1.Impact of ischemia time and storage periods on RNA quality of fresh-frozen breast cancer and esophageal cancer tissue samples in biobank
Yang-si ZHENG ; Xuan-hao LIN ; Fan LI ; Kun-sheng XIAO ; Xi-feng CHEN ; Chun-peng LIU ; Pei-xiu YAO ; Shao-hong WANG
Fudan University Journal of Medical Sciences 2025;52(3):437-445
Objective To investigate the effects of ischemia time and storage periods on RNA quality in fresh-frozen breast cancer(BC)and esophageal cancer(EC)tissue samples in order to establish evidence-based protocols for biobank sample management.Methods The tumor(T)and paired normal(N)tissue samples from 6 cases of BC and 6 cases of EC were collected and cryopreserved in Biobank,Shantou Central Hospital.Mirror paraffin-embedded tissues were simultaneously prepared into sections for morphological analysis.The samples were divided into two groups of<15 min and 15-30 min according to ischemia time,and RNA quality was analyzed at 4 storage periods of 8-10 months(T1),14-16 months(T2),26-28 months(T3)and 38-40 months(T4).Results In 96 analyzed samples,93.8%(90/96)exhibited high quality(RIN≥6),with 89.6%(43/48)in BC and 97.9%(47/48)in EC.Significant differences in RIN were observed between BC group and EC group(8.050 vs.8.600,P=0.009).In EC group,RIN value was significantly negatively correlated with RNA yield(P<0.001).Moreover,RIN values of tumor-normal pairs exhibited markedly significant differences(7.550 vs.9.000,P<0.001).In contrast,no significant difference was detected in BC group(8.200 vs.7.700,P=0.348).Statistical analysis showed that RIN value was positively correlated with 28S/18S(P<0.001),but had no correlation with tumor content(P=0.676)and necrotic content(P=0.055).Neither ischemia time(<15 min vs.15-30 min:8.200 vs.8.300,P=0.932)nor storage periods(T1-T4:8.400,7.700,8.450,8.600,P=0.163)compromised RNA quality.Conclusion Organ origin and tissue type could influence RNA quality of fresh-frozen tissue samples.However,limited ischemia time(≤30 min)and long-term storage period(38-40 months)do not adversely affect RNA quality in fresh-frozen breast cancer and esophageal cancer tissue samples.
2.Diagnostic value of ultrasonic shear wave elastography for clinically significant prostate cancer
Fang-rui YANG ; Yong-hao JI ; Li-tao RUAN ; Jian-xue LIU ; Yao-ren ZHANG ; Xiao ZHANG ; Qin-yun WAN ; Si-fan REN
National Journal of Andrology 2025;31(6):505-511
Objective:To explore the diagnostic value of shear wave elastography(SWE)for clinically significant prostate cancer(csPCa).Methods:We retrospectively analyzed the clinical data of 359 cases with suspected prostate cancer(PCa)in Baoji Central Hospital from June 2017 to July 2023.All the patients underwent the following examinations in the order of serum prostate-spe-cific antigen(PSA)testing,transrectal ultrasonography(TRUS),measurement of the stiffness of the entire prostate gland by SWE,and TRUS-guided prostate puncture biopsy.The stiffness of the entire prostate gland was defined as the average of Young's modulus at both sides of the base,middle,and apex of the prostate,including the maximum Young's modulus(Emax),mean Young's modulus(Emean),and minimum Young's modulus(Emin).We analyzed the correlation of the parameters of the stiffness of the entire prostate gland with the pathological results,focusing on their diagnostic performance for csPCa.Results:Of the 359 cases,189 were diag-nosed by pathological puncture biopsy as BPH,26 as non-csPCa,and 144 as csPCa.The PSA level,Emax,Emean and Emin were significantly higher in the csPCa than those in the BPH and non-csPCa groups(all P<0.01),but showed no statistically significant difference between the BPH and non-csPCa groups(all P>0.05).The area under the receiver operating characteristic curve(AUC),optimal cut-off value,sensitivity,specificity,positive predictive value(PPV),negative predictive value(NPV)and accura-cy of Emax in the diagnosis of csPCa were 0.852,143.92 kPa,72.22%,84.65%,75.91%,81.98%and 79.67%;those of Emean were 0.868,82.42 kPa,67.36%,91.16%,83.62%,80.66%and 81.62%;and those of Emin were 0.682,32.73 kPa,47.22%,89.30%,73.91%,71.54%and 72.14%,respectively.In the non-csPCa group,Emax,Emean and Emin were found be-low the optimal cut-off value in 73.08%(19/26),92.31%(24/26)and 88.46%(23/26),respectively.Conclusion:The stiff-ness of the entire prostate gland measured by SWE contributes to the diagnosis of csPCa,reduces unnecessary detection of non-csPCa,and provides some reference for its active surveillance.
3.Paclitaxel induces immunogenic cell death in vascular smooth muscle cells
Chenming SI ; Yanyan HE ; Tianxiao LI ; Jia LIANG ; Yao LIU ; Yang LIU ; Chenqing LI ; Chi MA ; Hui Ferdinand K ; Yingkun HE
Chinese Journal of Neuromedicine 2025;24(2):119-130
Objective:To investigate whether paclitaxel (PTX) can induce immunogenic cell death (ICD) in vascular smooth muscle cells (VSMCs), and explore the new molecular mechanism of PTX-coated balloon angioplasty in intracranial atherosclerotic stenosis.Methods:(1) Cell culture and identification: VSMCs were induced into synthetic vascular smooth muscle cells (sVSMCs); the mRNA and protein expressions of smooth muscle protein 22-α (SM22-α) and α-smooth muscle actin (α-SMA) in VSMCsS and sVSMCs were detected by real-time fluorescent quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) and Western blotting, respectively. Human acute monocytic leukemia cell line THP-1 was induced into dendritic cells (DCs); the CD86 and CD83 expressions in THP-1 and DCs were detected by flow cytometry. (2) Cell viability detection: cell counting kit-8 (CCK-8) assay was used to detect the cell viability of sVSMCs after 0, 0.01, 0.05, 0.5, 5, 10, 50, and 100 μmol/L PTX or under 0, 50, 100, 200, 400, and 600 mmHg (1 mmHg=0.133 kPa) pressures. (3) ICD marker detection: sVSMCs were collected and divided into blank-control group, dimethyl sulfoxide (DMSO) group and PTX group (cultured with 3.2 μmol/L PTX) at normal state and pressure procedure (188 mmHg), respectively; calreticulin (CRT) expression was detected by immunofluorescent staining; adenosine triphosphate (ATP) expression was detected by luciferase assay, and high mobility group protein B1 (HMGB1) expression was detected by enzyme-linked immunosorbent assay (ELISA). (4) ICD-related immune activation assay detection: sVSMCs and DCs were collected and divided into DCs group, PTX+DCs group (cultured with 3.2 μmol/L PTX), DCs+sVSMCs group, and PTX+DCs+sVSMCs group (cultured with 3.2 μmol/L PTX); CD86 and CD83 expressions were detected by flow cytometry; interleukin (IL)-2, IL-10 and interferon-γ (IFN-γ) levels were detected by ELISA. The sVSMCs, DCs and CD8 +T cells were collected and divided into sVSMCs group, sVSMCs+DCs group, sVSMCs+CD8 +T cell group, sVSMCs+DCs+CD8 +T cell group, PTX+sVSMCs group (cultured with 3.2 μmol/L PTX), and PTX+sVSMCs+DCs+CD8 +T cell group (cultured with 3.2 μmol/L PTX); proliferation of these cells was detected by cell clone formation assay. Results:(1) The SM22-α and α-SMA mRNA and protein expressions in the sVSMCs group were significantly lower than those in the VSMCs group ( P<0.05); rate of double-positive CD83 and CD86 in the DCs group was significantly higher than that in the THP-1 group ( P<0.05). (2) The sVSMCs viability decreased in a concentration-dependent manner after PTX treatment at concentrations of 0, 0.01, 0.05, 0.5, 5, 10, 50, and 100 μmol/L, respectively, with significant differences ( P<0.05); half maximal inhibitory concentration (IC 50) of PTX on sVSMCs was 3.2 μmol/L; no significant difference in sVSMCs viability after 3.2 μmol/L PTX treatment was noted under 0, 50, 100, 200, 400, and 600 mmHg pressures ( P>0.05). (3) Under normal state and pressure procedure, CRT fluorescent intensity of sVSMCs in the PTX group (42.00±3.50, 24.19±2.41) was significantly higher than that in the blank-control group (8.60±1.8, 8.42±1.7) and DMSO group (10.23±1.47, 9.71±1.01), ATP luminescence intensity (17 399.33±2 035.58, 17 445.67±2 449.34) was significantly higher than that in the blank-control group (9 021.33±726.84, 10 271.33±2 194.22) and DMSO group (11 977.33±960.91, 11 683.33±419.50), and HMGB1 concentration ([3 258.31±502.08] pg/mL, [3 265.27±246.06] pg/mL) was significantly higher than that in the blank-control group ([1 156.48±184.96] pg/mL, [1 205.20±196.36] pg/mL) and DMSO group ([1 309.59±75.03] pg/mL, [1 265.51±14.52] pg/mL, P<0.05). (4) The PTX+DCs+sVSMCs group had significantly higher CD83, CD86, IFN-γ and IL-2 expressions and lower IL-10 expression than the DCs group, PTX+DCs group, and DCs+sVSMCs group ( P<0.05); the PTX+sVSMCs group and PTX+sVSMCs+DCs+CD8 +T cell group had significantly lower clone formation rate compared with the sVSMCs group, sVSMCs+DCs group, sVSMCs+CD8 +T cell group, and sVSMCs+DCs+CD8 +T cell group ( P<0.05). Conclusion:PTX can promote ICD in VSMCs by promoting DCs activation and enhancing CD8 +T cell toxicity.
4.Mechanism of mitochondrial DNA-ROS-Drp1 axis in regulating phenotypic transformation of vascular smooth muscle cells
Chenqing LI ; Yanyan HE ; Yingkun HE ; Bing ZHANG ; Jia LIANG ; Yao LIU ; Chenming SI ; Yang LIU ; Yu WANG ; Chi MA ; Tianxiao LI
Chinese Journal of Neuromedicine 2025;24(10):997-1012
Objective:To investigate the mechanism of mitochondrial DNA (mtDNA)-reactive oxygen species (ROS)-dynamin-related protein 1 (Drp1) axis in regulating phenotypic transformation of vascular smooth muscle cells (VSMCs).Methods:(1) VSMCs were divided into a control group, a synthetic VSMCs group, and a Drp1 siRNA+synthetic VSMCs group; cells in the Drp1 siRNA+synthetic VSMCs group were transfected with 50 nmol/L Drp1 siRNA for 48 h; cells in the latter two groups were treated with 20 ng/mL platelet-derived growth factor (PDGF)-BB, while cells in the control group were treated with an equal volume of solvent. After another 24 h of culture, Drp1 expression in VSMCs, and mitochondrial Drp1 and mitofusin 2 (Mfn2) expressions were detected by Western blotting, and changes in mitochondrial morphology were detected by mitochondrial fluorescent staining. (2) VSMCs were divided into a control group, a synthetic VSMCs group, and a mitochondrial fission inhibitor 1 (Mdivi-1)+synthetic VSMCs group; cells in the Mdivi-1+synthetic VSMCs group were pretreated with 50 μmol/L Mdivi-1 for 2 h; and cells in the latter two groups were treated with 20 ng/mL PDGF-BB, while cells in the control group were treated with an equal volume of solvent. After 24 hours of continued culture, expressions of α-smooth muscle actin (α-SMA), smooth muscle protein 22-α (SM22-α), proliferating cell nuclear antigen (PCNA), and Cyclin D1 were detected by Western blotting; invasion and migration abilities of VSMCs were detected by Transwell assay and scratch wound healing assay, respectively. (3) VSMCs were divided into a control group, a synthetic VSMCs group, and a N-acetylcysteine (NAC)+synthetic VSMCs group; cells in the NAC+synthetic VSMCs group were pretreated with 5 mmol/L NAC for 1 h; cells in the latter two groups were treated with 20 ng/mL PDGF-BB, while cells in the control group were treated with an equal volume of solvent. After 24 h of continued culture, expressions of Drp1, phosphorylated (p)-Drp1, α-SMA, SM22-α, PCNA, and Cyclin D1 were detected by Western blotting; changes in mitochondrial morphology were detected by mitochondrial fluorescent staining; intracellular ROS level was detected by 2', 7' -dichlorodihydrofluorescein diacetate (DCFH-DA) fluorescent probe; cell invasion and migration abilities were detected by Transwell assay and scratch wound healing assay, respectively. (4) VSMCs were divided into a control group, a synthetic VSMCs group, and a 5-Aza-2'-deoxycytidine (5-Aza-dC)+synthetic VSMCs group; cells in the 5-Aza-dC+synthetic VSMCs group were pretreated with 2 μmol/L 5-Aza-dC for 1 h; and then, cells in the latter two groups were treated with 20 ng/mL PDGF-BB, while cells in the control group were treated with an equal volume of solvent. After 24 h of continued culture, agarose gel electrophoresis was used to analyze the methylation degree in the mitochondrial D-loop region; intracellular ROS level was detected using DCFH-DA fluorescent probe; expressions of mitochondrial DNMT1, α-SMA, SM22-α, PCNA, and Cyclin D1 were detected by Western blotting; invasion and migration abilities were detected by Transwell assay and scratch wound healing assay, respectively.Results:(1) Compared with the control group and synthetic VSMCs group, the Drp1 siRNA+synthetic VSMCs group had significantly decreased Drp1 protein expression ( P<0.05). Compared with the control group, the synthetic VSMCs group had significantly increased Drp1 protein expression and decreased Mfn2 protein expression in the mitochondria ( P<0.05); compared with the synthetic VSMCs group, the Drp1 siRNA+synthetic VSMCs group had statistically decreased Drp1 protein expression and increased Mfn2 protein expression in the mitochondria ( P<0.05). Results of mitochondrial fluorescent staining showed that mitochondria in the control group were with filamentous structure, while mitochondrial fission in the synthetic VSMCs group was enhanced, and morphology of mitochondria in the Drp1 siRNA+synthetic VSMCs group tended to be continuous and complete. (2) Compared with the control group, the synthetic VSMCs group had statistically decreased α-SMA and SM22-α protein expressions and increased PCNA and Cyclin D1 protein expressions ( P<0.05). Compared with the synthetic VSMCs group, the Mdivi-1+synthetic VSMCs group had significantly increased α-SMA and SM22-α protein expressions and decreased PCNA and Cyclin D1 protein expressions ( P<0.05). Results of Transwell and scratch wound healing assays showed that compared with the control group, the synthetic VSMCs group had larger number of migrating cells and faster cell scratch healing; compared with the synthetic VSMCs group, the Mdivi-1+synthetic VSMCs group had smaller number of migrating cells and slower cell scratch healing. (3) Compared with the control group (1.10±0.02), the synthetic VSMCs group (1.53±0.02) had significantly increased p-Drp1 protein expression ( P<0.05). Compared with the synthetic VSMCs group, the NAC+synthetic VSMCs group (0.90±0.02) had statistically decreased p-Drp1 protein expression ( P<0.05). Results of mitochondrial fluorescent staining showed that mitochondria in cells of the control group were in a filamentous structure, while mitochondrial fission in cells of the synthetic VSMCs group was enhanced, and morphology of mitochondria in the NAC+synthetic VSMCs group tended to be continuous and complete. Results of DCFH-DA fluorescent probe showed that ROS level in the synthetic VSMCs group was higher than that in the control group, and ROS level in the NAC+synthetic VSMCs group was lower than that in the synthetic VSMCs group. Compared with the control group, the synthetic VSMCs group had significantly decreased α-SMA and SM22-α protein expressions and increased PCNA and Cyclin D1 protein expressions ( P<0.05). Compared with the synthetic VSMCs group, the NAC+synthetic VSMCs group had significantly increased α-SMA and SM22-α protein expressions and decreased PCNA and Cyclin D1 protein expressions ( P<0.05). Results of Transwell and scratch wound healing assays showed that compared with the control group, the synthetic VSMCs group had larger number of migrating cells and faster cell scratch healing; compared with the synthetic VSMCs group, the NAC+synthetic VSMCs group had smaller number of migrating cells and slower cell scratch healing. (4) Results of agarose gel electrophoresis showed that compared with the control group, the synthetic VSMCs group had significantly increased methylation rate in the mitochondrial D-loop region ( P<0.05); compared with the synthetic VSMCs group, the 5-Aza-dC+synthetic VSMCs group had statistically decreased methylation rate in the mitochondrial D-loop region ( P<0.05). Compared with the control group, the synthetic VSMCs group had statistically increased mitochondrial DNMT1 protein expression (1.03±0.03 vs. 0.55±0.03, P<0.05); and compared with the synthetic VSMCs group, the the 5-Aza-dC+synthetic VSMCs group (0.62±0.03) had significantly decreased mitochondrial DNMT1 protein expression ( P<0.05). Results of DCFH-DA fluorescent probe showed that ROS level in the synthetic VSMCs group was higher than that in the control group; ROS level in the 5-Aza-dC+synthetic VSMCs group was lower than that in the synthetic VSMCs group. Compared with the control group, the synthetic VSMCs group had significantly decreased α-SMA and SM22-α protein expressions and increased PCNA and Cyclin D1 protein expressions ( P<0.05). Compared with the synthetic VSMCs group, the 5-Aza-dC+synthetic VSMCs group had significantly increased α-SMA and SM22-α protein expressions and decreased PCNA and Cyclin D1 protein expressions ( P<0.05). Results of Transwell and scratch wound healing assays showed that compared with the control group, the synthetic VSMCs group had larger number of migrating cells and faster scratch healing. Compared with the synthetic VSMCs group, the 5-Aza-dC+synthetic VSMCs group had smaller number of migrating cells and slower scratch healing. Conclusion:The mtDNA-ROS-Drp1 axis may regulate the phenotypic transformation of VSMCs by modulating mitochondrial epigenetic modifications.
5.Advances in research on lower-limb biomechanics of Tai Ji Quan exercise intervention for knee osteoarthritis
Hongyu YUE ; Jiahe CUI ; Fangfang XIE ; Yang LI ; Mengran SI ; Fei YAO ; Jue HONG
Journal of Acupuncture and Tuina Science 2025;23(4):359-366
Knee osteoarthritis(KOA)is a prevalent chronic degenerative disorder among older adults,with biomechanical factors playing a crucial role in its pathogenesis and progression.This article aims to direct clinical studies on Tai Ji Quan(Shadow Boxing)therapeutic intervention for KOA by analyzing biomechanical factors in the pathogenesis of KOA and generalizing the biomechanical characteristics of Tai Ji Quan exercise and its impact on the gait pattern,overall mechanical balance,muscle function,plantar pressure,and proprioception of KOA patients,as well as summarizing the limitations in current clinical research.
6.Protective effect of sub-hypothermic mechanical perfusion combined with membrane lung oxygenation on a yorkshire model of brain injury after traumatic blood loss.
Xiang-Yu SONG ; Yang-Hui DONG ; Zhi-Bo JIA ; Lei-Jia CHEN ; Meng-Yi CUI ; Yan-Jun GUAN ; Bo-Yao YANG ; Si-Ce WANG ; Sheng-Feng CHEN ; Peng-Kai LI ; Heng CHEN ; Hao-Chen ZUO ; Zhan-Cheng YANG ; Wen-Jing XU ; Ya-Qun ZHAO ; Jiang PENG
Chinese Journal of Traumatology 2025;28(6):469-476
PURPOSE:
To investigate the protective effect of sub-hypothermic mechanical perfusion combined with membrane lung oxygenation on ischemic hypoxic injury of yorkshire brain tissue caused by traumatic blood loss.
METHODS:
This article performed a random controlled trial. Brain tissue of 7 yorkshire was selected and divided into the sub-low temperature anterograde machine perfusion group (n = 4) and the blank control group (n = 3) using the random number table method. A yorkshire model of brain tissue injury induced by traumatic blood loss was established. Firstly, the perfusion temperature and blood oxygen saturation were monitored in real-time during the perfusion process. The number of red blood cells, hemoglobin content, NA+, K+, and Ca2+ ions concentrations and pH of the perfusate were detected. Following perfusion, we specifically examined the parietal lobe to assess its water content. The prefrontal cortex and hippocampus were then dissected for histological evaluation, allowing us to investigate potential regional differences in tissue injury. The blank control group was sampled directly before perfusion. All statistical analyses and graphs were performed using GraphPad Prism 8.0 Student t-test. All tests were two-sided, and p value of less than 0.05 was considered to indicate statistical significance.
RESULTS:
The contents of red blood cells and hemoglobin during perfusion were maintained at normal levels but more red blood cells were destroyed 3 h after the perfusion. The blood oxygen saturation of the perfusion group was maintained at 95% - 98%. NA+ and K+ concentrations were normal most of the time during perfusion but increased significantly at about 4 h. The Ca2+ concentration remained within the normal range at each period. Glucose levels were slightly higher than the baseline level. The pH of the perfusion solution was slightly lower at the beginning of perfusion, and then gradually increased to the normal level. The water content of brain tissue in the sub-low and docile perfusion group was 78.95% ± 0.39%, which was significantly higher than that in the control group (75.27% ± 0.55%, t = 10.49, p < 0.001), and the difference was statistically significant. Compared with the blank control group, the structure and morphology of pyramidal neurons in the prefrontal cortex and CA1 region of the hippocampal gyrus were similar, and their integrity was better. The structural integrity of granulosa neurons was destroyed and cell edema increased in the perfusion group compared with the blank control group. Immunofluorescence staining for glail fibrillary acidic protein and Iba1, markers of glial cells, revealed well-preserved cell structures in the perfusion group. While there were indications of abnormal cellular activity, the analysis showed no significant difference in axon thickness or integrity compared to the 1-h blank control group.
CONCLUSIONS
Mild hypothermic machine perfusion can improve ischemia and hypoxia injury of yorkshire brain tissue caused by traumatic blood loss and delay the necrosis and apoptosis of yorkshire brain tissue by continuous oxygen supply, maintaining ion homeostasis and reducing tissue metabolism level.
Animals
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Perfusion/methods*
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Disease Models, Animal
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Brain Injuries/etiology*
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Swine
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Male
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Hypothermia, Induced/methods*
7.Associations of Ureaplasma urealyticum infection with male infertility and intrauterine insemination outcomes.
Yang-Yang WAN ; Xiao-Yun SHI ; Wen-Jing LIU ; Shun BAI ; Xin CHEN ; Si-Yao LI ; Xiao-Hua JIANG ; Li-Min WU ; Xian-Sheng ZHANG ; Juan HUA
Asian Journal of Andrology 2025;27(2):219-224
Ureaplasma urealyticum (UU) is one of the most commonly occurring pathogens associated with genital tract infections in infertile males, but the impact of seminal UU infection in semen on intrauterine insemination (IUI) outcomes is poorly understood. We collected data from 245 infertile couples who underwent IUI at The First Affiliated Hospital of USTC (Hefei, China) between January 2021 and January 2023. The subjects were classified into two groups according to their UU infection status: the UU-positive group and the UU-negative group. We compared semen parameters, pregnancy outcomes, and neonatal birth outcomes to investigate the impact of UU infection on IUI outcomes. There were no significantly statistical differences in various semen parameters, including semen volume, sperm concentration, total and progressive motility, sperm morphology, leukocyte count, the presence of anti-sperm antibody, and sperm DNA fragmentation index (DFI), between the UU-positive and UU-negative groups of male infertile patients (all P > 0.05). However, the high DNA stainability (HDS) status of sperm differed between the UU-positive and UU-negative groups, suggesting that seminal UU infection may affect sperm nuclear maturation ( P = 0.04). Additionally, there were no significant differences in pregnancy or neonatal birth outcomes between the two groups (all P > 0.05). These results suggest that IUI remains a viable and cost-effective option for infertile couples with UU infection who are facing infertility issues.
Humans
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Male
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Ureaplasma Infections/complications*
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Female
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Infertility, Male/therapy*
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Ureaplasma urealyticum/isolation & purification*
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Pregnancy
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Adult
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Pregnancy Outcome
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Semen Analysis
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Insemination, Artificial
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Semen/microbiology*
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China
8.Single-cell Protein Localization Method Based on Class Perception Graph Convolutional Network
Hao-Yang TANG ; Xin-Yue YAO ; Meng-Meng WANG ; Si-Cong YANG
Progress in Biochemistry and Biophysics 2025;52(9):2417-2427
ObjectiveThis study proposes a novel single-cell protein localization method based on a class perception graph convolutional network (CP-GCN) to overcome several critical challenges in protein microscopic image analysis, including the scarcity of cell-level annotations, inadequate feature extraction, and the difficulty in achieving precise protein localization within individual cells. The methodology involves multiple innovative components designed to enhance both feature extraction and localization accuracy. MethodsFirst, a class perception module (CPM) is developed to effectively capture and distinguish semantic features across different subcellular categories, enabling more discriminative feature representation. Building upon this, the CP-GCN network is designed to explore global features of subcellular proteins in multicellular environments. This network incorporates a category feature-aware module to extract protein semantic features aligned with label dimensions and establishes a subcellular relationship mining module to model correlations between different subcellular structures. By doing so, it generates co-occurrence embedding features that encode spatial and contextual relationships among subcellular locations, thereby improving feature representation. To further refine localization, a multi-scale feature analysis approach is employed using the K-means clustering algorithm, which classifies multi-scale features within each subcellular category and generates multi-cell class activation maps (CAMs). These CAMs highlight discriminative regions associated with specific subcellular locations, facilitating more accurate protein localization. Additionally, a pseudo-label generation strategy is introduced to address the lack of annotated single-cell data. This strategy segments multicellular images into single-cell images and assigns reliable pseudo-labels based on the CAM-predicted regions, ensuring high-quality training data for single-cell analysis. Under a transfer learning framework, the model is trained to achieve precise single-cell-level protein localization, leveraging both the extracted features and pseudo-labels for robust performance. ResultsExperimental validation on multiple single-cell test datasets demonstrates that the proposed method significantly outperforms existing approaches in terms of robustness and localization accuracy. Specifically, on the Kaggle 2021 dataset, the method achieves superior mean average precision (mAP) metrics across 18 subcellular categories, highlighting its effectiveness in diverse protein localization tasks. Visualization of the generated CAM results further confirms the model’s capability to accurately localize subcellular proteins within individual cells, even in complex multicellular environments. ConclusionThe integration of the CP-GCN network with a pseudo-labeling strategy enables the proposed method to effectively capture heterogeneous cellular features in protein images and achieve precise single-cell protein localization. This advancement not only addresses key limitations in current protein image analysis but also provides a scalable and accurate solution for subcellular protein studies, with potential applications in biomedical research and diagnostic imaging. The success of this method underscores the importance of combining advanced deep learning architectures with innovative training strategies to overcome data scarcity and improve localization performance in biological image analysis. Future work could explore the extension of this framework to other types of microscopic imaging and its application in large-scale protein interaction studies.
9.Application value of risk prediction model for acute kidney injury after donation of cardiac death liver transplantation based on machine learning algorithm
Guanrong CHEN ; Jinyan CHEN ; Xin HU ; Ronggao CHEN ; Yingchen HUANG ; Yao JIANG ; Zhongzhou SI ; Jiayin YANG ; Jinzhen CAI ; Li ZHUANG ; Zhicheng ZHOU ; Shusen ZHENG ; Xiao XU
Chinese Journal of Digestive Surgery 2025;24(2):236-248
Objective:To investigate the application value of risk prediction model for acute kidney injury (AKI) after donation of cardiac death (DCD) liver transplantation based on machine learning algorithm.Methods:The retrospective cohort study was conducted. The clinicopathological data of 1 001 pairs of DCD liver transplant donors and recipients at five hospitals, including The First Affiliated Hospital of Zhejiang University School of Medicine et al, in the Chinese Liver Transplan-tation Registry from January 2015 to December 2023 were collected. Of the donors, there were 825 males and 176 females. Of the recipients, there were 806 males and 195 females, aged 52 (range, 18-75)years. There were 281 recipients included using oversampling technique, and all 1 282 recipients were divided to the training set of 897 recipients and the validation set of 385 recipients by a ratio of 7∶3 using computer-generated random numbers. Seven prediction models, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), Support Vector Machine (SVM), Logistic Regression (LR), Decision Tree (DT), K-Nearest Neighbors (KNN), and Categorical Boosting (CatBoost), were constructed for AKI after liver transplantation based on machine learning algorithm. Observation indicators: (1) comparison of clinicopathological characteristics between recipients with and without AKI and donors; (2) follow-up and survival of recipients with and without AKI; (3) construction and validation of nomogram prediction model of AKI after liver transplantation; (4) construction and validation of machine learning prediction model of AKI after liver transplantation. Comparison of measurement data with normal distribution between groups was conducted using the independent sample t test. Comparison of measurement data with skewed distribution between groups was conducted using the Mann-Whitney U test, and comparison among groups was conducted using the Kruskal-Wallis H test. Comparison of count data between groups was conducted using the chi-square test or corrected chi-square test. Kaplan-Meier method was used to calculate survival rates and plot survival curves. Logistic regression model was performed for univariate and multivariate analyses. The receiver operating characteristic (ROC) curve was plotted to calculate area under curve (AUC) and 95% confidence interval ( CI). The performance of prediction model was evaluated using DeLong test, accuracy, sensitivity, specificity. The calibration curve was plotted to evaluate the performance of predicted probability and actual probability. The interpretability analysis of machine learning algorithm and SHapley Additive exPlanations was used to explain the model decision separately. Results:(1) Comparison of clinicopathological characteristics between recipients with and without AKI and donors. Of 1 001 recipients, there were 360 cases with AKI and 641 cases without AKI after liver transplantation. There were significant differences in body mass index (BMI), hepatic encepha-lopathy, hepatitis B surfact antigen (HBsAg), hepatorenal syndrome (HRS) and donor diabetes, donor blood urea nitrogen, donor alanine aminotransferase, donor aspartate aminotransferase, mass of graft, volume of blood loss during liver transplantation, warm ischema time of donor liver, and operation time between recipients with and without AKI ( Z=-4.337, χ2=9.751, 9.088, H=11.142, χ2=5.286, Z=-3.360, -2.539, -3.084, -1.730, -3.497, -1.996, -2.644, P<0.05). (2) Follow-up and survival of recipients with and without AKI. All the 1 001 recipients received follow-up. The recipients with AKI after liver transplantation were followed up for 18.6(range, 0-102.3)months, and recipients without AKI after liver transplantation were followed up for 31.9(range, 0.1-105.5)months. The 1-, 3-, and 5-year overall survival rates were 72.1%, 63.5%, and 59.3% of recipients with AKI, versus 86.7%, 76.7%, and 72.5% of recipients without AKI, respectively, showing a significant difference in overall survival between them ( χ2=26.028, P<0.05). (3) Construction and validation of nomogram predic-tion model of AKI after liver transplantation. Results of multivariate analysis showed that recipient BMI, recipient creatinine, recipient HBsAg, recipient HRS, donor blood urea nitrogen, donor crea-tinine, anhepatic phase and volume of blood loss during liver transplantation were independent risk factors for AKI of recipients after liver transplantation ( odds ratio=1.113, 0.998, 0.605, 1.580, 1.047, 0.998, 1.006, 1.157, 95% CI as 1.070-1.157, 0.996-1.000, 0.450-0.812, 1.021-2.070, 1.021-1.074, 0.996-0.999, 1.000-1.012, 1.045-1.281, P<0.05). The nomogram prediction model of AKI after liver transplantation was constructed based on the results of multivariate analysis. Results of ROC curve showed that the AUC of 0.666 (95% CI as 0.637-0.696). (4) Construction and validation of machine learning prediction model of AKI after liver transplantation. Based on the Lasso regression analysis, seven machine learning algorithm prediction models, including RF, XGBoost, SVM, LR, DT, KNN, and CatBoost, were constructed, with ROC curves of the validation set plotted. The AUC of above models were 0.863, 0.841, 0.721, 0.637, 0.620, 0.708, 0.731, accuracies were 0.764, 0.782, 0.701, 0.592, 0.605, 0.605, 0.681, sensitivities were 0.764, 0.789, 0.719, 0.588, 0.694, 0.694, 0.704, specificities were 0.763, 0.774, 0.683, 0.597, 0.511, 0.511, 0.656, respectively. Delong test showed that the RF model with the highest AUC of 0.863(95% CI as 0.828-0.899). Calibration curve analysis showed the predicted probability closest to the actual probability of RF model, indicating the model with a good validation value. Further sorting of SHAP of different clinical factors based on RF model showed that recipient BMI, donor blood urea nitrogen, volume of blood loss during liver transplantation, donor age had large effects on the output outcomes. Conclusion:The nomogram prediction model and seven machine learning algorithm prediction models for AKI after DCD liver transplantation are constructed, and the RF model based on machine learning has a better predictive performance.
10.Analysis of completion rate of tumor evaluation at initial assessment and after neoadjuvant therapy for mid and low rectal cancer : a national multicenter real-world study
Kexuan LI ; Tixian XIAO ; Xiaodong WANG ; Bin WU ; Guole LIN ; Yuchen GUO ; Ming QU ; Si WU ; Xiaodong YANG ; Yinshengbo′er BAO ; Baohua WANG ; Fan ZHANG ; Xiangwang YU ; Beizhan NIU ; Junyang LU ; Lai XU ; Guannan ZHANG ; Zhen SUN ; Guoyou ZHANG ; Yan SHI ; Hong JIANG ; Yongjing TIAN ; Yongxiang LI ; Hongwei YAO ; Jun XUE ; Quan WANG ; Lie YANG ; Qian LIU ; Yi XIAO
Chinese Journal of Digestive Surgery 2025;24(1):113-119
Objective:To investigate the completion rate of tumor evaluation at initial assessment and after neoadjuvant therapy for mid and low rectal cancer patients in the national multicenter real-world database.Methods:The prospective real-world study was conducted. The clinicopathological data of 1 074 patients who underwent surgical treatment for mid and low rectal cancer in 47 national medical institutions, including Peking Union Medical College Hospital et al, from May 12,2023 to May 11,2024 were collected. Observation indicators: (1) clinical characteristics of patients with mid and low rectal cancer; (2) initial colonoscopy and pathologic evaluation of tumors in patients with mid and low rectal cancer; (3) initial imaging evaluation of patients with mid and low rectal cancer; (4) imaging evaluation after neoadjuvant therapy for patients with mid and low rectal cancer. Measurement data with normal distribution were represented as Mean± SD, and measurement data with skewed distribution were represented as M( Q1, Q3). Count data were described as absoluter numbers and/or percentages. Results:(1) Clinical characteristics of patients with mid and low rectal cancer. Of the 1 074 patients, there were 713 males and 361 females, aged 63(56,70)years. The body mass index of 1 074 patients was 24(21,26)kg/m 2.For American Society of Anesthesiologists classification, there were 147 cases of stage Ⅰ, 641 cases of stage Ⅱ, 157 cases of stage Ⅲ, 2 cases of stage Ⅳ, and there were 127 cases missing data. (2) Initial colonoscopy and pathologic evaluation of tumors in patients with mid and low rectal cancer. Of the 1 074 patients, there were 787 cases (73.28%) undergoing complete colonoscopy, and there were only 197 cases (18.34%) undergoing immunohistochemical evaluation of all four mismatch repair proteins. (3) Initial imaging evaluation of patients with mid and low rectal cancer. Of the 1 074 patients, there were 842(78.40%) patients completing magnetic resonance imaging (MRI) or ultrasound evaluation, and there were 914(85.10%) patients completing chest, abdomen, and pelvis enhanced computed tomography (CT) evaluation. In the 149 patients completing rectal ultrasound evaluation, there were 122 cases (81.88%) comple-ting T staging evaluation, and there were 81 cases (54.36%) completing N staging evaluation. In the 808 patients completing rectal MRI evaluation, there were 708 cases (87.62%) completing T staging evaluation, and there were 590 cases (73.02%) completing N staging evaluation. (4) Imaging evalua-tion after neoadjuvant therapy for patients with mid and low rectal cancer. Of the 388 patients with neoadjuvant therapy, there were 332 patients (85.57%) completing MRI or ultrasound evaluation, and there were 327 patients (84.28%) completing chest, abdomen, and pelvis enhanced CT evalua-tion. In the 70 patients completing rectal ultrasound evaluation, there were 65 cases (92.86%) com-pleting T staging evaluation, and there were 49 cases (70.00%) completing N staging evaluation. In the 327 patients completing rectal MRI evaluation, there were 246 cases (75.23%) completing T staging, and there were 228 cases (69.72%) completing N staging evaluation. Conclusion:The com-pletion rate of tumor imaging evaluation at initial assessment and after neoadjuvant therapy for mid and low rectal cancer patients on a national scale is relatively good.

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