and chemokines,and its specific immune and inflammatory responses exert antitumor effects.BCG was first used during the 1970s as an intravesical treatment agent for bladder cancer,which effectively improved immune antitumor activity and prevented tumor recurrence.More recently,nano-BCG and genetically engineered BCG have been proposed as treatment alternatives for bladder cancer due to their ability to induce stronger and more stable immune responses.In this study,we outline the development of nano-BCG and genetically engineered BCG for bladder cancer immunotherapy and review their potential and associated challenges.
3.Association of complement C3 with urine protein level and proteinuria remission status in patients with primary membranous nephropathy
Si CHEN ; Ying PAN ; Yifei LU ; Li QIAN ; Qing LI ; Yili XU ; Suyan DUAN ; Lin WU ; Bo ZHANG ; Changying XING ; Huijuan MAO ; Yanggang YUAN
Chinese Journal of Nephrology 2024;40(9):705-715
Objective:To investigate the correlation between complement C3 and urine protein level and proteinuria remission status in patients with primary membranous nephropathy (PMN), and better guide individualized clinical treatment.Methods:It was a single-center retrospective study. The clinical data of PMN patients who underwent renal biopsy in the First Affiliated Hospital of Nanjing Medical University from January 2017 to June 2022 were collected. Patients with 24 h urinary protein ≥ 3.5 g were followed up after receiving standard treatment, and the last outpatient or inpatient review was used as the end point of follow-up. 24 h urine protein was collected to evaluate the remission status of proteinuria. Kaplan-Meier method was used to analyze the correlation between serum and renal complements and proteinuria remission. Cox regression analysis method was used to analyze the correlation between serum C3 level and renal tissue C3 deposition and proteinuria remission.Results:This study included 507 PMN patients with 312 (61.54%) males, aged 54 (43, 64) years old. Compared with 24 h urinary protein < 3.5 g group, proportion of males ( χ2=22.479, P<0.001), age ( Z=-2.521, P=0.012), systolic blood pressure ( Z=-4.148, P<0.001), diastolic blood pressure ( Z=-4.084, P<0.001), serum anti-phospholipase A2 receptor (PLA2R) antibody titer ( Z=-7.019, P<0.001), total cholesterol ( Z=-8.796, P<0.001), triglyceride ( Z=-6.158, P<0.001), low density lipoprotein cholesterol ( Z=-8.716, P<0.001), serum creatinine ( Z=-7.368, P<0.001), serum C3 ( Z=-3.663, P<0.001), serum C4 ( Z=-6.560, P<0.001), proportion of glucocorticoid use ( χ2=116.417, P<0.001) and proportion of immunosuppressant use ( χ2=53.839, P<0.001) were all higher, while serum albumin ( Z=12.518, P<0.001), estimated glomerular filtration rate ( Z=6.345, P<0.001) and serum IgG ( Z=7.321, P<0.001) were all lower in 24 h urinary protein ≥3.5 g group. There were 268 patients included in the follow-up cohort with baseline 24 h urinary protein of 7.15 (5.14, 10.24) g, serum anti-PLA2R antibody titer of 61.44 (14.35, 193.24) RU/ml, serum C3 of 1.005 (0.864, 1.150) g/L, and serum C4 of 0.260 (0.214, 0.317) g/L. Kaplan-Meier survival curve showed that the incomplete remission rate of proteinuria in serum C3 > 1.005 g/L group was lower than that in serum C3 ≤ 1.005 g/L group (log-rank χ2=4.757, P=0.029). There was no significant difference in the incomplete remission rate of proteinuria between serum C4 ≤ 0.260 g/L group and serum C4 > 0.260 g/L group (log-rank χ2=3.543, P=0.060). Renal C1q (log-rank χ2=0.167, P=0.683) and C4 (log-rank χ2=1.927, P=0.165) deposition had no significant effects on proteinuria remission in PMN patients. The incomplete remission rate of proteinuria in patients with renal C3 deposition was higher than that in patients without renal C3 deposition (log-rank χ2=7.018, P=0.008). Univariate Cox regression analysis showed that serum C3 level and C3 deposition in renal tissues were influencing factors of incomplete remission of proteinuria (both P<0.05), while adjusting for gender, age, mean arterial pressure, serum anti-PLA2R antibody, serum albumin and 24 h urinary protein, serum C3 ≤ 1.005 g/L ( HR=1.374, 95% CI 1.021-1.849, P=0.036), C3 deposition in renal tissues ( HR=1.949, 95% CI 1.098-3.460, P=0.023), and serum C3 ≤ 1.005 g/L combined with C3 deposition in renal tissues ( HR=1.472, 95% CI 1.093-1.983, P=0.011) were independent influencing factors of incomplete remission of proteinuria. Conclusions:The serum C3 level and C3 deposition in renal tissues are closely related to urinary protein level and proteinuria remission status in PMN patients. The patients with higher urinary protein have higher serum C3. For patients with massive proteinuria, serum C3 ≤ 1.005 g/L, C3 deposition in renal tissues, serum C3 ≤ 1.005 g/L combined with C3 deposition in renal tissues are independent risk factors of incomplete remission of proteinuria.
4.Exemplifying interspecies variation of liposome in vivo fate by the effects of anti-PEG antibodies.
Ercan WU ; Juan GUAN ; Yifei YU ; Shiqi LIN ; Tianhao DING ; Yuxiu CHU ; Feng PAN ; Mengyuan LIU ; Yang YANG ; Zui ZHANG ; Jian ZHANG ; Changyou ZHAN ; Jun QIAN
Acta Pharmaceutica Sinica B 2024;14(11):4994-5007
The different fate of liposomes among species has been discovered and mentioned in many studies, but the underlying mechanisms have not been explored. In the present work, we concentrated on the in vivo fate of PEGylated liposomes (sLip) in three commonly used species (mice, rats, and dogs). It was exhibited that the accelerated blood clearance (ABC) phenomenon and hypersensitivity in large animals (beagle dogs) were much more significant than that in rodents. We demonstrated that anti-PEG IgM (partially) and complement (mostly) determined the elimination of sLip and linked the distinct interspecies performances with the diverse complement capacity among species. Based on the data from animals and clinical patients, it was revealed that the fate of sLip in large animals was closer to that in humans, for the sufficient complement capacity could expose the potential adverse reactions caused by anti-PEG antibodies. Our results suggested that the distinctive interspecies performances of sLip were highly related to the physiological variabilities among species, which should not be overlooked in the innovation and translation of nanomedicines.
5.Association of sleep quality, depressive symptoms with non suicidal self injury among rural middle school students
LUO Yunjiao, YAN Na, PEI Yifei, CHEN Qian, WANG Jingjing, TANG Jie, WANG Yuhao, WANG Wei
Chinese Journal of School Health 2023;44(2):224-228
Objective:
To investigate the association of sleep quality, depressive symptoms and their interaction with non suicidal self injury (NSSI) among rural middle school students, so as to provide a reference for early prevention and control of NSSI among rural middle school students.
Methods:
A multi stage cluster sampling method was used to randomly select four rural middle schools in Xuzhou, Jiangsu Province. A total of 1 723 middle school students were investigated according to the principle of grade stratification and class random selection. Paper questionnaires (including demographic factors, Non Suicidal Self Injury Short Scale, Pittsburgh Sleep Quality Index, Patient Health Questionnare-9) were used to conduct the questionnaire survey. Logistic regression model was used to analyze the association of sleep quality, depressive symptoms and their interaction with NSSI among rural middle school students.
Results:
Totally 30.5% of middle school students had NSSI. Univariate results showed that girls (33.0%) had a higher incidence of NSSI than boys(27.3%), and those with sleep disorders and depressive symptoms had a higher incidence of NSSI, which was 46.8%, 43.6%. The results of multivariate Logistic regression showed that the risk of NSSI in students with sleep disorder was 1.80 times that in those without sleep disorder( OR 95%CI=1.42-2.28, P <0.01). The risk of NSSI in students with depressive symptoms was 3.32 times higher than that in those without depressive symptoms( OR 95%CI=2.60-4.24, P <0.01). The interaction results showed that there was additive interaction between sleep disturbance and depressive symptoms on the occurrence of NSSI behavior in rural middle school students, and the relative excess risk, attributable proportion and synergy index were 1.80, 0.30 and 1.57, respectively.
Conclusion
Sleep disorder and depressive symptoms are risk factors for NSSI among rural middle school students, and there is additive interaction between them.
6.Application of progressive case teaching method based on core competency in standardized nursing training
Xiaoying CHEN ; Fei CHEN ; Jinyu QIAN ; Yifei ZHANG ; Zonghua WANG ; Lei LIU ; Jishu XIAN
Chinese Journal of Medical Education Research 2023;22(7):1088-1093
Objective:To explore the application effect of progressive case teaching method based on core competency in standardized nursing training.Methods:A total of 63 nursing students rotated in department of neurosurgery from June 2020 to June 2022 were selected as the research objects and randomized into experimental group ( n=31) and control group ( n=32). The experimental group adopted the progressive case teaching method based on core competency, and the control group adopted the conventional teaching mode. The data was analyzed using SPSS 26.0 to conduct t-test or non-parametric test based on the data normality for comparing the theory results, objective structure clinical examination (OSCE) scores, core competency, self-directed learning ability scores, teaching satisfaction and nursing satisfaction of patients in two wards between the two groups. Results:The theoretical results ( t=4.74, P<0.001) and OSCE scores ( t=3.81, P<0.001) of the experimental group were better than those of the control group. The scores of core competency and autonomous learning ability ( t=4.32, P<0.001) of the experimental group were better than those of the control group. The teaching satisfaction score ( t=2.21, P=0.044) and patient satisfaction score ( t=2.92, P=0.011) of the observation group were better than those of the control group. Conclusion:The progressive case teaching method based on core competency can improve the post competency of nurses, and also improve the teaching satisfaction rate and patient satisfaction rate, which is worthy of being carried out in the subsequent teaching activities.
7.The comprehensive analysis of clinical characteristics and magnetic resonance imaging of non-malignant patients assigned to PI-RADS 5 score
Yamin WANG ; Linghui LIANG ; Yifei CHENG ; Jinwei SHANG ; Ruizhe ZHAO ; Wei XIA ; Yiyang LIU ; Chao LIANG ; Shangqian WANG ; Jian QIAN ; Gong CHENG ; Lixin HUA
Chinese Journal of Urology 2023;44(2):92-96
Objective:To analyze the clinical features and magnetic resonance imaging of non-malignant patients assigned to Prostate Imaging Reporting And Data System (PI-RADS) 5 score.Methods:We performed a retrospective review of 289 patients who underwent magnetic resonance ultrasound targeted combined system biopsy with PI-RADS 5 lesions in the First Affiliated Hospital of Nanjing Medical University between May 2019 and July 2021. The median age 72 (66, 77)years, median body mass index 24.4(22.3, 27.1)kg/m 2, median prostate volume (PV) 37.39(29.39, 48.86) ml, median PSA 22.24(10.91, 62.69) ng/ml, and median PSAD 0.53(0.30, 1.52)ng/ml 2 were recorded. According to the biopsy pathological results, all patients were divided into benign lesion group and prostate cancer group. PSA, PSAD, PV, and apparent diffusion coefficient (ADC) values were compared, and magnetic resonance imaging and clinical characteristics of patients with biopsy benign lesions were analyzed. Results:There were 11 cases (3.8%) with benign lesion and 278 cases (96.2%) with prostate cancer. The characters of 11 negative biopsy cases were displayed as follows: median age 69(66, 79)years, median body mass index 22.0(21.0, 25.5)kg/m 2, median PV 62.90(38.48, 71.96)ml, median PSA 5.55(2.99, 20.52)ng/ml, median PSAD 0.16(0.07, 0.24) ng/ml 2, median ADC 714.47(701.91, 801.26)×10 -6 mm 2/s, abnormal digital rectal and amination in 5 cases, smoking in 7 cases, and alcohol consumption in 4 cases. The median PV [62.90(38.48, 71.96) vs. 37.21(29.22, 47.82)ml, P<0.01], the PSA value [5.55(2.99, 20.52) vs. 23.53(11.14, 65.98)ng/ml, P<0.01], and the PSAD value [0.16(0.07, 0.24) vs. 0.58(0.31, 1.57)ng/ml 2, P<0.01] were significantly different between benign condition group and prostate carcinoma group. Benign condition group included 5 chronic prostatitis, 2 acute prostatitis (1 with focal adenocarcinoma), 2 granulomatous inflammation, and 2 tuberculous granulomatous inflammation. In 7 benign cases, PSA was less than 10 ng/ml, combined with frequent urination, urgency of urination and incontinence were founded. In 8 benign cases, the area of lesion was more than 50% of the total prostate area in the axial position and the imaging of magnetic resonance were diffused, with regular shape and uniform signal. The imaging of symmetrical distribution was in 6 cases. Conclusions:The benign condition with PI-RADS 5 lesions included chronic prostatitis, acute prostatitis, granulomatous inflammation and tuberculous granulomatous inflammation, among which prostatitis was the most common cause. The PSA value were less than 10 ng/ml in most benign cases, with symptoms such as frequent urination, urgency of urination and incontinence. The imaging of magnetic resonance were diffused, symmetrically distributed, with regular shape and uniform signal.
8.CHESS endoscopic ruler in objective measurement of diameter of esophageal varices in liver cirrhosis and portal hypertension: a prospective multicenter study
Shengjuan HU ; Jianping HU ; Shaoqi YANG ; Xiaoguo LI ; Yanhong DENG ; Ruichun SHI ; Xiaoqin LI ; Hailong QI ; Qian SHEN ; Fang HE ; Jun ZHU ; Bin MA ; Xiaobing YU ; Jianyang GUO ; Yuehua YU ; Haijiang YONG ; Wentun YAO ; Ting YE ; Hua WANG ; Wenfu DONG ; Jianguo LIU ; Qiang WEI ; Jing TIAN ; Haoxiang HE ; Changhui HE ; Yifei HUANG ; Yang BU ; Xiaolong QI
Chinese Journal of Digestion 2023;43(3):193-198
Objective:To investigate the safety and feasibility of the CHESS endoscpic ruler (CHESS ruler), and the consistency between the measured values and the interpretation values by endoscopic physician experience.Methods:From January 2021 to January 2022, a total of 105 liver cirrhosis patients with portal hypertension were prospectively enrolled from General Hospital, Xixia Branch Hospital, Ningnan Hospital of People′s Hospital of Ningxia Hui Autonomous Region (29 cases), and the First People′s Hospital of Yinchuan (25 cases), General Hospital of Ningxia Medical University (18 cases), Wuzhong People′s Hospital (10 cases), the Fifth People′s Hospital of Ningxia Hui Autonomous Region (10 cases), Shizuishan Second People′s Hospital (6 cases), Yinchuan Second People′s Hospital (5 cases), and Zhongwei People′s Hospital (2 cases) 8 hospitals. The clinical characteristics of all the patients, including gender, age, nationality, etiolog of liver cirrhosis, and Child-Pugh classification of liver function were recorded. A big gastroesophageal varices was defined as diameter of varices ≥5 mm. Endoscopist (associated chief physician) performed gastroscopy according to the routine gastroscopy procedures, and the diameter of the biggest esophageal varices was measured by experience and images were collected, and then objective measurement was with the CHESS ruler and images were collected. The diameter of esophageal varices of 10 randomly selected patients (random number table method) was determined by 6 endoscopists (attending physician or associated chief physician) with experience or measured by CHESS ruler. Kappa test was used to test the consistency in the diameter of esophageal varices between measured values by CHESS ruler and the interpretation values by endoscopic physician experience.Results:Among 105 liver cirrhosis patients with portal hypertension, male 65 cases and female 40 cases, aged (54.8±12.2) years old, Han nationality 82 cases, Hui nationality 21 cases and Mongolian nationality 2 cases. The etiology of liver cirrhosis included chronic hepatitis B (79 cases), alcoholic liver disease (7 cases), autoimmune hepatitis (7 cases), chronic hepatitis C (2 cases), and other etiology (10 cases). Liver function of 32 cases was Child-Pugh A, Child-Pugh B 57 cases, and Child-Pugh C 16 cases. All 105 liver cirrhosis patients with cirrhotic portal hypertension were successfully measured the diameter of gastroesophageal varices by CHESS ruler, and the success rate of application of CHESS ruler was 100.0% (105/105). The procedure time from the CHESS ruler into the body to the exit of the body after measurement was (3.50±2.55) min. No complications happened in all the patients during measurement. Among 105 liver cirrhosis patients with cirrhotic portal hypertension, 96 cases (91.4%) were recognized as big gastroesophageal varices by the endoscopists. Totally 93 cases (88.6%) were considered as big gastroesophageal varices by CHESS ruler. Eight cases were recognized as big gastroesophageal varices by the endoscopist, however not by the CHESS ruler; 5 cases were recognized as big gastroesophageal varices by the CHESS ruler, but not by the endoscopists; 4 cases were not recognized as big gastroesophageal varices both by the endoscopists and CHESS ruler; 88 cases were recognized as big gastroesophageal varices both by the endoscopists and CHESS ruler. The missed diagnostic rate of big gastroesophageal varices by the endoscopists experience was 5.4% (5/93), and the Kappa value of consistency coefficient between the measurement by the CHESS ruler and the interpretation by endoscopists experience was 0.31 (95% confidence interval 0.03 to 0.60). The overall Kappa value of consistency coefficient by 6 endoscopists measured by CHESS ruler in big gastroesophageal varices diagnosis was 0.77 (95% confidence interval 0.61 to 0.93).Conclusion:As an objective measurement tool, CHESS ruler can make up for the deficiency of subjective judgment by endoscopists, accurately measure the diameter of gastroesophageal varices, and is highly feasible and safe.
9.How adverse and benevolent childhood experiences influence depression and suicidal ideation in Chinese undergraduates: a latent class analysis.
Jie TANG ; Jingjing WANG ; Yifei PEI ; Shiferaw Blen DEREJE ; Qian CHEN ; Na YAN ; Yunjiao LUO ; Yuhao WANG ; Wei WANG
Environmental Health and Preventive Medicine 2023;28():17-17
BACKGROUND:
There has been minimal research on the role of benevolent childhood experiences (BCEs) and how such events may offer protection from the insidious effects of adverse childhood experiences (ACEs) or later in life.
OBJECTIVES:
This research aims to learn how BCEs and ACEs interact to affect adolescents' psychological distress.
METHODS:
Cross-sectional survey was conducted in three cities (Xuzhou, Nanjing, and Wuhan) in China from March 2021 to May 2021. Latent class analysis (LCA) was used to classify the patterns of ACEs and BCEs. We adopted hierarchical multivariable regression to examine the influences of ACEs and BCEs on depression and suicidal ideation.
RESULTS:
To explore the relationship between childhood experience and suicidal ideation and depression, LCA revealed three patterns of ACEs: (1) emotional abuse (10.57%); (2) high ACEs (0.55%); and (3) low ACEs classes (88.88%). Adolescents with emotional abuse (depression: OR = 3.82, 95%CI = 2.80-5.22, P < 0.001; suicidal ideation: OR = 5.766, 95%CI = 3.97-8.38, P < 0.001) and high ACEs class (suicidal ideation: OR = 5.93, 95%CI = 1.19-29.66, P < 0.05) had an increased risk of psychological distress (reference: low ACEs). LCA revealed four patterns of BCEs: (1) relationship support (14.54%); (2) low BCEs (4.85%); (3) high BCEs (55.34%); and (4) high quality of life classes (25.28%). Adolescents with a high quality of life (depression: OR = 0.09, 95%CI = 0.05-0.16, P < 0.001; suicidal ideation: OR = 0.22, 95%CI = 0.12-0.40, P < 0.001) and high BCEs (depression: OR = 0.05, 95%CI = 0.03-0.09, P < 0.001; suicidal ideation: OR = 0.15, 95%CI = 0.09-0.26, P < 0.001) protected the mental health of adolescents (reference: low BCEs).
CONCLUSIONS
High ACEs and emotional abuse classes were significantly associated with poorer mental health symptoms, including suicidal ideation and depression. In contrast, high BCEs and high quality of life classes were associated with better mental health. These findings point out that it is more necessary to identify and support victims of ACEs, and it is urgent to increase BCEs in early childhood.
Adolescent
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Humans
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Cross-Sectional Studies
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Depression
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East Asian People
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Latent Class Analysis
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Quality of Life
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Suicidal Ideation
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Adverse Childhood Experiences
10.Application of magnetic resonance sacral neurography combined with 3D printing in sacral nerve modulation in neurogenic bladder patients with special comorbidities
Changsheng ZHAN ; Yinfeng QIAN ; Wei CHEN ; Xuemei ZHAO ; Xiaoqin LIU ; Cheng ZHANG ; Yifei ZHANG ; Chaozhao LIANG
Chinese Journal of Urology 2023;44(10):781-782
This paper discusses the application of MRN combined with 3D printing in SNM in neurogenic bladder patients with special comorbidities. In this study, 21 cases of neurogenic bladder patients with special comorbidities involved, including 14 cases into the control group and 7 cases in the experimental group. Traditional X-ray guidance was used in the control group, while the MRN combined with 3D printing navigation template positioning was used in the experimental group. Compared with those in the control group, the X-ray fluoroscopy, number of punctures, puncture time, intraoperative adjustment and testing time were significantly decreased in the experimental group. The difference of implantable pulse generator implantation rates between the two groups was statistically significant.


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