88 results on '"Shen, N."'
Search Results
2. DNA hydrogels and their derivatives in biomedical engineering applications.
- Author
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Wu R, Li W, Yang P, Shen N, Yang A, Liu X, Ju Y, Lei L, and Fang B
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- Humans, Animals, Drug Delivery Systems methods, Biomedical Engineering methods, Biosensing Techniques methods, Cell Culture Techniques methods, Hydrogels chemistry, DNA chemistry, Tissue Engineering methods, Biocompatible Materials chemistry
- Abstract
Deoxyribonucleotide (DNA) is uniquely programmable and biocompatible, and exhibits unique appeal as a biomaterial as it can be precisely designed and programmed to construct arbitrary shapes. DNA hydrogels are polymer networks comprising cross-linked DNA strands. As DNA hydrogels present programmability, biocompatibility, and stimulus responsiveness, they are extensively explored in the field of biomedicine. In this study, we provide an overview of recent advancements in DNA hydrogel technology. We outline the different design philosophies and methods of DNA hydrogel preparation, discuss its special physicochemical characteristics, and highlight the various uses of DNA hydrogels in biomedical domains, such as drug delivery, biosensing, tissue engineering, and cell culture. Finally, we discuss the current difficulties facing DNA hydrogels and their potential future development., (© 2024. The Author(s).)
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- 2024
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3. The causal role between circulating immune cells and diabetic nephropathy: a bidirectional Mendelian randomization with mediating insights.
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Shen N, Lu S, Kong Z, Gao Y, Hu J, Si S, Wang J, Li J, Han W, Wang R, and Lv Z
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Diabetic nephropathy (DN) is a critical inflammatory condition linked to diabetes, affecting millions worldwide. This study employs Mendelian randomization (MR) to explore the causal relationship between immune cell signatures and DN, analyzing over 731 immune signatures and incorporating data from 1400 metabolites to investigate potential mediators. Despite no statistically significant influence of DN on immunophenotypes after FDR correction, some phenotypes with unadjusted low P-values warranted mention, including CD34 on Hematopoietic Stem Cell (Myeloid cell Panel), CD45 on CD33
- HLA DR- (Myeloid cell Panel). Furthermore, three immunophenotypes were identified to have a significant impact on DN risk: CD16- CD56 on HLA DR+ NK (TBNK Panel), CD45 on HLA DR+ T cell (TBNK Panel), and CD33dim HLA DR+ CD11b+ AC (Myeloid cell Panel). Our findings underscore the critical role of immune cells in DN, highlighting potential mediators and offering new insights into its underlying mechanisms., (© 2024. The Author(s).)- Published
- 2024
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4. CDCA5 accelerates progression of breast cancer by promoting the binding of E2F1 and FOXM1.
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Xiong Y, Shi L, Li L, Yang W, Zhang H, Zhao X, and Shen N
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- Humans, Female, Animals, Cell Line, Tumor, Middle Aged, Apoptosis, Prognosis, Mice, Nude, Cell Movement, Promoter Regions, Genetic genetics, Mice, Inbred BALB C, Mice, Gene Knockdown Techniques, Adaptor Proteins, Signal Transducing, Breast Neoplasms pathology, Breast Neoplasms genetics, Breast Neoplasms metabolism, Forkhead Box Protein M1 metabolism, Forkhead Box Protein M1 genetics, Cell Cycle Proteins metabolism, Cell Cycle Proteins genetics, Disease Progression, E2F1 Transcription Factor metabolism, E2F1 Transcription Factor genetics, Cell Proliferation, Protein Binding, Gene Expression Regulation, Neoplastic
- Abstract
Background: Breast cancer is one of the most common malignant tumors in women. Cell division cycle associated 5 (CDCA5), a master regulator of sister chromatid cohesion, was reported to be upregulated in several types of cancer. Here, the function and regulation mechanism of CDCA5 in breast cancer were explored., Methods: CDCA5 expression was identified through immunohistochemistry staining in breast cancer specimens. The correlation between CDCA5 expression with clinicopathological features and prognosis of breast cancer patients was analyzed using a tissue microarray. CDCA5 function in breast cancer was explored in CDCA5-overexpressed/knockdown cells and mice models. Co-IP, ChIP and dual-luciferase reporter assay assays were performed to clarify underlying molecular mechanisms., Results: We found that CDCA5 was expressed at a higher level in breast cancer tissues and cell lines, and overexpression of CDCA5 was significantly associated with poor prognosis of patients with breast cancer. Moreover, CDCA5 knockdown significantly suppressed the proliferation and migration, while promoted apoptosis in vitro. Mechanistically, we revealed that CDCA5 played an important role in promoting the binding of E2F transcription factor 1 (E2F1) to the forkhead box M1 (FOXM1) promoter. Furthermore, the data of in vitro and in vivo revealed that depletion of FOXM1 alleviated the effect of CDCA5 overexpression on breast cancer. Additionally, we revealed that the Wnt/β-catenin signaling pathway was required for CDCA5 induced progression of breast cancer., Conclusions: We suggested that CDCA5 promoted progression of breast cancer via CDCA5/FOXM1/Wnt axis, CDCA5 might serve as a novel therapeutic target for breast cancer treatment., (© 2024. The Author(s).)
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- 2024
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5. Open surgery with a lateral neck approach in cases of foreign body impaction that penetrating the neck through the esophagus: a single-center experience.
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Xu F, Shen N, Liu D, Zhu T, Xue L, Luo X, and Zhou X
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- Humans, Male, Female, Adult, Retrospective Studies, Middle Aged, Young Adult, Adolescent, Aged, Foreign Bodies surgery, Esophagus surgery, Neck surgery
- Abstract
Background: Because the cases are quite scarce, we aimed to review cases of foreign body impaction penetrating the neck through the esophagus to analyze the characteristics of these cases. The open surgery skills of the surgeon, the treatment procedure and the surgeons' experience in the rare diseases were analyzed., Methods: We collected and analyzed all cases from 2015-2020 in our hospital. Surgical skills and procedures for fasting and anti-infection treatment were reviewed retrospectively. Follow-up was telephone communication., Results: Our series included 15 cases. Tenderness in the pre-cervical site was a physical sign for screening. Thirteen cases underwent a lateral neck open surgery with the incision including the left side of neck and only two cases were incised from the right side of the neck. Pus was found 3 days after the impaction in one case, the shortest time observed in our series. The esophageal laceration was only sutured primarily in 5 cases (33.33%) among all fifteen cases. After sufficient drainage (average more than 9 days), antibiotic treatment and fasting (normally 2-3 weeks), patients gradually began to switch to solid foods from fluids after complete blood counts and confirmations from esophageal radiography result. No severe complications occurred, and all the patients have no swallowing dis-function and recovered well., Conclusion: Surgery should be performed as soon as possible after impaction. Lateral neck approach surgery and the therapeutic procedure described in this article are safe and effective treatments., (© 2024. The Author(s).)
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- 2024
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6. Blockade of the ADAM8-Fra-1 complex attenuates neuroinflammation by suppressing the Map3k4/MAPKs axis after spinal cord injury.
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Qian Z, Li R, Zhao T, Xie K, Li P, Li G, Shen N, Gong J, Hong X, Yang L, and Li H
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- Animals, Mice, Antigens, CD, Cell Movement drug effects, Inflammation pathology, Inflammation drug therapy, Mice, Inbred C57BL, Proto-Oncogene Proteins c-fos drug effects, Proto-Oncogene Proteins c-fos metabolism, ADAM Proteins metabolism, ADAM Proteins antagonists & inhibitors, ADAM Proteins genetics, MAP Kinase Signaling System drug effects, Membrane Proteins metabolism, Membrane Proteins genetics, Microglia metabolism, Microglia drug effects, Neuroinflammatory Diseases drug therapy, Neuroinflammatory Diseases metabolism, Spinal Cord Injuries metabolism, Spinal Cord Injuries pathology, Spinal Cord Injuries drug therapy
- Abstract
Background: Mechanical spinal cord injury (SCI) is a deteriorative neurological disorder, causing secondary neuroinflammation and neuropathy. ADAM8 is thought to be an extracellular metalloproteinase, which regulates proteolysis and cell adherence, but whether its intracellular region is involved in regulating neuroinflammation in microglia after SCI is unclear., Methods: Using animal tissue RNA-Seq and clinical blood sample examinations, we found that a specific up-regulation of ADAM8 in microglia was associated with inflammation after SCI. In vitro, microglia stimulated by HMGB1, the tail region of ADAM8, promoted microglial inflammation, migration and proliferation by directly interacting with ERKs and Fra-1 to promote activation, then further activated Map3k4/JNKs/p38. Using SCI mice, we used BK-1361, a specific inhibitor of ADAM8, to treat these mice., Results: The results showed that administration of BK-1361 attenuated the level of neuroinflammation and reduced microglial activation and recruitment by inhibiting the ADAM8/Fra-1 axis. Furthermore, treatment with BK-1361 alleviated glial scar formation, and also preserved myelin and axonal structures. The locomotor recovery of SCI mice treated with BK-1361 was therefore better than those without treatment., Conclusions: Taken together, the results showed that ADAM8 was a critical molecule, which positively regulated neuroinflammatory development and secondary pathogenesis by promoting microglial activation and migration. Mechanically, ADAM8 formed a complex with ERK and Fra-1 to further activate the Map3k4/JNK/p38 axis in microglia. Inhibition of ADAM8 by treatment with BK-1361 decreased the levels of neuroinflammation, glial formation, and neurohistological loss, leading to favorable improvement in locomotor functional recovery in SCI mice., (© 2024. The Author(s).)
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- 2024
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7. Correction: Genome Med 15, 115 & Genome Med 16, 3.
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Shen N
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- 2024
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8. Platelet-rich plasma alleviates neuropathic pain in osteoarthritis by downregulating microglial activation.
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Yan X, Ye Y, Wang L, Xue J, Shen N, and Li T
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- Animals, Male, Rats, Activating Transcription Factor 3 metabolism, Ganglia, Spinal metabolism, Disease Models, Animal, Injections, Intra-Articular, Calcium-Binding Proteins metabolism, Iodoacetic Acid toxicity, Microfilament Proteins, Platelet-Rich Plasma, Neuralgia therapy, Neuralgia metabolism, Microglia metabolism, Rats, Sprague-Dawley, Osteoarthritis, Knee therapy, Down-Regulation
- Abstract
Background: The development of neuropathic pain (NP) is one of the reasons why the pain is difficult to treat, and microglial activation plays an important role in NP. Recently, platelet-rich plasma (PRP) has emerged as a novel therapeutic method for knee osteoarthritis (KOA). However, it's unclarified whether PRP has analgesic effects on NP induced by KOA and the underlying mechanisms unknown., Purpose: To observe the analgesic effects of PRP on NP induced by KOA and explore the potential mechanisms of PRP in alleviating NP., Methods: KOA was induced in male rats with intra-articular injections of monosodium iodoacetate (MIA) on day 0. The rats received PRP or NS (normal saline) treatment at days 15, 17, and 19 after modeling. The Von Frey and Hargreaves tests were applied to assess the pain-related behaviors at different time points. After euthanizing the rats with deep anesthesia at days 28 and 42, the corresponding tissues were taken for subsequent experiments. The expression of activating transcription factor 3 (ATF3) in dorsal root ganglia (DRG) and ionized-calcium-binding adapter molecule-1(Iba-1) in the spinal dorsal horn (SDH) was detected by immunohistochemical staining. In addition, the knee histological assessment was performed by hematoxylin-eosin (HE) staining., Results: The results indicated that injection of MIA induced mechanical allodynia and thermal hyperalgesia, which could be reversed by PRP treatment. PRP downregulated the expression of ATF3 within the DRG and Iba-1 within the SDH. Furthermore, an inhibitory effect on cartilage degeneration was observed in the MIA + PRP group only on day 28., Conclusion: These results indicate that PRP intra-articular injection therapy may be a potential therapeutic agent for relieving NP induced by KOA. This effect could be attributed to downregulation of microglial activation and reduction in nerve injury., (© 2024. The Author(s).)
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- 2024
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9. Chronic atrophic gastritis and risk of incident upper gastrointestinal cancers: a systematic review and meta-analysis.
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Li J, Pan J, Xiao D, Shen N, Wang R, Miao H, Pu P, Zhang H, Yv X, and Xing L
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- Humans, Risk Factors, Chronic Disease, Incidence, Esophageal Neoplasms epidemiology, Esophageal Neoplasms pathology, Stomach Neoplasms epidemiology, Stomach Neoplasms pathology, Male, Odds Ratio, Female, Publication Bias, Gastritis, Atrophic complications, Gastritis, Atrophic epidemiology, Gastrointestinal Neoplasms epidemiology, Gastrointestinal Neoplasms pathology
- Abstract
Background: Previous literature has explored the relationship between chronic atrophic gastritis (CAG) and isolated cancers within the upper gastrointestinal cancers; However, an integrative synthesis across the totality of upper gastrointestinal cancers was conspicuously absent. The research objective was to assess the relationship between CAG and the risk of incident upper gastrointestinal cancers, specifically including gastric cancer, oesophageal cancer, and oesophagogastric junction cancer., Methods: Rigorous systematic searches were conducted across three major databases, namely PubMed, Embase and Web of Science, encompassing the timeline from database inception until August 10, 2023. We extracted the necessary odds ratio (OR) and their corresponding 95% confidence interval (CI) for subsequent meta-analysis. Statistical analyses were conducted using Stata 17.0 software., Results: This meta-analysis included a total of 23 articles encompassing 5858 patients diagnosed with upper gastrointestinal cancers. CAG resulted in a statistically significant 4.12-fold elevated risk of incident gastric cancer (OR = 4.12, 95% CI 3.20-5.30). Likewise, CAG was linked to a 2.08-fold increased risk of incident oesophageal cancer (OR = 2.08, 95%CI 1.60-2.72). Intriguingly, a specific correlation was found between CAG and the risk of incident oesophageal squamous cell carcinoma (OR = 2.29, 95%CI 1.77-2.95), while no significant association was detected for oesophageal adenocarcinoma (OR = 0.62, 95%CI 0.17-2.26). Moreover, CAG was correlated with a 2.77-fold heightened risk of oesophagogastric junction cancer (OR = 2.77, 95%CI 2.21-3.46). Notably, for the same type of upper gastrointestinal cancer, it was observed that diagnosing CAG through histological methods was linked to a 33-77% higher risk of developing cancer compared to diagnosing CAG through serological methods., Conclusion: This meta-analysis indicated a two- to fourfold increased risk of gastric cancer, oesophageal cancer, and oesophagogastric junction cancer in patients with CAG. Importantly, for the same upper gastrointestinal cancer, the risk of incident cancer was higher when CAG was diagnosed histologically compared to serological diagnosis. Further rigorous study designs are required to explore the impact of CAG diagnosed through both diagnostic methods on the risk of upper gastrointestinal cancers., (© 2024. The Author(s).)
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- 2024
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10. Publisher Correction: Association of urinary chlorpyrifos, paraquat, and cyproconazole levels with the severity of fatty liver based on MRI.
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Ma P, Gao H, Shen N, Zhang L, Zhang Y, Zheng K, Xu B, Qin J, He J, Xu T, Li Y, Wu J, Yuan Y, and Xue B
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- 2024
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11. Association of urinary chlorpyrifos, paraquat, and cyproconazole levels with the severity of fatty liver based on MRI.
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Ma P, Gao H, Shen N, Zhang L, Zhang Y, Zheng K, Xu B, Qin J, He J, Xu T, Li Y, Wu J, Yuan Y, and Xue B
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- Humans, Paraquat, Magnetic Resonance Imaging, Chlorpyrifos urine, Pesticides, Non-alcoholic Fatty Liver Disease, Triazoles
- Abstract
Background: The objective of this study was to detect the urinary levels of chlorpyrifos, paraquat, and cyproconazole in residents living in Fuyang City and to analyze the correlation between these urinary pesticides levels and the severity of fatty liver disease (FLD)., Methods: All participants' fat fraction (FF) values were recorded by MRI (Magnetic resonance imaging). First-morning urine samples were collected from 53 participants from Fuyang Peoples'Hospital. The levels of three urinary pesticides were measured using β-glucuronidase hydrolysis followed by a. The results were analyzed by using Pearson correlation analysis and binary logistic regression analysis to reveal the correlation between three urinary pesticides and the severity of fatty liver., Results: 53 individuals were divided into 3 groups based on the results from MRI, with 20 cases in the normal control group, 16 cases in the mild fatty liver group, and 17 cases in the moderate and severe fatty liver group. Urinary chlorpyrifos level was increased along with the increase of the severity of fatty liver. Urinary paraquat level was significantly higher both in the low-grade fatty liver group and moderate & serve grade fatty liver group compared with the control group. No significant differences in urinary cyproconazole levels were observed among the three groups. Furthermore, urinary chlorpyrifos and paraquat levels were positively correlated with FF value. And chlorpyrifos was the risk factor that may be involved in the development of FLD and Receiver Operating Characteristic curve (ROC curve) analysis showed that chlorpyrifos and paraquat may serve as potential predictors of FLD., Conclusion: The present findings indicate urinary chlorpyrifos and paraquat were positively correlated with the severity of fatty liver. Moreover, urinary chlorpyrifos and paraquat have the potential to be considered as the predictors for development of FLD. Thus, this study may provide a new perspective from the environmental factors for the diagnosis, prevention, and treatment of FLD., (© 2024. The Author(s).)
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- 2024
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12. Unilateral biportal endoscopic lumbar interbody fusion (ULIF) versus endoscopic transforaminal lumbar interbody fusion (Endo-TLIF) in the treatment of lumbar spinal stenosis along with intervertebral disc herniation: a retrospective analysis.
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Fan Z, Wu X, Guo Z, Shen N, Chen B, and Xiang H
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- Humans, Retrospective Studies, Lumbar Vertebrae diagnostic imaging, Lumbar Vertebrae surgery, Treatment Outcome, Endoscopy methods, Minimally Invasive Surgical Procedures methods, Intervertebral Disc Displacement diagnostic imaging, Intervertebral Disc Displacement surgery, Spinal Stenosis diagnostic imaging, Spinal Stenosis surgery, Spinal Fusion methods
- Abstract
Objective: This study aims to compare the clinical effects and imaging data of patients who underwent endoscopic transforaminal lumbar interbody fusion (Endo-TLIF) with those who received unilateral biportal endoscopic lumbar interbody fusion (ULIF)., Methods: A retrospective analysis was conducted on the clinical data of 69 patients presenting with typical intermittent claudication and signs and symptoms indicative of unilateral lower extremity nerve root compression, meeting inclusion criteria between April 2022 and June 2022. Among the cohort, 35 patients underwent ULIF group, while 34 patients underwent Endo-TLIF group. We compared perioperative parameters, including intraoperative blood loss, duration of hospital stay, and operation time between the two groups. Pre-operative and post-operative changes in the height and cross-sectional area of the target intervertebral space were also compared between the groups. Finally, we evaluated bone graft size and interbody fusion rates at 6 and 12 months post-surgery using the Brantigan scoring system., Results: The ULIF group had significantly shorter operative times compared to the Endo-TLIF group (P < 0.05). Conversely, the Endo-TLIF group exhibited significantly shorter hospital stays compared to the ULIF group (P < 0.05). However, there were no significant differences in intraoperative bleeding between the two groups (P > 0.05). Furthermore, both groups exhibited postoperative increases in vertebral canal volume compared to baseline (P < 0.05), with no significant difference in the change in the cross-sectional area of the target intervertebral space between the two surgical methods (P > 0.05). Interbody fusion rates were comparable between the two groups at both 6 and 12 months after surgery (P > 0.05). Lastly, the ULIF group had a significantly larger area of bone graft than the Endo-TLIF group (P < 0.05)., Conclusion: In summary, the ULIF technique, as a novel spinal endoscopy approach, is a safer and more effective minimally invasive surgical method for addressing lumbar spinal stenosis and intervertebral disc herniation in patients. Both surgical methods have their own advantages and drawbacks. With the development of technology and related instruments, the limitations of both techniques can be mitigated for to a certain extent, and they can be applied by more doctors in diverse medical fields in the future., (© 2024. The Author(s).)
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- 2024
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13. Microenvironment Remodeling Self-Healing Hydrogel for Promoting Flap Survival.
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Ju Y, Yang P, Liu X, Qiao Z, Shen N, Lei L, and Fang B
- Abstract
Random flap grafting is a routine procedure used in plastic and reconstructive surgery to repair and reconstruct large tissue defects. Flap necrosis is primarily caused by ischemia-reperfusion injury and inadequate blood supply to the distal flap. Ischemia-reperfusion injury leads to the production of excessive reactive oxygen species, creating a pathological microenvironment that impairs cellular function and angiogenesis. In this study, we developed a microenvironment remodeling self-healing hydrogel [laminarin-chitosan-based hydrogel-loaded extracellular vesicles and ceria nanozymes (LCH@EVs&CNZs)] to improve the flap microenvironment and synergistically promote flap regeneration and survival. The natural self-healing hydrogel (LCH) was created by the oxidation laminarin and carboxymethylated chitosan via a Schiff base reaction. We loaded this hydrogel with CNZs and EVs. CNZs are a class of nanomaterials with enzymatic activity known for their strong scavenging capacity for reactive oxygen species, thus alleviating oxidative stress. EVs are cell-secreted vesicular structures containing thousands of bioactive substances that can promote cell proliferation, migration, differentiation, and angiogenesis. The constructed LCH@EVs&CNZs demonstrated a robust capacity for scavenging excess reactive oxygen species, thereby conferring cellular protection in oxidative stress environments. Moreover, these constructs notably enhance cell migration and angiogenesis. Our results demonstrate that LCH@EVs&CNZs effectively remodel the pathological skin flap microenvironment and marked improve flap survival. This approach introduces a new therapeutic strategy combining microenvironmental remodeling with EV therapy, which holds promise for promoting flap survival., Competing Interests: Competing interests: The authors declare that they have no competing interests., (Copyright © 2024 Yikun Ju et al.)
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- 2024
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14. ST218 Klebsiella pneumoniae became a high-risk clone for multidrug resistance and hypervirulence.
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Yang P, Liu C, Du P, Yi J, Wu Z, Zheng J, Shen N, Cui L, and Lu M
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- Humans, beta-Lactamases genetics, Retrospective Studies, Escherichia coli, Drug Resistance, Multiple, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Klebsiella pneumoniae, Klebsiella Infections microbiology
- Abstract
Background: The occurrence of multidrug-resistant and hypervirulent Klebsiella pneumoniae (MDR-hvKp) worldwide poses a great challenge for public health. Few studies have focused on ST218 MDR-hvKp., Methods: Retrospective genomic surveillance was conducted at the Peking University Third Hospital from 2017 and clinical information was obtained. To understand genomic and microbiological characteristics, antimicrobial susceptibility testing, plasmid conjugation and stability, biofilm formation, serum killing, growth curves and whole-genome sequencing were performed. We also assessed the clinical and microbiological characteristics of ST218 compared with ST23., Results: A total of eleven ST218 Kp isolates were included. The most common infection type was lower respiratory tract infection (72.7%, 8/11) in our hospital, whereas ST23 hvKp (72.7%, 8/11) was closely associated with bloodstream infection. Notably, nosocomial infections caused by ST218 (54.5%, 6/11) was slightly higher than ST23 (36.4%, 4/11). All of the ST218 and ST23 strains presented with the virulence genes combination of iucA + iroB + peg344 + rmpA + rmpA2. Interestingly, the virulence score of ST218 was lower than ST23, whereas one ST218 strain (pPEKP3107) exhibited resistance to carbapenems, cephalosporins, β-lactamase/inhibitors and quinolones and harbored an ~ 59-kb IncN type MDR plasmid carrying resistance genes including bla
NDM-1 , dfrA14 and qnrS1. Importantly, blaNDM-1 and qnrS1 were flanked with IS26 located within the plasmid that could successfully transfer into E. coli J53. Additionally, PEKP2044 harbored an ~ 41-kb resistance plasmid located within tetA indicating resistance to doxycycline., Conclusion: The emergence of blaNDM-1 revealed that there is great potential for ST218 Kp to become a high-risk clone for MDR-hvKp, indicating the urgent need for enhanced genomic surveillance., (© 2024. The Author(s).)- Published
- 2024
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15. Anti-Toxoplasma gondii antibodies as a risk factor for the prevalence and severity of systemic lupus erythematosus.
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Li Z, Lei Z, Yang W, Jing C, Sun X, Yang G, Zhao X, Zhang M, Xu M, Tang Y, Wang Q, Zhao J, Zhou Z, Wen Z, Chen X, Peng Q, Wang G, Zhang P, Sun E, Shen N, Xu W, Li Z, Yang H, and Yin Z
- Subjects
- Humans, Seroepidemiologic Studies, Prevalence, Immunoglobulin G, Risk Factors, DNA, Autoantibodies, Lupus Erythematosus, Systemic complications, Lupus Erythematosus, Systemic epidemiology
- Abstract
Background: Systemic lupus erythematosus (SLE) is a complex systemic autoimmune disease characterized by the presence of numerous autoantibodies. The interaction of infectious agents (viruses, bacteria and parasites) and a genetically susceptible host may be a key mechanism for SLE. Toxoplasma gondii is a widespread intracellular parasite that has been implicated in the pathogenesis of autoimmune diseases. However, the relationship between T. gondii infection and the increased risk of SLE in Chinese populations remains unclear., Methods: The seroprevalence of T. gondii infection was assessed in 1771 serum samples collected from Chinese individuals (908 healthy controls and 863 SLE patients) from different regions of China using an enzyme-linked immunosorbent assay. Serum autoantibodies and clinical information were obtained and analysed., Results: Our observations revealed a higher prevalence of anti-T. gondii antibodies (ATxA) immunoglobulin G (IgG) in serum samples from SLE patients (144/863, 16.7%) than in those from the healthy controls (53/917, 5.8%; P < 0.0001), indicating a 2.48-fold increased risk of SLE in the ATxA-IgG
+ population, after adjustment for age and sex (95% confidence interval [CI] 1.70-3.62, P < 0.0001). ATxA-IgG+ SLE patients also showed a 1.75-fold higher risk of developing moderate and severe lupus symptoms (95% CI 1.14-2.70, P = 0.011) compared to ATxA-IgG- patients. Relative to ATxA-IgG- patients, ATxA-IgG+ patients were more likely to develop specific clinical symptoms, including discoid rash, oral ulcer, myalgia and alopecia. Seven antibodies, namely anti-ribosomal RNA protein (rRNP), anti-double stranded DNA (dsDNA), anti-cell membrane DNA (cmDNA), anti-scleroderma-70 (Scl-70), anti-cardiolipin (CL), anti-beta2-glycoprotein-I (B2GPI) and rheumatoid factor (RF), occurred more frequently in ATxA-IgG+ patients. When combined with anti-dsDNA and RF/anti-rRNP/anti-cmDNA/ESR, ATxA-IgG significantly increased the risk for severe lupus., Conclusions: Our results suggest that ATxA-IgG may be a significant risk factor for SLE prevalence and severity in Chinese populations., (© 2024. The Author(s).)- Published
- 2024
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16. ZDHHC5-mediated S-palmitoylation of FAK promotes its membrane localization and epithelial-mesenchymal transition in glioma.
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Wang Y, Shen N, Yang Y, Xia Y, Zhang W, Lu Y, Wang Z, Yang Z, and Wang Z
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- Humans, Cell Line, Tumor, Cell Movement, Epithelial-Mesenchymal Transition, Lipoylation, Signal Transduction, Glioblastoma metabolism, Glioma pathology
- Abstract
Background: Abnormal activation of FAK is associated with tumor development and metastasis. Through interactions with other intracellular signalling molecules, FAK influences cytoskeletal remodelling, modulation of adhesion signalling, and activation of transcription factors, promoting migration and invasion of tumor cells. However, the exact mechanism that regulates these processes remains unresolved. Herein, our findings indicate that the S-palmitoylation of FAK is crucial for both its membrane localization and activation., Methods: The palmitoylation of FAK in U251 and T98G cells was assessed by an acyl-PEG exchange (APE) assay and a metabolic incorporation assay. Cellular palmitoylation was inhibited using 2-bromopalmitate, and the palmitoylation status and cellular localization of FAK were determined. A metabolic incorporation assay was used to identify the potential palmitoyl acyltransferase and the palmitoylation site of FAK. Cell Counting Kit-8 (CCK8) assays, colony formation assays, and Transwell assays were conducted to assess the impact of ZDHHC5 in GBM. Additionally, intracranial GBM xenografts were utilized to investigate the effects of genetically silencing ZDHHC5 on tumor growth., Results: Inhibiting FAK palmitoylation leads to its redistribution from the membrane to the cytoplasm and a decrease in its phosphorylation. Moreover, ZDHHC5, a protein-acyl-transferase (PAT), catalyzes this key modification of FAK at C456. Knockdown of ZDHHC5 abrogates the S-palmitoylation and membrane distribution of FAK and impairs cell proliferation, invasion, and epithelial-mesenchymal transition (EMT). Taken together, our research reveals the crucial role of ZDHHC5 as a PAT responsible for FAK S-palmitoylation, membrane localization, and activation., Conclusions: These results imply that targeting the ZDHHC5/FAK axis has the potential to be a promising strategy for therapeutic interventions for glioblastoma (GBM). Video Abstract., (© 2024. The Author(s).)
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- 2024
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17. MAGPIE: accurate pathogenic prediction for multiple variant types using machine learning approach.
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Liu Y, Zhang T, You N, Wu S, and Shen N
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- Humans, Genome, Human, Machine Learning
- Abstract
Identifying pathogenic variants from the vast majority of nucleotide variation remains a challenge. We present a method named Multimodal Annotation Generated Pathogenic Impact Evaluator (MAGPIE) that predicts the pathogenicity of multi-type variants. MAGPIE uses the ClinVar dataset for training and demonstrates superior performance in both the independent test set and multiple orthogonal validation datasets, accurately predicting variant pathogenicity. Notably, MAGPIE performs best in predicting the pathogenicity of rare variants and highly imbalanced datasets. Overall, results underline the robustness of MAGPIE as a valuable tool for predicting pathogenicity in various types of human genome variations. MAGPIE is available at https://github.com/shenlab-genomics/magpie ., (© 2023. The Author(s).)
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- 2024
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18. De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data.
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Zhang T, Jia H, Song T, Lv L, Gulhan DC, Wang H, Guo W, Xi R, Guo H, and Shen N
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- Humans, Reproducibility of Results, Sequence Analysis, RNA methods, Mutation, Gene Expression Profiling methods, Cluster Analysis, Software, Single-Cell Analysis methods, Melanoma genetics
- Abstract
Identifying expressed somatic mutations from single-cell RNA sequencing data de novo is challenging but highly valuable. We propose RESA - Recurrently Expressed SNV Analysis, a computational framework to identify expressed somatic mutations from scRNA-seq data. RESA achieves an average precision of 0.77 on three in silico spike-in datasets. In extensive benchmarking against existing methods using 19 datasets, RESA consistently outperforms them. Furthermore, we applied RESA to analyze intratumor mutational heterogeneity in a melanoma drug resistance dataset. By enabling high precision detection of expressed somatic mutations, RESA substantially enhances the reliability of mutational analysis in scRNA-seq. RESA is available at https://github.com/ShenLab-Genomics/RESA ., (© 2023. The Author(s).)
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- 2023
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19. N6-methyladenosine-modified circRIMS2 mediates synaptic and memory impairments by activating GluN2B ubiquitination in Alzheimer's disease.
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Wang X, Xie J, Tan L, Lu Y, Shen N, Li J, Hu H, Li H, Li X, and Cheng L
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- Animals, Mice, Adenosine, Memory Disorders genetics, Methyltransferases, Mice, Inbred C57BL, Mice, Transgenic, Peptides metabolism, Alzheimer Disease metabolism, MicroRNAs genetics, Receptors, N-Methyl-D-Aspartate metabolism, RNA, Circular genetics
- Abstract
Background: Synaptic degeneration occurs in the early stage of Alzheimer's disease (AD) before devastating symptoms, strongly correlated with cognitive decline. Circular RNAs (circRNAs) are abundantly enriched in neural tissues, and aberrant expression of circRNAs precedes AD symptoms, significantly correlated with clinical dementia severity. However, the direct relationship between circRNA dysregulation and synaptic impairment in the early stage of AD remains poorly understood., Methods: Hippocampal whole-transcriptome sequencing was performed to identify dysregulated circRNAs and miRNAs in 4-month-old wild-type and APP/PS1 mice. RNA antisense purification and mass spectrometry were utilized to unveil interactions between circRIMS2 and methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3). The roles of circRIMS2/miR-3968 in synaptic targeting of UBE2K-mediated ubiquitination of GluN2B subunit of NMDA receptor were evaluated via numerous lentiviruses followed by morphological staining, co-immunoprecipitation and behavioral testing. Further, a membrane-permeable peptide was used to block the ubiquitination of K1082 on GluN2B in AD mice., Results: circRIMS2 was significantly upregulated in 4-month-old APP/PS1 mice, which was mediated by METTL3-dependent N6-methyladenosine (m6A) modification. Overexpression of circRIMS2 led to synaptic and memory impairments in 4-month-old C57BL/6 mice. MiR-3968/UBE2K was validated as the downstream of circRIMS2. Elevated UBE2K induced synaptic dysfunction of AD through ubiquitinating K1082 on GluN2B. Silencing METTL3 or blocking the ubiquitination of K1082 on GluN2B with a short membrane-permeable peptide remarkably rescued synaptic dysfunction in AD mice., Conclusions: In conclusion, our study demonstrated that m6A-modified circRIMS2 mediates the synaptic and memory impairments in AD by activating the UBE2K-dependent ubiquitination and degradation of GluN2B via sponging miR-3968, providing novel therapeutic strategies for AD., (© 2023. The Author(s).)
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- 2023
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20. Multisensory stimulation bundles on sleep and neurobehavioral development in the first year after birth in very preterm infants: a randomized crossover controlled study protocol.
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Tang X, Sha S, Shen N, Zhu Z, Qin Y, Shen J, and Bei F
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- Infant, Infant, Newborn, Humans, Child, Cross-Over Studies, Patient Discharge, Sleep, Randomized Controlled Trials as Topic, Infant, Premature, Aftercare
- Abstract
Background: Disrupted sleep is believed to contribute to short- and long-term neurodevelopmental problems in very preterm infants (VPIs). This study presents a protocol for an evaluator-blinded, randomized crossover trial. It aims to assess the sleep efficiency of hospitalized VPIs by providing multisensory stimulation bundles. Furthermore, it aims to observe the intervention impacts on sleep during hospitalization of the VPIs and their sleep and neurodevelopmental outcomes during the first year of post-discharge follow-up., Methods: The study will be conducted in the neonatology department of a tertiary pediatric teaching hospital. All the eligible VPIs will undergo two types of care in random order: "standard care" (2 weeks) and "standard care plus multisensory stimulation bundles," each lasting 2 weeks. A generated list of random numbers will be used for case sequence allocation. Sleep outcomes will be evaluated using the Actiwatch-2 Actigraph. Moreover, the amplitude-integrated electroencephalography and the Griffiths Mental Development Scales will be used to measure the neurodevelopmental outcomes during hospitalization and in the first year of follow-up of the VPIs., Discussion: The intervention protocol of this study differs from that of other traditional interventions by producing precise and consistent supportive stimulations, similar to maternal tactile, auditory, posture, and visual effects for hospitalized VPIs. This protocol could be an effective measure to facilitate sleep and early neurodevelopment of VPIs. The expected outcomes will help confirm the implementation and generalization of the multisensory stimulation bundles' care protocol in neonatology departments. We expect that the study will positively impact hospitalized VPIs, especially in their sleep and early neurodevelopmental outcomes. It will also provide a new perspective regarding parent and infant interaction strategies, particularly for newborn intensive care units that limit visits because of the global spread of COVID-19., Trial Registration: Chinese Clinical Trial Registry ChiCTR 2200059099. Registered on 25 April 2022, https://www.chictr.org.cn/showproj.html?proj=166980 ; the Hospital Research Ethics Committee (approval number: SCMCIRB-K2021086-1, Version 01), approved on 21 January 2022., (© 2023. The Author(s).)
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- 2023
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21. The triglyceride-glucose index predicts 1-year major adverse cardiovascular events in end-stage renal disease patients with coronary artery disease.
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Xie E, Ye Z, Wu Y, Zhao X, Li Y, Shen N, Gao Y, and Zheng J
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- Humans, Glucose, Triglycerides, Blood Glucose, Biomarkers, Risk Factors, Risk Assessment, Coronary Artery Disease diagnosis, Coronary Artery Disease therapy, Cardiovascular System, Kidney Failure, Chronic diagnosis, Kidney Failure, Chronic epidemiology, Kidney Failure, Chronic therapy, Myocardial Infarction diagnosis, Myocardial Infarction epidemiology
- Abstract
Background: The triglyceride-glucose (TyG) index has been suggested as a dependable indicator for predicting major adverse cardiovascular events (MACE) in individuals with cardiovascular conditions. Nevertheless, there is insufficient data on the predictive significance of the TyG index in end-stage renal disease (ESRD) patients with coronary artery disease (CAD)., Methods: This study, conducted at multiple centers in China, included 959 patients diagnosed with dialysis and CAD from January 2015 to June 2021. Based on the TyG index, the participants were categorized into three distinct groups. The study's primary endpoint was the combination of MACE occurring within one year of follow-up, including death from any cause, non-fatal myocardial infarction, and non-fatal stroke. We assessed the association between the TyG index and MACE using Cox proportional hazard models and restricted cubic spline analysis. The TyG index value was evaluated for prediction incrementally using C-statistics, continuous net reclassification improvement (NRI), and integrated discrimination improvement (IDI)., Results: The three groups showed notable variations in the risk of MACE (16.3% in tertile 1, 23.5% in tertile 2, and 27.2% in tertile 3; log-rank P = 0.003). Following complete adjustment, patients with the highest TyG index exhibited a notably elevated risk of MACE in comparison to those in the lowest tertile (hazard ratio [HR] 1.63, 95% confidence interval [CI] 1.14-2.35, P = 0.007). Likewise, each unit increase in the TyG index correlated with a 1.37-fold higher risk of MACE (HR 1.37, 95% CI 1.13-1.66, P = 0.001). Restricted cubic spline analysis revealed a connection between the TyG index and MACE (P for nonlinearity > 0.05). Furthermore, incorporating the TyG index to the Global Registry of Acute Coronary Events risk score or baseline risk model with fully adjusted factors considerably enhanced the forecast of MACE, as demonstrated by the C-statistic, continuous NRI, and IDI., Conclusions: The TyG index might serve as a valuable and dependable indicator of MACE risk in individuals with dialysis and CAD, indicating its potential significance in enhancing risk categorization in clinical settings., (© 2023. The Author(s).)
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- 2023
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22. Predictive value of the stress hyperglycemia ratio in dialysis patients with acute coronary syndrome: insights from a multi-center observational study.
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Xie E, Ye Z, Wu Y, Zhao X, Li Y, Shen N, Gao Y, and Zheng J
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- Humans, Risk Assessment, Renal Dialysis adverse effects, Risk Factors, Prognosis, Acute Coronary Syndrome diagnosis, Acute Coronary Syndrome therapy, Acute Coronary Syndrome complications, Hyperglycemia diagnosis, Hyperglycemia complications, Diabetes Mellitus
- Abstract
Background: Various studies have indicated that stress hyperglycemia ratio (SHR) can reflect true acute hyperglycemic status and is associated with poor outcomes in patients with acute coronary syndrome (ACS). However, data on dialysis patients with ACS are limited. The Global Registry of Acute Coronary Events (GRACE) risk score is a well-validated risk prediction tool for ACS patients, yet it underestimates the risk of major events in patients receiving dialysis. This study aimed to evaluate the association between SHR and adverse cardiovascular events in dialysis patients with ACS and explore the potential incremental prognostic value of incorporating SHR into the GRACE risk score., Methods: This study enrolled 714 dialysis patients with ACS from January 2015 to June 2021 at 30 tertiary medical centers in China. Patients were stratified into three groups based on the tertiles of SHR. The primary outcome was major adverse cardiovascular events (MACE), and the secondary outcomes were all-cause mortality and cardiovascular mortality., Results: After a median follow-up of 20.9 months, 345 (48.3%) MACE and 280 (39.2%) all-cause mortality occurred, comprising 205 cases of cardiovascular death. When the highest SHR tertile was compared to the second SHR tertile, a significantly increased risk of MACE (adjusted hazard ratio, 1.92; 95% CI, 1.48-2.49), all-cause mortality (adjusted hazard ratio, 2.19; 95% CI, 1.64-2.93), and cardiovascular mortality (adjusted hazard ratio, 2.70; 95% CI, 1.90-3.83) was identified in the multivariable Cox regression model. A similar association was observed in both diabetic and nondiabetic patients. Further restricted cubic spline analysis identified a J-shaped association between the SHR and primary and secondary outcomes, with hazard ratios for MACE and mortality significantly increasing when SHR was > 1.08. Furthermore, adding SHR to the GRACE score led to a significant improvement in its predictive accuracy for MACE and mortality, as measured by the C-statistic, net reclassification improvement, and integrated discrimination improvement, especially for those with diabetes., Conclusions: In dialysis patients with ACS, SHR was independently associated with increased risks of MACE and mortality. Furthermore, SHR may aid in improving the predictive efficiency of the GRACE score, especially for those with diabetes. These results indicated that SHR might be a valuable tool for risk stratification and management of dialysis patients with ACS., (© 2023. The Author(s).)
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- 2023
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23. Association of triglyceride-glucose index with coronary severity and mortality in patients on dialysis with coronary artery disease.
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Xie E, Ye Z, Wu Y, Zhao X, Li Y, Shen N, Guo X, Gao Y, and Zheng J
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- Humans, Blood Glucose, Cohort Studies, Triglycerides, Risk Assessment, Renal Dialysis, Risk Factors, Biomarkers, Glucose, Coronary Artery Disease
- Abstract
Background: The triglyceride-glucose (TyG) index is validated as a reliable biomarker of insulin resistance and an independent predictor of cardiovascular prognosis. However, the prognostic value of the TyG index in patients on dialysis with coronary artery disease (CAD) remained unexplored. This study aimed to determine the association between the TyG index and CAD severity and mortality in these patients., Methods: A total of 1061 dialysis patients with CAD were enrolled in this multi-center cohort study from January 2015 to June 2021. The extent and severity of CAD were evaluated using the multivessel disease and Gensini score (GS). Patients were followed up for all-cause death and cardiovascular death., Results: The multivariable logistic regression model indicated that the TyG index was significantly associated with multivessel disease (odds ratio [OR] 1.51, 95% confidence interval [CI] 1.18-1.94, P = 0.001), and high GS (OR 1.33, 95% CI 1.10-1.61, P = 0.003). After adjusting for baseline risk factors, the hazards of all-cause death and cardiovascular death were 1.23 (95% CI 1.06-1.43, P = 0.007), and 1.33 (95% CI 1.11-1.59, P = 0.002), independent of CAD severity. Restricted cubic spline analysis identified a dose-response association between the TyG index and both CAD severity and mortality (all P for nonlinearity > 0.05). When modeling the TyG index as a categorical variable, these independent associations remained. Subgroup analyses did not substantially modify the results. Furthermore, incorporating the TyG index into the existing risk prediction model improved the predictive accuracy for all-cause death and cardiovascular death, as evaluated by C-statistic, continuous net reclassification improvement, and integrated discrimination improvement., Conclusions: In patients on dialysis with CAD, the TyG index was significantly associated with more severe CAD as well as mortality. These results highlight the clinical importance of the TyG index for assessing CAD severity and risk stratification in patients on dialysis with CAD., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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24. Point-wise spatial network for identifying carcinoma at the upper digestive and respiratory tract.
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Zhou L, Jiang H, Li G, Ding J, Lv C, Duan M, Wang W, Chen K, Shen N, and Huang X
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- Humans, Respiratory System, Semantics, Artificial Intelligence, Carcinoma
- Abstract
Problem: Artificial intelligence has been widely investigated for diagnosis and treatment strategy design, with some models proposed for detecting oral pharyngeal, nasopharyngeal, or laryngeal carcinoma. However, no comprehensive model has been established for these regions., Aim: Our hypothesis was that a common pattern in the cancerous appearance of these regions could be recognized and integrated into a single model, thus improving the efficacy of deep learning models., Methods: We utilized a point-wise spatial attention network model to perform semantic segmentation in these regions., Results: Our study demonstrated an excellent outcome, with an average mIoU of 86.3%, and an average pixel accuracy of 96.3%., Conclusion: The research confirmed that the mucosa of oral pharyngeal, nasopharyngeal, and laryngeal regions may share a common appearance, including the appearance of tumors, which can be recognized by a single artificial intelligence model. Therefore, a deep learning model could be constructed to effectively recognize these tumors., (© 2023. BioMed Central Ltd., part of Springer Nature.)
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- 2023
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25. Evaluation of the immunoprotective effects of eight recombinant proteins from Baylisascaris schroederi in mice model.
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Xiong L, Chen L, Chen Y, Shen N, Hua R, and Yang G
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- Mice, Animals, Interleukin-10 metabolism, Interleukin-5, Recombinant Proteins genetics, Recombinant Proteins metabolism, Immunoglobulin G metabolism, Immunoglobulin A, Immunoglobulin E, Mice, Inbred BALB C, Ascariasis, Ursidae parasitology, Vaccines metabolism, Ascaridoidea
- Abstract
Background: Baylisascaris schroederi is the most common and harmful intestinal parasitic nematode of giant pandas, causing ascariasis. Although drug deworming is the main measure to control ascariasis in captive giant pandas, prolonged and repeated use of deworming drugs might induce resistance in nematodes and drug residues in giant pandas. Therefore, developing a safe and effective vaccine might provide a novel strategy to prevent ascariasis in captive giant pandas., Methods: Four highly expressed secretome genes encoding excretory and secretory proteins of B. schroederi, including transthyretin-like protein 46 (BsTLP), uncharacterized protein (BsUP), hypothetical protein 1 (BsHP1), and hypothetical protein 2 (BsHP2) and four functional genes [(encoding Galectin (BsGAL), glutathione S-transferase (BsGST), fatty acid-binding protein (BsFABP), and thioredoxin peroxidase (BsTPX)] were identified based on genome and transcriptome databases of B. schroederi and used to construct recombinant proteins via prokaryotic expression. Kunming mice were vaccinated subcutaneously twice with the recombinant proteins (50 μg/mouse) mixed with Quil A adjuvant with a 2-week interval and then orally challenged with 3000 infective eggs. The immunoprotective effects of the eight recombinant proteins on mice were assessed comprehensively using surface lesion histology scores of the mouse liver and lung, larval worm reduction, serum antibody levels (IgG, IgE, IgA, IgG1, and IgG2a), and cytokine production [interferon gamma (IFN-γ), interleukin (IL)-2, IL-4, IL-5, and IL-10]., Results: Mice vaccinated with recombinant (r)BsUP (76.5%), rBsGAL (74.7%), and rBsHP2 (71.5%) showed a significant (P < 0.001) reduction in the larval worm rate compared with that in the adjuvant control. Besides, the surface lesions in the liver and lung of the vaccinated mice were alleviated. Serum levels of total IgG, IgE, IgA, IgG1, IgG2a, and cytokines, including IL-10, IL-5, and IFN-γ, were significantly higher (P < 0.001) than those in the control group., Conclusions: The results showed that candidate three vaccines (rBsUP, rBsGAL, and rBsHP2) could provide effective protection against egg infection in mice associated with a mixed Th1/2-type immune response., (© 2023. The Author(s).)
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- 2023
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26. Engineered Escherichia coli platforms for tyrosine-derivative production from phenylalanine using phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system.
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Satoh Y, Fukui K, Koma D, Shen N, and Lee TS
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Background: Aromatic compounds derived from tyrosine are important and diverse chemicals that have industrial and commercial applications. Although these aromatic compounds can be obtained by extraction from natural producers, their growth is slow, and their content is low. To overcome these problems, many of them have been chemically synthesized from petroleum-based feedstocks. However, because of the environmental burden and depleting availability of feedstock, microbial cell factories are attracting much attention as sustainable and environmentally friendly processes., Results: To facilitate development of microbial cell factories for producing tyrosine derivatives, we developed simple and convenient tyrosine-producing Escherichia coli platforms with a bacterial phenylalanine hydroxylase, which converted phenylalanine to tyrosine with tetrahydromonapterin as a cofactor, using a synthetic biology approach. By introducing a tetrahydrobiopterin-regeneration system, the tyrosine titer of the plasmid-based engineered strain was 4.63 g/L in a medium supplemented with 5.00 g/L phenylalanine with a test tube. The strains were successfully used to produce industrially attractive compounds, such as tyrosol with a yield of 1.58 g/L by installing a tyrosol-producing module consisting of genes encoding tyrosine decarboxylase and tyramine oxidase on a plasmid. Gene integration into E. coli chromosomes has an advantage over the use of plasmids because it increases genetic stability without antibiotic feeding to the culture media and enables more flexible pathway engineering by accepting more plasmids with artificial pathway genes. Therefore, we constructed a plasmid-free tyrosine-producing platform by integrating five modules, comprising genes encoding the phenylalanine hydroxylase and tetrahydrobiopterin-regeneration system, into the chromosome. The platform strain could produce 1.04 g/L of 3,4-dihydroxyphenylalanine, a drug medicine, by installing a gene encoding tyrosine hydroxylase and the tetrahydrobiopterin-regeneration system on a plasmid. Moreover, by installing the tyrosol-producing module, tyrosol was produced with a yield of 1.28 g/L., Conclusions: We developed novel E. coli platforms for producing tyrosine from phenylalanine at multi-gram-per-liter levels in test-tube cultivation. The platforms allowed development and evaluation of microbial cell factories installing various designed tyrosine-derivative biosynthetic pathways at multi-grams-per-liter levels in test tubes., (© 2023. The Author(s).)
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- 2023
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27. Immune regulation and prognosis indicating ability of a newly constructed multi-genes containing signature in clear cell renal cell carcinoma.
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Gui Z, Du J, Wu N, Shen N, Yang Z, Yang H, Wang X, Zhao N, Zeng Z, Wei R, Ma W, and Wang C
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- Humans, Prognosis, Immunotherapy, Carcinoma, Renal Cell genetics, Carcinoma, Kidney Neoplasms genetics
- Abstract
Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal malignancy, although newly developing targeted therapy and immunotherapy have been showing promising effects in clinical treatment, the effective biomarkers for immune response prediction are still lacking. The study is to construct a gene signature according to ccRCC immune cells infiltration landscape, thus aiding clinical prediction of patients response to immunotherapy., Methods: Firstly, ccRCC transcriptome expression profiles from Gene Expression Omnibus (GEO) database as well as immune related genes information from IMMPORT database were combine applied to identify the differently expressed meanwhile immune related candidate genes in ccRCC comparing to normal control samples. Then, based on protein-protein interaction network (PPI) and following module analysis of the candidate genes, a hub gene cluster was further identified for survival analysis. Further, LASSO analysis was applied to construct a signature which was in succession assessed with Kaplan-Meier survival, Cox regression and ROC curve analysis. Moreover, ccRCC patients were divided as high and low-risk groups based on the gene signature followed by the difference estimation of immune treatment response and exploration of related immune cells infiltration by TIDE and Cibersort analysis respectively among the two groups of patients., Results: Based on GEO and IMMPORT databases, a total of 269 differently expressed meanwhile immune related genes in ccRCC were identified, further PPI network and module analysis of the 269 genes highlighted a 46 genes cluster. Next step, Kaplan-Meier and Cox regression analysis of the 46 genes identified 4 genes that were supported to be independent prognosis indicators, and a gene signature was constructed based on the 4 genes. Furthermore, after assessing its prognosis indicating ability by both Kaplan-Meier and Cox regression analysis, immune relation of the signature was evaluated including its association with environment immune score, Immune checkpoint inhibitors expression as well as immune cells infiltration. Together, immune predicting ability of the signature was preliminary explored., Conclusions: Based on ccRCC genes expression profiles and multiple bioinformatic analysis, a 4 genes containing signature was constructed and the immune regulation of the signature was preliminary explored. Although more detailed experiments and clinical trials are needed before potential clinical use of the signature, the results shall provide meaningful insight into further ccRCC immune researches., (© 2023. The Author(s).)
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- 2023
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28. Association between the triglyceride glucose index and in-hospital and 1-year mortality in patients with chronic kidney disease and coronary artery disease in the intensive care unit.
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Ye Z, An S, Gao Y, Xie E, Zhao X, Guo Z, Li Y, Shen N, and Zheng J
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- Humans, Hospitals, Intensive Care Units, Glucose, Triglycerides, Blood Glucose, Biomarkers, Risk Factors, Coronary Artery Disease diagnosis, Coronary Artery Disease therapy, Cardiovascular Diseases, Renal Insufficiency, Chronic diagnosis, Renal Insufficiency, Chronic therapy
- Abstract
Objective: This study aimed to explore the association between the triglyceride glucose index (TyG) and the risk of in-hospital and one-year mortality in patients with chronic kidney disease (CKD) and cardiovascular disease (CAD) admitted to the intensive care unit (ICU)., Methods: The data for the study were taken from the Medical Information Mart for Intensive Care-IV database which contained over 50,000 ICU admissions from 2008 to 2019. The Boruta algorithm was used for feature selection. The study used univariable and multivariable logistic regression analysis, Cox regression analysis, and 3-knotted multivariate restricted cubic spline regression to evaluate the association between the TyG index and mortality risk., Results: After applying inclusion and exclusion criteria, 639 CKD patients with CAD were included in the study with a median TyG index of 9.1 [8.6,9.5]. The TyG index was nonlinearly associated with in-hospital and one-year mortality risk in populations within the specified range., Conclusion: This study shows that TyG is a predictor of one-year mortality and in-hospital mortality in ICU patients with CAD and CKD and inform the development of new interventions to improve outcomes. In the high-risk group, TyG might be a valuable tool for risk categorization and management. Further research is required to confirm these results and identify the mechanisms behind the link between TyG and mortality in CAD and CKD patients., (© 2023. The Author(s).)
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- 2023
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29. Improving the resident assessment process: application of App-based e-training platform and lean thinking.
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Yuan W, Li Z, Han J, Chu H, Lu S, Gu S, and Shen N
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- Humans, Pandemics, Learning, Students, Mobile Applications, COVID-19
- Abstract
Background: The assessment system for standardized resident training is crucial for developing competent doctors. However, it is complex, making it difficult to manage. The COVID-19 pandemic has also aggravated the difficulty of assessment. We, therefore, integrated lean thinking with App-based e-training platform to improve the assessment process through Define-Measure-Analyze-Improve-Control (DMAIC) cycles. This was designed to avoid unnecessary activities that generate waste., Methods: Panels and online surveys were conducted in 2021-2022 to find the main issues that affect resident assessment and the root causes under the frame of waste. An online app was developed. Activities within the process were improved by brainstorming. Online surveys were used to improve the issues, satisfaction, and time spent on assessment using the app., Results: A total of 290 clinical educators in 36 departments responded to the survey, and 153 clinical educators used the online app for assessment. Unplanned delay or cancellation was defined as the main issue. Eleven leading causes accounted for 87.5% of the issues. These were examiner time conflict, student time conflict, insufficient examiners, supervisor time conflict, grade statistics, insufficient exam assistants, reporting results, material archiving, unfamiliarity with the process, uncooperative patients, and feedback. The median rate of unplanned delay or cancellation was lower with use of the app (5% vs 0%, P < 0.001), and satisfaction increased (P < 0.001). The median time saved by the app across the whole assessment process was 60 (interquartile range 60-120) minutes., Conclusions: Lean thinking integrated with an App-based e-training platform could optimize the process of resident assessment. This could reduce waste and promote teaching and learning in medical education., (© 2023. The Author(s).)
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- 2023
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30. Osteosarcoma transcriptome data exploration reveals STC2 as a novel risk indicator in disease progression.
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Wang Z, Zeng Z, Gao F, Gui Z, Du J, Shen N, Shang Y, Yang Z, Shang L, Wei R, Ma W, and Wang C
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- Adolescent, Child, Humans, Transcriptome, Disease Progression, Risk Factors, Gene Expression Profiling methods, Computational Biology methods, Gene Expression Regulation, Neoplastic, Glycoproteins genetics, Glycoproteins metabolism, Intercellular Signaling Peptides and Proteins genetics, Intercellular Signaling Peptides and Proteins metabolism, Osteosarcoma genetics, Osteosarcoma pathology, Bone Neoplasms genetics, Bone Neoplasms pathology
- Abstract
Background: Osteosarcoma has been the most common primary bone malignant tumor in children and adolescents. Despite the considerable improvement in the understanding of genetic events attributing to the rapid development of molecular pathology, the current information is still lacking, partly due to the comprehensive and highly heterogeneous nature of osteosarcoma. The study is to identify more potential responsible genes during the development of osteosarcoma, thus identifying promising gene indicators and aiding more precise interpretation of the disease., Methods: Firstly, from GEO database, osteosarcoma transcriptome microarrays were used to screen the differential expression genes (DEGS) in cancer comparing to normal bone samples, followed by GO/KEGG interpretation, risk score assessment and survival analysis of the genes, for the purpose of selecting a credible key gene. Further, the basic physicochemical properties, predicted cellular location, gene expression in human cancers, the association with clinical pathological features and potential signaling pathways involved in the key gene's regulation on osteosarcoma development were in succession explored., Results: Based on the selected GEO osteosarcoma expression profiles, we identified the differential expression genes in osteosarcoma versus normal bone samples, and the genes were classified into four groups based on the difference level, further genes interpretation indicated that the high differently level (> 8 fold) genes were mainly located extracellular and related to matrix structural constituent regulation. Meanwhile, module function analysis of the 67 high differential level (> 8 fold) DEGS revealed a 22-gene containing extracellular matrix regulation associated hub gene cluster. Further survival analysis of the 22 genes revealed that STC2 was an independent prognosis indicator in osteosarcoma. Moreover, after validating the differential expression of STC2 in cancer vs. normal tissues using local hospital osteosarcoma samples by IHC and qRT-PCR experiment, the gene's physicochemical property revealed STC2 as a cellular stable and hydrophilic protein, and the gene's association with osteosarcoma clinical pathological parameters, expression in pan-cancers and the probable biological functions and signaling pathways it involved were explored., Conclusion: Using multiple bioinformatic analysis and local hospital samples validation, we revealed the gain of expression of STC2 in osteosarcoma, which associated statistical significantly with patients survival, and the gene's clinical features and potential biological functions were also explored. Although the results shall provide inspiring insights into further understanding of the disease, further experiments and detailed rigorous clinical trials are needed to reveal its potential drug-target role in clinical medical use., (© 2023. The Author(s).)
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- 2023
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31. Fusion plasmid enhanced the endemic extensively drug resistant Klebsiella pneumoniae clone ST147 harbored bla OXA-48 to acquire the hypervirulence and cause fatal infection.
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Liu C, Du P, Yang P, Lu M, and Shen N
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- Humans, Klebsiella genetics, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Retrospective Studies, Plasmids genetics, beta-Lactamases genetics, Klebsiella pneumoniae genetics, Klebsiella Infections microbiology
- Abstract
Background: Klebsiella Pneumoniae (Kp) sequence type (ST) 147 has emerged globally and spread rapidly, particularly the extensively drug resistant (XDR) isolates. However, the infections caused by this subtype is rare reported in China for now. The clinical, microbiological and genomic characteristics are unclear., Methods: A systemic retrospective study was conducted in a Chinese tertiary hospital. Clinical information of the infection cases was collected, and whole-genome sequencing and phenotypic experiments were performed on the ST147 isolates. The resistance and virulence genes were identified, and the plasmids harboring these genes were further studied., Results: Six ST147 isolates from six patients among 720 available clincial Kp isolates were detected. Notably, two isolates, PEKP4035 and PEKP4265, represented both XDR and hypervirulence by acquiring bla
OXA-48 , blaCTX-M-15 and key virulence genes, iucA + rmpA2, representing no fitness cost and resulting fatal infection. Four of the six ST147 isolates presented with more nucleotide differences, whereas the PEKP4035 and PEKP4265 both isolated from the intensive care unit possessed 20 single nucleotide polymorphisms among one year, indicating the prolonged survive and transmission. Interestingly, the two isolates harbored the same fused plasmid composed of sul2 and iucA + rmpA2, which might be generated by recombination of a plasmid like KpvST101_OXA-48 with the pLVPK plasmid via IS26. Besides, two ~ 70 kb plasmids conferring multiple-drug resistance were also identified among the two isolates, which presented resistance genes including blaOXA-48 , blaCTX-M-16 , strA and strB. Interestingly, we reported that blaCTX-M-15 , a common resistance gene within ST147, has successfully transferred into the chromosome by ISEcp1., Conclusions: XDR hypervirulent ST147 Kp is emerging, suggesting enhanced surveillance is essential., (© 2023. The Author(s).)- Published
- 2023
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32. The prediction of in-hospital mortality in chronic kidney disease patients with coronary artery disease using machine learning models.
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Ye Z, An S, Gao Y, Xie E, Zhao X, Guo Z, Li Y, Shen N, Ren J, and Zheng J
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- Humans, Hospital Mortality, Algorithms, Machine Learning, Coronary Artery Disease, Renal Insufficiency, Chronic
- Abstract
Objective: Chronic kidney disease (CKD) patients with coronary artery disease (CAD) in the intensive care unit (ICU) have higher in-hospital mortality and poorer prognosis than patients with either single condition. The objective of this study is to develop a novel model that can predict the in-hospital mortality of that kind of patient in the ICU using machine learning methods., Methods: Data of CKD patients with CAD were extracted from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. Boruta algorithm was conducted for the feature selection process. Eight machine learning algorithms, such as logistic regression (LR), random forest (RF), Decision Tree, K-nearest neighbors (KNN), Gradient Boosting Decision Tree Machine (GBDT), Support Vector Machine (SVM), Neural Network (NN), and Extreme Gradient Boosting (XGBoost), were conducted to construct the predictive model for in-hospital mortality and performance was evaluated by average precision (AP) and area under the receiver operating characteristic curve (AUC). Shapley Additive Explanations (SHAP) algorithm was applied to explain the model visually. Moreover, data from the Telehealth Intensive Care Unit Collaborative Research Database (eICU-CRD) were acquired as an external validation set., Results: 3590 and 1657 CKD patients with CAD were acquired from MIMIC-IV and eICU-CRD databases, respectively. A total of 78 variables were selected for the machine learning model development process. Comparatively, GBDT had the highest predictive performance according to the results of AUC (0.946) and AP (0.778). The SHAP method reveals the top 20 factors based on the importance ranking. In addition, GBDT had good predictive value and a certain degree of clinical value in the external validation according to the AUC (0.865), AP (0.672), decision curve analysis, and calibration curve., Conclusion: Machine learning algorithms, especially GBDT, can be reliable tools for accurately predicting the in-hospital mortality risk for CKD patients with CAD in the ICU. This contributed to providing optimal resource allocation and reducing in-hospital mortality by tailoring precise management and implementation of early interventions., (© 2023. The Author(s).)
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- 2023
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33. A comparison of patients with neck abscesses caused by esophageal foreign body impaction vs. inflammatory disease: a retrospective study.
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Wang X, Xu F, Liu D, Luo X, Zhou X, Huang X, and Shen N
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- Humans, Abscess complications, Abscess surgery, Retrospective Studies, Esophageal Perforation, Foreign Bodies complications, Foreign Bodies surgery
- Abstract
Objectives: During clinical practice, we have detected a few cases of neck abscesses in patients diagnosed with esophageal foreign body impaction (EFB) but without the primary inflammatory disease. However, we do not know if neck abscesses caused by an inflammatory source are more like to be associated with a more severe progression or poorer prognosis. In this study, we aimed to identify differences between these two groups of patients by comparing progression and prognosis., Materials and Methods: We retrospectively reviewed all patients who underwent neck abscess incisions between January 2011 and March 2022 and divided these patients into two groups: an EFB group and an inflammation group. Data were described by percentages, means, and standard deviations (SDs). Fisher's precision probability test was used to compare differences between the EFB and inflammation groups. Categorical variables were analyzed by Pearson's Chi-squared test. In addition, three factors including hospital days, intensive care unit (ICU) stay, and drainage-tube removal time were used for multivariate analysis to identify independent correlations separately., Results: We enrolled a total of 33 patients with neck abscesses who received surgical incisions; the EFB group included 14 (42%) cases, while the inflammatory group included 19 (58%) cases. No significant differences were identified between the two groups in terms of surgery type (with or without mediastinotomy) and postoperative management (negative pressure drainage or postoperative irrigation). There were no significant differences between the two groups in terms of hospital stay, the timing of drainage-tube removal, the risk of ICU admission, and the probability of receiving intubation and tracheotomy. The incidence rate of esophageal perforation differed significantly between the two groups (p < 0.001). However, there were no significant differences in terms of other preoperative or postoperative comorbidities. The multivariate analysis revealed that the application of mediastinotomy (HR = 0.216 [0.049, 0.963]; p = 0.044) was correlated with a longer stay in the hospital. The time from symptoms to surgery was associated with a longer drainage tube removal time (HR = 0.392 [0.159, 0.967]; P = 0.042) and longer ICU stay (OR = 79.754[1.513, 4203.182]; P = 0.03)., Conclusion: Patients with neck abscesses associated with EFB and inflammation received the same therapeutic management, and there were no significant differences between these two groups in terms of prognosis. Furthermore, esophageal perforation was found to be irrelevant to the aggravation of neck abscesses, and there was no need for additional surgery to repair a perforated esophagus in patients with neck abscesses., Level of Evidence: Retrospective cohort (2b)., (© 2022. The Author(s).)
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- 2022
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34. Convergence of two serotypes within the epidemic ST11 KPC-producing Klebsiella pneumoniae creates the "Perfect Storm" in a teaching hospital.
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Liu C, Yang P, Zheng J, Yi J, Lu M, and Shen N
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- Anti-Bacterial Agents pharmacology, Carbapenems, Female, Hospitals, Teaching, Humans, Klebsiella pneumoniae genetics, Male, Retrospective Studies, Serogroup, Virulence genetics, Carbapenem-Resistant Enterobacteriaceae genetics, Klebsiella Infections epidemiology
- Abstract
Objectives: ST11 KPC-producing Klebsiella pneumoniae (Kp) is highly prevalent in China. We investigated the inter- and intra- host transmission and evolution characteristics of ST11 KPC-producing Kp., Methods: A retrospective study was conducted in a hospital. The clinical data and antimicrobial resistance (AMR) phenotypes were collected. Whole genome sequencing was performed. The transmission route was reconstructed by combining single nucleotide polymorphisms (SNPs) with the clinical information. Hypervirulent Kp (HvKp) was defined as the presence of some combination of peg-344, iroB, iucA, rmpA, or rmpA2., Results: Fifty-eight Kp strains isolated from thirty-five patients were enrolled. The information of one isolate was missing. The mean age of the patients was 74.3 ± 18.0 years, and 18 (50.0%) were female. Fifteen patients (41.7%, 15/36) presented with poor prognosis. All the strains were identified as ST11, and 57 strains harbored bla
KPC-2 . Two distinguished clades were identified based on the 1,325 high quality SNPs. In clade 1, carbapenem-resistant (CR)-hvKp accounted for 48.3% of the strains (28/58), which mostly presented as KL64 subclones, whereas CR-classical Klebsiella pneumoniae (cKp) commonly possessing KL47 were clustered in Clade 2. One CR-hvKp strain might have originated from the CR-cKp strain from within-host evolution. Even worse, a prolonged transmission of CR-hvKp has led to its spread into healthcare institutes., Conclusion: Two endemic subclones of ST11 KPC-producing Kp, KL64-CR-hvKp and KL47-CR-cKp, were transmitted in parallel within the hospital and/or the healthcare institute, suggesting that the ongoing genomic surveillance should be enhanced., (© 2022. The Author(s).)- Published
- 2022
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35. Identifying and adapting interventions to reduce documentation burden and improve nurses' efficiency in using electronic health record systems (The IDEA Study): protocol for a mixed methods study.
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Strudwick G, Jeffs L, Kemp J, Sequeira L, Lo B, Shen N, Paterson P, Coombe N, Yang L, Ronald K, Wang W, Pagliaroli S, Tajirian T, Ling S, and Jankowicz D
- Abstract
Background: Although EHR systems have become a critical part of clinical care, nurses are experiencing a growing burden due to documentation requirements, taking time away from other important clinical activities. There is a need to address the inefficiencies and challenges that nurses face when documenting in and using EHRs. The objective of this study is to engage nurses in generating ideas on how organizations can support and optimize nurses' experiences with their EHR systems, thereby improving efficiency and reducing EHR-related burden. This work will ensure the identified solutions are grounded in nurses' perspectives and experiences and will address their specific EHR-related needs., Methods: This mixed methods study will consist of three phases. Phase 1 will evaluate the accuracy of the EHR system's analytics platform in capturing how nurses utilize the system in real-time for tasks such as documentation, chart review, and medication reconciliation. Phase 2 consists of a retrospective analysis of the nursing-specific analytics platform and focus groups with nurses to understand and contextualize their usage patterns. These focus groups will also be used to identify areas for improvement in the utilization of the EHR. Phase 3 will include focus groups with nurses to generate and adapt potential interventions to address the areas for improvement and assess the perceived relevance, feasibility, and impact of the potential interventions., Discussion: This work will generate insights on addressing nurses' EHR-related burden and burnout. By understanding and contextualizing inefficiencies and current practices, opportunities to improve EHR systems for nursing professional practice will be identified. The study findings will inform the co-design and implementation of interventions that will support adoption and impact. Future work will include the evaluation of the developed interventions, and research on scaling and disseminating the interventions for use in different organizations, EHR systems, and jurisdictions in Canada., (© 2022. The Author(s).)
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- 2022
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36. Risk factors for kidney stone disease recurrence: a comprehensive meta-analysis.
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Wang K, Ge J, Han W, Wang D, Zhao Y, Shen Y, Chen J, Chen D, Wu J, Shen N, Zhu S, Xue B, and Xu X
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- Female, Humans, Male, Prospective Studies, Recurrence, Retrospective Studies, Risk Factors, Kidney Calculi diagnosis
- Abstract
Background: Kidney stone disease (KSD) is a common illness that causes an economic burden globally. It is easy for patients to relapse once they have suffered from this disease. The reported recurrence rate of KSD ranged from 6.1% to 66.9%. We performed this meta-analysis to identify various potential risk factors for the recurrence of KSD., Methods: The PubMed, Embase and Web of Science databases were searched using suitable keywords from inception to Mar 2022. A total of 2,663 records were collected initially. After screening the literature according to the inclusion and exclusion criteria, 53 articles (40 retrospective studies; 13 prospective studies) including 488,130 patients were enrolled. The study protocol was registered with PROSPERO (No. CRD42020171771)., Results: The pooled results indicated that 12 risk factors including younger age (n = 18), higher BMI (n = 16), family history of kidney stones (n = 12), personal history of kidney stones (n = 11), hypertension (n = 5), uric acid stone (n = 4), race of Caucasian (n = 3), suspected kidney stone episode before the first confirmed stone episode (n = 3), surgery (n = 3), any concurrent asymptomatic (nonobstructing) stone (n = 2), pelvic or lower pole kidney stone (n = 2), and 24 h urine test completion (n = 2) were identified to be associated with KSD recurrence. In the subgroup analysis, patients with higher BMI (OR = 1.062), personal history of nephrolithiasis (OR = 1.402), or surgery (OR = 3.178) had a higher risk of radiographic KSD recurrence., Conclusions: We identified 12 risk factors related to the recurrence of KSD. The results of this analysis could serve to construct recurrence prediction models. It could also supply a basis for preventing the recurrence of KSD., (© 2022. The Author(s).)
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- 2022
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37. Graphene quantum dots rescue angiogenic retinopathy via blocking STAT3/Periostin/ERK signaling.
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Zhao N, Gui X, Fang Q, Zhang R, Zhu W, Zhang H, Li Q, Zhou Y, Zhao J, Cui X, Gao G, Tang H, Shen N, Chen T, Song H, and Shen W
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- Animals, Cell Proliferation, Cells, Cultured, Human Umbilical Vein Endothelial Cells, Humans, Mice, Signal Transduction, Graphite pharmacology, Quantum Dots therapeutic use, Retinal Diseases
- Abstract
Background: Pathological retinal angiogenesis resulting from a variety of ocular diseases including oxygen induced retinopathy, diabetic retinopathy and ocular vein occlusion, is one of the major reasons for vision loss, yet the therapeutic option is limited. Multiple nanoparticles have been reported to alleviate angiogenic retinopathy. However, the adverse effect cannot be ignored due to the relatively large scale. Graphene quantum dots (GQDs) have shown potential in drug delivery and have been proved biocompatible. In this study, Graphene quantum dots are extensively investigated for their application in angiogenic retinopathy therapy., Results: We showed that GQDs were biocompatible nanomaterials in vitro and in vivo. The nanoparticles have a dose-dependent inhibitory effect on proliferation, migration, tube formation and sprouting of human umbilical vein endothelial cells (HUVECs). Further data show that GQDs could inhibit pathological retinal neovascularization in an oxygen-induced retinopathy (OIR) model. The data of RNA sequencing suggested that periostin is involved in this process. GQDs inhibit the expression of periostin via STAT3, and further regulated cell cycle-related protein levels through ERK pathway. The signaling pathway was conformed in vivo using OIR mouse model., Conclusions: The present study indicated that GQDs could be a biocompatible anti-angiogenic nanomedicine in the treatment of pathological retinal neovascularization via disrupting periostin/ERK pathway and subsequent cell cycle., (© 2022. The Author(s).)
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- 2022
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38. Urinary galectin-3 binding protein (G3BP) as a biomarker for disease activity and renal pathology characteristics in lupus nephritis.
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Ding H, Shen Y, Lin C, Qin L, He S, Dai M, Okitsu SL, DeMartino JA, Guo Q, and Shen N
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- Biomarkers metabolism, Cross-Sectional Studies, Galectin 3, Humans, Antigens, Neoplasm urine, Biomarkers, Tumor urine, Kidney pathology, Lupus Nephritis pathology
- Abstract
Objective: There is an urgent need to identify novel biomarkers of LN to reflect renal histological changes. This study aims to investigate urinary G3BP levels in LN patients and their association with renal disease activity both clinically and pathologically., Methods: This is a cross-sectional study. A total of 119 lupus nephritis patients were recruited. Thirty patients with chronic kidney diseases (CKD) and 27 healthy volunteers were also recruited as controls. Urinary G3BP was tested by ELISA. Renal histopathology was reviewed by an experienced renal pathologist. Other clinical variables were collected through chart review., Results: The levels of uG3BP were significantly increased in active LN patients compared to those in inactive LN (p<0.001), CKD patients (p=0.01), and healthy controls (p<0.001). ROC analysis indicated a good discrimination ability of uG3BP to differentiate active LN from CKD patients (AUC=0.7), inactive LN (AUC=0.76), or healthy controls (AUC=0.87). uG3BP was positively correlated with SLEDAI (ρ=0.352, p<0.001), rSLEDAI (ρ=0.302, p<0.001), and SLICC RAS (ρ=0.465, p<0.001), indicating a role as a biomarker of disease activity. It also correlated with clinical parameters, including 24-h urine protein, ESR, and serum C3 levels. In patients with 24-h urine protein > 3.0 g/24h, uG3BP levels were higher in proliferative LN than in membranous LN (p=0.04). They could discriminate the two pathogenic types of LN (AUC=0.72), and they also positively correlated with AI (ρ=0.389, p=0.008) and scores of hyaline deposits (ρ=0.418, p=0.006). While in patients with 24-h urine protein ≤ 3.0 g/24h, uG3BP levels were not significantly different between proliferative and membranous LN, and there was no apparent relationship between uG3BP levels with AI or with scores of hyaline deposits, but they correlated positively with scores of cellular/fibrocellular crescents (ρ=0.328, p=0.04)., Conclusion: uG3BP is a non-invasive biomarker for clinically and histologically reflecting disease activity. It is associated with active histological changes and can be used as a surrogate biomarker when the renal biopsy is impractical., (© 2022. The Author(s).)
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- 2022
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39. Isolation and identification of a feather degrading Bacillus tropicus strain Gxun-17 from marine environment and its enzyme characteristics.
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Shen N, Yang M, Xie C, Pan J, Pang K, Zhang H, Wang Y, and Jiang M
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- Animals, Bacillus, Chickens metabolism, China, Hydrogen-Ion Concentration, Keratins analysis, Keratins chemistry, Keratins metabolism, Peptide Hydrolases metabolism, Temperature, Caseins metabolism, Feathers chemistry
- Abstract
Background: Feathers are the most abundant agricultural waste produced by poultry farms. The accumulation of a large number of feathers not only seriously pollutes the environment but also causes the waste of protein resources. The degradation of feather waste by keratinase-producing strains is currently a promising method. Therefore, screening high-producing keratinase strains from marine environment and studying the fermentation conditions, enzymatic properties and feather degradation mechanism are crucial for efficient degradation of feathers., Results: A novel efficient feather-degrading bacteria, Gxun-17, isolated from the soil sample of a marine duck farm of Beibu Gulf in Guangxi, China, was identified as Bacillus tropicus. The optimum fermentation conditions were obtained by single factor and orthogonal tests as follows: feather concentration of 15 g/L, maltose concentration of 10.0 g/L, MgSO
4 concentration of 0.1 g/L, initial pH of 7.0 and temperature of 32.5 °C. The strain completely degraded the feathers within 48 h, and the highest keratinase activity was 112.57 U/mL, which was 3.18-fold that obtained with the basic medium (35.37 U/mL). Detecting the keratinase activity and the content of sulphur-containing compounds in the fermentation products showed that the degradation of feathers by the strain might be a synergistic effect of the enzyme and sulphite. The keratinase showed optimal enzyme activity at pH 7.0 and temperature of 60 °C. The keratinase had the best performance on the casein substrate. When casein was used as the substrate, the Km and Vmax values were 15.24 mg/mL and 0.01 mg/(mL·min), respectively. Mg2+ , Ca2+ , K+ , Co2+ , Al3+ , phenylmethylsulphonyl fluoride and isopropanol inhibited keratinase activity, which indicated that it was a serine keratinase. Conversely, the keratinase activity strongly increased with the addition of Mn2+ and β-mercaptoethanol., Conclusions: A novel feather-degrading B. tropicus Gxun-17 was obtained from marine environment. The strain adapted the extreme conditions such as low temperature, high salt and high pressure. Thus, the keratinase had high activity, wide range of temperature and pH, salt tolerance and other characteristics, which had potential application value., (© 2022. The Author(s).)- Published
- 2022
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40. A new approach for reducing pollutants level: a longitudinal cohort study of physical exercises in young people.
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Xu Y, Gao H, Du Z, Liu H, Cheng Q, Zhang F, Ye J, Wang A, Dou Y, Ma B, Zhao N, Zhu F, Xu X, Shen N, Wu J, and Xue B
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- Adolescent, Benzhydryl Compounds urine, Cohort Studies, Dimethoate, Exercise, Female, Humans, Longitudinal Studies, Male, Environmental Pollutants
- Abstract
Background: The present study aimed to evaluate the elimination of three common pollutants (dimethoate, benzo(a)pyrene (BaP) and bisphenol A (BPA) by different physical exercises and to assess the possible factors which could affect the pollutants elimination., Methods: A total of 200 individuals who chose different kinds of exercises in accordance to their own wish were recruited. The levels of urinary pollutants were measured using β-glucuronidase hydrolysis followed by a high-performance liquid chromatography tandem mass spectrometry-based method., Results: Totally, the levels of dimethoate, BaP and BPA were reduced after physical exercises. However, the elimination of BaP in male was higher than that in female but the elimination of BPA in female was higher than that in male. Multivariate logistic regression showed that the degree of heart rate (HR) change was a protective factor affecting the improvement effect of dimethoate, BaP and BPA while BMI (body mass index) was a risk factor. Nevertheless, sex was a risk factor affecting the improvement of dimethoate and BaP but had a lower efficacy on BPA improvement., Conclusion: The present findings indicate that physical exercises can be considered as a novel approach to eliminate pollutants level in human body and can also give suggestions for choosing specific physical exercises to male and female individuals. Moreover, those who are with higher BMI need to lose weight before eliminating pollutant level through physical exercises., (© 2022. The Author(s).)
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- 2022
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41. Serum creatinine/cystatin C ratio as a surrogate marker for sarcopenia in patients with gastric cancer.
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Sun J, Yang H, Cai W, Zheng J, Shen N, Yang X, Pan B, Zhang W, Chen X, and Shen X
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- Biomarkers, Creatinine, Cystatin C, Humans, Male, Retrospective Studies, Sarcopenia diagnosis, Sarcopenia diagnostic imaging, Stomach Neoplasms complications
- Abstract
Background: Sarcopenia is an age-related syndrome that may have negative impact on surgical outcomes and long-term survival of patients with gastric cancer. Serum creatinine/cystatin C (Cr/CysC) ratio has attracted attention as a surrogate marker for sarcopenia but has not been adequately studied in patients with gastric cancer. The purpose of this study was to investigate the validity of serum Cr/CysC ratio as a predictor of sarcopenia, evaluate a statistical cut-off value, and assess the relationship between Cr/CysC ratio and prognosis of patients with gastric cancer., Methods: We retrospectively studied 327 patients who underwent surgery for gastric cancer from June 2009 to October 2021. The skeletal muscle mass index was calculated using computed tomography (CT). We determined the relevance of serum Cr/CysC ratio as a surrogate maker for sarcopenia by comparing it with various biomarkers. The Concordance index (C-index) was calculted to measure whether the Cr/CysC ratio can prognosis of patients with gastric cancer., Results: Serum Cr/CysC was significantly correlated with with Skeletal Muscle Index (SMI) (r = 0.221, p < 0.001) and Skeletal Muscle Area (SMA) (r = 0.258, p < 0.001). The area under the curve for sarcopenia was significantly larger for serum Cr/CysC ratio than for other biomarkers (Cr/CysC: 0.644, CysC: 0.535, Cr: 0.556). Patients in the high-Cr/CysC group have longer survival time than that in low-Cr/CysC group, defined by the cutoff value 0.67. The C-index of both Cr/CysC ratio and SMI with OS was 0.63., Conclusions: Serum Cr/CysC ratio can be used accurately, inexpensively, and easily to evaluate sarcopenia in male patients with gastric cancer. Our study shows that patients with Cr/CysC below 0.67 had possibility of sarcopenia and would be poor prognosis., (© 2022. The Author(s).)
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- 2022
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42. Online re-examination of postgraduate medical students during the COVID-19 pandemic.
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Gu S, Yuan W, Zhang A, Huo G, Jiang M, Han J, and Shen N
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- Humans, Pandemics, Retrospective Studies, SARS-CoV-2, COVID-19, Education, Medical, Undergraduate, Students, Medical
- Abstract
Background: Postgraduate entrance examination (the Unified National Graduate Entrance Examination) is the major way for Chinese medical undergraduate student to apply for postgraduate studies. It consists of two stages: the preliminary basic written test and the re-examination in form of both written tests and interviews. With the spread of COVID-19, the traditional on-site re-examination of postgraduates must be changed to online re-examination. By comparing the re-examination process and admission results of online and on-site re-examination, we studied the feasibility of online re-examination for postgraduates and measures to improve it., Methods: This was a retrospective cohort study using data from the Unified National Graduate Entrance Examination. Our sample population was the applicants to Peking University Third Hospital (PUTH) who completed re-examinations. In total, 281 records were successively selected from March 2017 to May 2020. By comparing the re-examination process and admission results of the 2020 online re-examination with those of the 2017-2019 on-site re-examinations, we analyzed the process, difficulties and improvement of online re-examination., Results: A total of 281 subjects were included, of whom 77.9% completed an on-site re-examination in 2017-2019 and 22.1% completed the 2020 online re-examination. In the on-site re-examinations, 70.8% of the students were admitted, and in the online re-examination, 74.2% of the students were admitted. There were no significant differences between the students who completed on-site and online re-examinations in terms of gender, recent graduation, cultivation type, graduate from a key university, and admission (P>0.05). The on-site and online re-examination results were very similar among the admitted students. The multivariable logistic regression analysis showed that online re-examination had no effect on student admissions. Students seeking professional degree were less likely to be admitted than those seeking academic degree, and those with a better standardized rank in medicine and a better standardized rank of re-examination score were more likely to be admitted., Conclusions: The online re-examination implemented in 2020 during the COVID-19 pandemic achieved the same selective effect as on-site re-examination. Effective time management, a standardized test question template, well-trained staff and effective technology are the keys to success., (© 2022. The Author(s).)
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- 2022
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43. Successful treatment of a kidney transplant patient with COVID-19 and late-onset Pneumocystis jirovecii pneumonia.
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Peng J, Ni M, Du D, Lu Y, Song J, Liu W, Shen N, Wang X, Zhu Y, Vallance BA, Sun Z, and Yu HB
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- Humans, Male, Middle Aged, COVID-19 complications, Kidney Transplantation adverse effects, Pneumonia, Pneumocystis diagnosis, Pneumonia, Pneumocystis drug therapy, COVID-19 Drug Treatment
- Abstract
Background: Solid transplant patients are susceptible to Pneumocystis jirovecii pneumonia (PJP). While the vast majority of PJP cases occur within the first 6 months after transplantation, very few PJP cases are seen beyond 1 year post-transplantation (late-onset PJP). PJP and coronavirus disease 2019 (COVID-19, caused by infection with SARS-CoV-2) share quite a few common clinical manifestations and imaging findings, making the diagnosis of PJP often underappreciated during the current COVID-19 pandemic. To date, only 1 case of kidney transplantation who developed COVID-19 and late-onset PJP has been reported, but this patient also suffered from many other infections and died from respiratory failure and multiple organ dysfunction syndrome. A successful treatment of kidney patients with COVID-19 and late-onset PJP has not been reported., Case Presentation: We present a case of a 55-year-old male kidney transplant patient with COVID-19 who also developed late-onset PJP. He received a combined treatment strategy, including specific anti-pneumocystis therapy, symptomatic supportive therapy, adjusted immunosuppressive therapy, and use of antiviral drugs/antibiotics, ending with a favorable outcome., Conclusions: This case highlights the importance of prompt and differential diagnosis of PJP in kidney transplant patients with SARS-CoV-2 infection. Further studies are required to clarify if kidney transplant patients with COVID-19 could be prone to develop late-onset PJP and how these patients should be treated., (© 2021. The Author(s).)
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- 2021
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44. Polysaccharide CM1 from Cordyceps militaris hinders adipocyte differentiation and alleviates hyperlipidemia in LDLR (+/-) hamsters.
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Yu WQ, Yin F, Shen N, Lin P, Xia B, Li YJ, and Guo SD
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- Animals, Cricetinae, Fungal Polysaccharides therapeutic use, Immunoblotting, Male, Real-Time Polymerase Chain Reaction, Adipocytes drug effects, Cell Differentiation drug effects, Cordyceps chemistry, Fungal Polysaccharides pharmacology, Hyperlipidemias drug therapy, Receptors, LDL metabolism
- Abstract
Background: Cordyceps militaris is cultured widely as an edible mushroom and accumulating evidence in mice have demonstrated that the polysaccharides of Cordyceps species have lipid-lowering effects. However, lipid metabolism in mice is significantly different from that in humans, making a full understanding of the mechanisms at play critical., Methods: After 5 months, the hamsters were weighed and sampled under anesthesia after overnight fasting. The lipid-lowering effect and mechanisms of the polysaccharide CM1 was investigated by cellular and molecular technologies. Furthermore, the effect of the polysaccharide CM1 (100 μg/mL) on inhibiting adipocyte differentiation was investigated in vitro., Results: CM1, a polysaccharide from C. militaris, significantly decreased plasma total cholesterol, triglyceride and epididymal fat index in LDLR
(+/-) hamsters, which have a human-like lipid profile. After 5 months' administration, CM1 decreased the plasma level of apolipoprotein B48, modulated the expression of key genes and proteins in liver, small intestine, and epididymal fat. CM1 also inhibited preadipocyte differentiation in 3T3-L1 cells by downregulating the key genes involved in lipid droplet formation., Conclusions: The polysaccharide CM1 lowers lipid and adipocyte differentiation by several pathways, and it has potential applications for hyperlipidemia prevention., (© 2021. The Author(s).)- Published
- 2021
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45. IMUP and GPRC5A: two newly identified risk score indicators in pancreatic ductal adenocarcinoma.
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Wei R, Qi G, Zeng Z, Shen N, Wang Z, Shen H, Gao L, Song C, Ma W, and Wang C
- Abstract
Background: Pancreatic cancer has been a threateningly lethal malignant tumor worldwide. Despite the promising survival improvement in other cancer types attributing to the fast development of molecular precise medicine, the current treatment situation of pancreatic cancer is still woefully challenging since its limited response to neither traditional radiotherapy and chemotherapy nor emerging immunotherapy. The study is to explore potential responsible genes during the development of pancreatic cancer, thus identifying promising gene indicators and probable drug targets., Methods: Different bioinformatic analysis were used to interpret the genetic events in pancreatic cancer development. Firstly, based on multiple cDNA microarray profiles from Gene Expression Omnibus (GEO) database, the genes with differently mRNA expression in cancer comparing to normal pancreatic tissues were identified, followed by being grouped based on the difference level. Then, GO and KEGG were performed to separately interpret the multiple groups of genes, and further Kaplan-Meier survival and Cox Regression analysis assisted us to scale down the candidate genes and select the potential key genes. Further, the basic physicochemical properties, the association with immune cells infiltration, mutation or other types variations besides expression gap in pancreatic cancer comparing to normal tissues of the selected key genes were analyzed. Moreover, the aberrant changed expression of key genes was validated by immunohistochemistry (IHC) experiment using local hospital tissue microarray samples and the clinical significance was explored based on TCGA clinical data., Results: Firstly, a total of 22,491 genes were identified to express differently in cancer comparing to normal pancreatic tissues based on 5 cDNA expression profiles, and the difference of 487/22491 genes was over eightfold, and 55/487 genes were shared in multi profiles. Moreover, after genes interpretation which showed the > eightfold genes were mainly related to extracellular matrix structural constituent regulation, Kaplan-Meier survival and Cox-regression analysis were performed continually, and the result indicated that of the 55 extracellular locating genes, GPRC5A and IMUP were the only two independent prognostic indicators of pancreatic cancer. Further, detailed information of IMUP and GPRC5A were analyzed including their physicochemical properties, their expression and variation ratio and their association with immune cells infiltration in cancer, as well as the probable signaling pathways of genes regulation on pancreatic cancer development. Lastly, local IHC experiment performed on PAAD tissue array which was produced with 62 local hospital patients samples confirmed that GPRC5A and IMUP were abnormally up-regulated in pancreatic cancer, which directly associated with worse patients both overall (OS) and recurrence free survival (RFS)., Conclusions: Using multiple bioinformatic analysis as well as local hospital samples validation, we revealed that GPRC5A and IMUP expression were abnormally up-regulated in pancreatic cancer which associated statistical significantly with patients survival, and the genes' biological features and clinical significance were also explored. However, more detailed experiments and clinical trials are obligatory to support their further potential drug-target role in clinical medical treatment., (© 2021. The Author(s).)
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- 2021
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46. Application of a protective sleeve is associated with decreased occupational anxiety during endotracheal intubation: a randomized controlled trial.
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Chen C, Shen N, Chen L, Luo T, Lu T, Liu D, Zhang Q, and Hei Z
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- Adult, Anesthesiologists statistics & numerical data, China, Female, Humans, Intubation, Intratracheal instrumentation, Male, Middle Aged, SARS-CoV-2, Anesthesiologists psychology, Anxiety prevention & control, Anxiety psychology, COVID-19 prevention & control, Intubation, Intratracheal methods, Personal Protective Equipment statistics & numerical data
- Abstract
Background: The high risk of cross-infection during tracheal intubation has caused excessive occupational anxiety for anaesthesiologists amid the novel coronavirus disease 2019 (COVID-19) pandemic. Currently, there is no effective way to attenuate their anxiety in clinical practice. We found that anaesthesiologist with better protective equipment might experience decreased levels of anxiety during intubation., Methods: In this study, 60 patients who underwent intubation and extubation in the operating room were enrolled, and then randomized 1:1 to either wear protective sleeves (protective sleeve group) or not (control group). Visual analogue scale (VAS) was used to measure the anxiety level of anaesthesiologists during intubation. The respiratory droplets of patients on the sleeve, and the anaesthesiologists' perception including the patient's oral malodour, exertion, satisfaction degree, waist discomfort and shoulder discomfort were recorded. The patients' anxiety, oppressed feelings and hypoxia and postoperative complications were all measured and recorded., Results: Compared with the control group, the anaesthesiologists in protective sleeve group achieved lower anxiety scores and better satisfaction degrees during the process of intubation and extubation (all P < 0.05). Respiratory droplets were observed only on the inner side, but not the external side, of the protective sleeves (P < 0.001). The incidence of the anaesthesiologists' perception of patients' oral malodour was significantly lower in the protective sleeve group (P = 0.02) and no patients developed hypoxemia or intubation-related complications in the protective sleeve group., Conclusion: Using protective devices for intubation might eliminate droplet transmission from patients to anaesthesiologists, while also decreasing their anxiety in a controlled operating room environment., Trial Registration: Chinese Clinical Trial. no. ChiCTR2000030705 . Registry at www.chictr.org.cn on 10/03/2020., (© 2021. The Author(s).)
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- 2021
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47. FAM49B promotes breast cancer proliferation, metastasis, and chemoresistance by stabilizing ELAVL1 protein and regulating downstream Rab10/TLR4 pathway.
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Li Y, Xiong Y, Wang Z, Han J, Shi S, He J, Shen N, Wu W, Wang R, Lv W, Deng Y, and Liu W
- Abstract
Background: Breast cancer (BC) is one of the most common cancers and the leading cause of death in women. Previous studies have demonstrated that FAM49B is implicated in several tumor progression, however, the role and mechanism of FAM49B in BC remain to be explored. Therefore, in this study, we aimed to systematically study the role of FAM49B in the proliferation, metastasis, apoptosis, and chemoresistance of BC, as well as the corresponding molecular mechanisms and downstream target., Methods: The ONCOMINE databases and Kaplan-Meier plotter databases were analyzed to find FAM49B and its prognostic values in BC. FAM49B expression in BC and adjacent non-tumor tissues was detected by western blot and IHC. Kaplan-Meier analysis was used to identify the prognosis of BC patients. After FAM49B knockdown in MCF-7 and MDA-MB-231 cells, a combination of co-immunoprecipitation, MTT, migration, and apoptosis assays, nude mouse xenograft tumor model, in addition to microarray detection and data analysis was used for further mechanistic studies., Results: In BC, the results showed that the expression level of FAM49B was significantly higher than that in normal breast tissue, and highly expression of FAM49B was significantly positively correlated with tumor volume, histological grade, lymph node metastasis rate, and poor prognosis. Knockdown of FAM49B inhibited the proliferation and migration of BC cells in vitro and in vivo. Microarray analysis revealed that the Toll-like receptor signaling pathway was inhibited upon FAM49B knockdown. In addition, the gene interaction network and downstream protein validation of FAM49B revealed that FAM49B positively regulates BC cell proliferation and migration by promoting the Rab10/TLR4 pathway. Furthermore, endogenous FAM49B interacted with ELAVL1 and positively regulated Rab10 and TLR4 expression by stabilizing ELAVL1. Moreover, mechanistic studies indicated that the lack of FAM49B expression in BC cells conferred more sensitivity to anthracycline and increased cell apoptosis by downregulating the ELAVL1/Rab10/TLR4/NF-κB signaling pathway., Conclusion: These results demonstrate that FAM49B functions as an oncogene in BC progression, and may provide a promising target for clinical diagnosis and therapy of BC., (© 2021. The Author(s).)
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- 2021
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48. Urinary levels of dimethoate, bisphenol A and benzo[a]pyrene in first-year students of Hohai University from different geographical regions.
- Author
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Xu YJ, Gao HL, Liu H, Zhao NW, Cheng Q, Zhang FR, Ye J, Wang AQ, Dou YJ, Ma B, Zhu F, Xu XL, Li CJ, Wu J, Shen N, and Xue B
- Subjects
- Adolescent, Benzhydryl Compounds, Dimethoate, Female, Humans, Male, Phenols, Students, Benzo(a)pyrene, Universities
- Abstract
Background: The objective of this study was to detect the urinary levels of dimethoate, benzo(a) pyrene (BaP), and bisphenol A (BPA) in first-year Hohai University students with different geographic origins., Methods: First-morning urine samples were collected from 540 healthy freshmen aged 17 to 19 years. Chemical levels were measured using β-glucuronidase hydrolysis followed by a high-performance liquid chromatography-tandem mass spectrometry-based method. Geometric means (GMs) of these three chemicals are presented by body mass index (BMI) and location in a volume-based and creatinine-standardized way., Results: GM concentrations of omethoate, BPA and 3-OHBaP were 9.47 μg/L (10.80 μg/g creatinine), 3.54 μg/L (4.04 μg/g creatinine) and 0.34 ng/L (0.39 ng/g creatinine), respectively. The GM concentration of omethoate in males was significantly higher than that in females. The individuals with a BMI higher than 23.9 had higher GM concentrations of omethoate, BPA, and 3-OHBaP. The inhabitants of Southwest China had significantly lower GM concentrations of omethoate, BPA, and 3-OHBaP than those who lived in other locations in China., Conclusion: The average level of environmental chemical accumulation in freshmen is lower in Southwest China and differs in youth who live in different regions. In addition, obesity is correlated with higher toxin levels in youth., (© 2021. The Author(s).)
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- 2021
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49. Application of PDCA cycle management for postgraduate medical students during the COVID-19 pandemic.
- Author
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Gu S, Zhang A, Huo G, Yuan W, Li Y, Han J, and Shen N
- Subjects
- Curriculum, Humans, Pandemics, SARS-CoV-2, COVID-19, Students, Medical
- Abstract
Background: The COVID-19 outbreak has exerted an enormous impact on various industries worldwide. During this pandemic, clinical teaching hospitals have faced unprecedented challenges regarding the management of postgraduate medical students since postgraduate students in clinical medicine have both student and resident identity characteristics. The purpose of this study was to explore the management effectiveness of Peking University Third Hospital (PUTH) based on PDCA (plan-do-check-act) cycle management and to further develop the medical student management system during the pandemic., Methods: The methods of document review, questionnaire surveys and interviews were used to continuously improve the management measures for postgraduate medical students during the COVID-19 pandemic by using the PDCA cycle., Results: Investigations were conducted on the management system, back-to-school arrangements, laboratory management, COVID-19 prevention and control training, online teaching, mentoring, dissertation progress, and emotional state of postgraduate medical students during the COVID-19 pandemic. We found that strengthening public health management knowledge training, increasing infectious-disease-related knowledge training, innovating online teaching methods, improving PDCA management model maps, and formulating improvement programmes are conducive to improving the quality of such management., Conclusion: Given the difficulties involved in the management of postgraduate medical students during the COVID-19 pandemic, managers need to comprehensively consider and conduct overall planning and use the PDCA management model to improve the management of postgraduate medical students during this period.
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- 2021
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50. Bioinformatic analysis identifying FGF1 gene as a new prognostic indicator in clear cell Renal Cell Carcinoma.
- Author
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Zhang X, Wang Z, Zeng Z, Shen N, Wang B, Zhang Y, Shen H, Lu W, Wei R, Ma W, and Wang C
- Abstract
Background: Clear cell renal cell carcinoma (ccRCC) has been the commonest renal cell carcinoma (RCC). Although the disease classification, diagnosis and targeted therapy of RCC has been increasingly evolving attributing to the rapid development of current molecular pathology, the current clinical treatment situation is still challenging considering the comprehensive and progressively developing nature of malignant cancer. The study is to identify more potential responsible genes during the development of ccRCC using bioinformatic analysis, thus aiding more precise interpretation of the disease METHODS: Firstly, different cDNA expression profiles from Gene Expression Omnibus (GEO) online database were used to screen the abnormal differently expressed genes (DEGs) between ccRCC and normal renal tissues. Then, based on the protein-protein interaction network (PPI) of all DEGs, the module analysis was performed to scale down the potential genes, and further survival analysis assisted our proceeding to the next step for selecting a credible key gene. Thirdly, immunohistochemistry (IHC) and quantitative real-time PCR (QPCR) were conducted to validate the expression change of the key gene in ccRCC comparing to normal tissues, meanwhile the prognostic value was verified using TCGA clinical data. Lastly, the potential biological function of the gene and signaling mechanism of gene regulating ccRCC development was preliminary explored., Results: Four cDNA expression profiles were picked from GEO database based on the number of containing sample cases, and a total of 192 DEGs, including 39 up-regulated and 153 down-regulated genes were shared in four profiles. Based on the DEGs PPI network, four function modules were identified highlighting a FGF1 gene involving PI3K-AKT signaling pathway which was shared in 3/4 modules. Further, both the IHC performed with ccRCC tissue microarray which contained 104 local samples and QPCR conducted using 30 different samples confirmed that FGF1 was aberrant lost in ccRCC. And Kaplan-Meier overall survival analysis revealed that FGF1 gene loss was related to worse ccRCC patients survival. Lastly, the pathological clinical features of FGF1 gene and the probable biological functions and signaling pathways it involved were analyzed using TCGA clinical data., Conclusions: Using bioinformatic analysis, we revealed that FGF1 expression was aberrant lost in ccRCC which statistical significantly correlated with patients overall survival, and the gene's clinical features and potential biological functions were also explored. However, more detailed experiments and clinical trials are needed to support its potential drug-target role in clinical medical use.
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- 2021
- Full Text
- View/download PDF
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