11,152 results on '"Ge D"'
Search Results
2. Modified Ce/Zr-MOF Nanoparticles Loaded with Curcumin for Alzheimer’s Disease via Multifunctional Modulation
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Yang Y, Wang Y, Jiang X, Mi J, Ge D, Tong Y, and Zhu Y
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metal-organic frameworks ,alzheimer’s disease ,drug delivery ,brain targeting ,oxidative stress ,Medicine (General) ,R5-920 - Abstract
Yan Yang,1,* Yiling Wang,1,* Xinran Jiang,1 Jiahao Mi,1 Dizhang Ge,2 Yuna Tong,3 Yuxuan Zhu1,2 1Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Science & Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, People’s Republic of China; 2Department of Pharmacy, People’s Hospital of Aba Tibetan and Qiang Autonomous Prefecture, Aba, 624000, People’s Republic of China; 3Department of Nephrology, The Third People’s Hospital of Chengdu, Chongqing Medical University, Chengdu, 610031, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yuna Tong; Yuxuan Zhu, Email tongyuna1985@163.com; zhuyuxuan6688@163.comIntroduction: Alzheimer’s disease (AD), a neurodegenerative condition, stands as the most prevalent form of dementia. Its complex pathological mechanisms and the formidable blood-brain barrier (BBB) pose significant challenges to current treatment approaches. Oxidative stress is recognized as a central factor in AD, underscoring the importance of antioxidative strategies in its treatment. In this study, we developed a novel brain-targeted nanoparticle, Ce/Zr-MOF@Cur-Lf, for AD therapy.Methods: Layer-by-layer self-assembly technology was used to prepare Ce/Zr-MOF@Cur-Lf. In addition, the effect on the intracellular reactive oxygen species level, the uptake effect by PC12 and bEnd.3 cells and the in vitro BBB permeation effect were investigated. Finally, the mouse AD model was established by intrahippocampal injection of Aβ1-42, and the in vivo biodistribution, AD therapeutic effect and biosafety of the nanoparticles were researched at the animal level.Results: As anticipated, Ce/Zr-MOF@Cur-Lf demonstrated efficient BBB penetration and uptake by PC12 cells, leading to attenuation of H2O2-induced oxidative damage. Moreover, intravenous administration of Ce/Zr-MOF@Cur-Lf resulted in rapid brain access and improvement of various pathological features of AD, including neuronal damage, amyloid-β deposition, dysregulated central cholinergic system, oxidative stress, and neuroinflammation.Conclusion: Overall, Ce/Zr-MOF@Cur-Lf represents a promising approach for precise brain targeting and multi-target mechanisms in AD therapy, potentially serving as a viable option for future clinical treatment.Keywords: metal-organic frameworks, Alzheimer’s disease, drug delivery, brain targeting, oxidative stress
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- 2024
3. Integrative Analyses of Pyrimidine Salvage Pathway-Related Genes Revealing the Associations Between UPP1 and Tumor Microenvironment
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Li Y, Jiang M, Wei Y, He X, Li G, Lu C, and Ge D
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pyrimidine salvage pathways ,upp1 ,microenvironment. ,Pathology ,RB1-214 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Yin Li,1,* Manling Jiang,2,3,* Yongqi Wei,1,* Xiang He,2 Guoping Li,2,* Chunlai Lu,1 Di Ge1 1Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China; 2Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People’s Hospital of Chengdu, Chengdu, Sichuan, People’s Republic of China; 3State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology, Taipa, Macao Special Administrative Region of China*These authors contributed equally to this workCorrespondence: Chunlai Lu; Di Ge, Email lu.chunlai@zs-hospital.sh.cn; ge.di@zs-hospital.sh.cnBackground: The pyrimidine salvage pathway plays a critical role in tumor progression and patient outcomes. The roles of pyrimidine salvage pathway-related genes (PSPGs) in cancer, however, are not fully understood. This study aims to depict the characteristics of PSPGs across various cancers.Methods: An integrative pan-cancer analysis of six PSPGs (CDA, UCK1, UCK2, UCKL1, UPP1, and UPP2) was conducted using TCGA data, single-cell RNA sequencing datasets, and patient samples. Single-cell transcriptome analysis and RT-qPCR were used to validate the relation between UPP1 and cytokines. Flow cytometry was performed to validate the role of UPP1 in immune checkpoint regulation. The correlation between UPP1 and tumor associated neutrophils (TAN) were investigated and validated by single-cell transcriptome analysis and tissue microarrays (TMAs).Results: PSPGs showed low mutation rates but significant copy number variations, particularly amplifications in UCKL1, UPP1, and UCK2 across various cancers. DNA methylation patterns varied, with notable negative correlations between methylation and gene expression in UPP1. PSPGs were broadly up-regulated in multiple cancers, with correlations to clinical staging and prognosis. Proteomic data further confirmed these findings. Functional analysis revealed PSPGs’ associations with tumor proliferation, metastasis, and various signaling pathways. UPP1 showed strong correlations with the tumor microenvironment (TME), particularly with cytokines, immune checkpoints, and various immune cells. Single-cell transcriptome analysis confirmed these associations, highlighting UPP1’s influence on cytokine expression and immune checkpoint regulation. In esophageal squamous cell carcinoma (ESCC), UPP1-high tumor cells were significantly associated with immunosuppressive cells in the TME. Spatial analysis using TMAs revealed that UPP1+ tumor cells were predominantly located at the invasive margin and closely associated with neutrophils, correlating with poorer patient prognosis.Conclusion: Our study depicted the multi-dimensional view of PSPGs in cancer, with a particular focus on UPP1’s role in the TME. Targeting UPP1 holds promise as a potential strategy for cancer therapy.Keywords: pyrimidine salvage pathways, UPP1, microenvironment
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- 2024
4. Baustein KI.
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Gerhard, Detlef, Köring, Timo, and Neges, Matthias
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ARTIFICIAL intelligence ,LIGHTWEIGHT construction ,SYSTEMS engineering ,MACHINE learning ,GEOMETRIC shapes ,NATURAL language processing - Abstract
Copyright of IM + io is the property of AWS-Institut fuer Digitale Produkte und Prozesse GmbH and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
5. The Value of Percutaneous Ultrasound-Guided Subacromial Bursography for Rotator Cuff Tear in Elderly Patients with Shoulder Pain
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Liu B, Ge D, Shan Y, Li Y, Lv J, and Gan S
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rotator cuff tear ,percutaneous ultrasound-guided subacromial bursography ,shoulder pain ,acromial slide cystography ,diagnosis ,Medicine (General) ,R5-920 - Abstract
Bili Liu, Dan Ge, Yue Shan, Yanping Li, Juan Lv, Shuzhi Gan Department of Ultrasound, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310007, People’s Republic of ChinaCorrespondence: Bili Liu, Department of Ultrasound, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, No. 453 Stadium Road, Xihu District, Hangzhou, Zhejiang Province, 310007, People’s Republic of China, Tel +86-057185827841, Email lbili_bl1@163.comObjective: Based on the analysis of the images of acromial slide, we explored the application of percutaneous ultrasound-guided subacromial bursography (PUSB) on rotator cuff tear (RCT) in diagnosing elderly patients with shoulder pain.Methods: Eighty-five patients who were clinically diagnosed with RCT and underwent PUSB examination in the department of ultrasound in our hospital were enrolled as the subjects. Independent samples t-test was used to analyze the general characteristics. Based on the gold standard of shoulder arthroscopy, the diagnostic efficacy of ultrasound, magnetic resonance imaging (MRI), and PUSB was evaluated. The sensitivity, specificity, positive and negative predictive values, and accuracy were calculated as well. The consistency of these techniques with shoulder arthroscopy in diagnosing the RCT stage was additionally compared using Kappa test.Results: In patients with large full-thickness RCT, the 100% detection rate was achieved by the techniques of ultrasound, MRI, and PUSB. For patients with small full-thickness RCT, the detection rate of PUSB (100%) was evidently higher than those of ultrasound and MRI. Similar results were shown in the detection rates of patients with bursal-side partial-thickness RCT (90.5%) and articular-side partial-thickness RCT (86.9%). More importantly, the sensitivity, specificity, and accuracy of PUSB in patients with both full-thickness RCT and partial-thickness RCT were significantly better than those of ultrasound and MRI.Conclusion: PUSB has a better efficacy in the detection of RCT than ultrasound and MRI, showing its feasibility as an important imaging method to evaluate the degree of RCT.Keywords: rotator cuff tear, percutaneous ultrasound-guided subacromial bursography, shoulder pain, acromial slide cystography, diagnosis
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- 2023
6. Flexible Measures to Depress Switching Over-Voltage in UHVAC Transmission System and Latest Research Results
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Chen, X., Shi, W., He, Z., Yu, H., Li, Z., Chen, W., Ge, D., Han, X., Sun, G., and Li, M.
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- 2023
7. Gegen Qinlian Decoction Alleviates Experimental Colitis and Concurrent Lung Inflammation by Inhibiting the Recruitment of Inflammatory Myeloid Cells and Restoring Microbial Balance
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Li Y, Li N, Liu J, Wang T, Dong R, Ge D, and Peng G
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gegen qinlian decoction ,ulcerative colitis ,lung and intestinal microbiota ,pulmonary inflammation ,myeloid cells ,Pathology ,RB1-214 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Yalan Li,1,* Na Li,1,* Jiajing Liu,1 Tieshan Wang,2 Ruijuan Dong,3 Dongyu Ge,3 Guiying Peng1 1Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China; 2Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, People’s Republic of China; 3Experimental Teaching Center, School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Guiying Peng, Email penggy@bucm.edu.cnObjective: Ulcerative colitis (UC) as one of the intractable diseases in gastroenterology seriously threatens human health. Respiratory pathology is a representative extraintestinal manifestation of UC affecting the quality of life of patients. Gegen Qinlian Decoction (GQD) is a classical traditional Chinese medicine prescription for UC or acute lung injury. This study was aimed to reveal the therapeutic effect of GQD on UC and its pulmonary complications and uncover its molecular mechanism mediated by myeloid cells and microbiota.Methods: Mice with DSS-induced colitis were orally administrated with GQD. Overall vital signs were assessed by body weight loss and disease activity index (DAI). Pulmonary general signs were evaluated by pulmonary pathology and lung function. The mechanism of GQD relieving UC was characterized by detecting myeloid cells (neutrophils, macrophages, inflammatory monocytes, and resident monocytes) in colonic and lung tissues, related inflammatory cytokines, as well as the microbiota in bronchoalveolar lavage fluid (BALF) and feces.Results: GQD significantly reduced weight loss, DAI scores, and lung injury but improved the lung function of colitis mice. The DSS-induced colonic and concurrent pulmonary inflammation were also alleviated by GQD, as indicated by the down-regulated expressions of inflammatory cytokines (TNF-α, IL-1β, IL-6, CCR2, and CCL2) and the suppressed recruitment of neutrophils and inflammatory monocytes. Meanwhile, GQD greatly improved intestinal microbiota imbalance by enriching Ruminococcaceae UCG-013 while decreasing Parabacteroides, [Eubacterium]_fissicatena_group, and Akkermansia in the feces of colitis mice. Expectantly, GQD also restored lung microbiota imbalance by clearing excessive Coprococcus 2 and Ochrobactrum in the BALF of colitis mice. Finally, significant correlations appeared between GQD-mediated specific bacteria and inflammatory cytokines or immune cells.Conclusion: GQD could alleviate UC by decreasing excessive inflammatory myeloid cells and cytokines, and reshaping the microbiota between the colon and lung, which contributes to clarifying the mechanism by which GQD ameliorates colitis-associated pulmonary inflammation.Keywords: Gegen Qinlian Decoction, ulcerative colitis, lung and intestinal microbiota, pulmonary inflammation, myeloid cells
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- 2022
8. Xuanbai Chengqi Decoction Ameliorates Pulmonary Inflammation via Reshaping Gut Microbiota and Rectifying Th17/Treg Imbalance in a Murine Model of Chronic Obstructive Pulmonary Disease
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Wang Y, Li N, Li Q, Liu Z, Li Y, Kong J, Dong R, Ge D, Li J, and Peng G
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xbcq ,copd ,intestinal microbiota ,th17/treg ,pulmonary inflammation ,Diseases of the respiratory system ,RC705-779 - Abstract
Yongan Wang,1,* Na Li,1,* Qiuyi Li,1 Zirui Liu,1 Yalan Li,1 Jingwei Kong,1 Ruijuan Dong,2 Dongyu Ge,2 Jie Li,3 Guiying Peng1 1Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, People’s Republic of China; 2Experimental Teaching Center, School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, People’s Republic of China; 3Department of Respiratory Medicine, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Guiying Peng; Jie Li Email penggy@bucm.edu.cn; lijie2007@126.comPurpose: Chronic obstructive pulmonary disease (COPD), a prevalent obstructive airway disease, has become the third most common cause of death globally. Xuanbai Chengqi decoction (XBCQ) is a traditional Chinese medicine prescription for the acute exacerbation of COPD. Here, we aimed to reveal the therapeutic effects of XBCQ administration and its molecular mechanisms mediated by Th17/Treg balance and gut microbiota.Methods: We determined the counts of Th17 and Treg cells in the serum of 15 COPD and 10 healthy subjects. Then, cigarette smoke extract-induced COPD mice were gavaged with low, middle, and high doses of XBCQ, respectively. Weight loss, pulmonary function and inflammation, Th17/Treg ratio, and gut microbiota were measured to evaluate the efficacy of XBCQ on COPD.Results: COPD patients had a higher Th17/Treg ratio in the serum than healthy controls, which was consistent with the results in the lung and colon of COPD mice. The middle dose of XBCQ (M-XBCQ) significantly decreased the weight loss and improved the pulmonary function (FEV0.2/FVC) in COPD mice. Moreover, M-XBCQ alleviated lung inflammation by rectifying the Th17/Treg imbalance, reducing the expressions of TNF-α, IL-1β, and MMP-9, and suppressing inflammatory cells infiltration. Meanwhile, M-XBCQ greatly improved the microbial homeostasis in COPD mice by accumulating probiotic Gordonibacter and Akkermansia but inhibiting the growth of pathogenic Streptococcus, which showed significant correlations with pulmonary injury.Conclusion: Oral M-XBCQ could alleviate COPD exacerbations by reshaping the gut microbiota and improving the Th17/Treg balance, which aids in elucidating the mechanism through which XBCQ as a therapy for COPD.Keywords: XBCQ, COPD, intestinal microbiota, Th17/Treg, pulmonary inflammation
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- 2021
9. Development and Validation of Prognostic Survival Nomograms for Patients with Anal Canal Cancer: A SEER-Based Study
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Tang J, Zhu L, Huang Y, Yang L, Ge D, Hu Z, and Wang C
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anal canal cancer ,cancer specific survival ,nomogram ,overall survival ,prognosis ,Medicine (General) ,R5-920 - Abstract
Jie Tang,1 Liqun Zhu,1 Yuejiao Huang,2,3 Lixiang Yang,4 Dangen Ge,5 Zhengyu Hu,6 Chun Wang1 1Department of Oncology, Liyang People’s Hospital, Liyang, 213300, People’s Republic of China; 2Medical School, Nantong University, Nantong, 226019, People’s Republic of China; 3Department of Medical Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226399, People’s Republic of China; 4Department of Neurosurgery, Affiliated Zhongda Hospital of Southeast University, Nanjing, 210009, People’s Republic of China; 5Department of Pharmacy, Liyang People’s Hospital, Liyang, 213300, People’s Republic of China; 6Department of General Surgery, Shanghai Tenth People’s Hospital, Affiliated to Tongji University School of Medicine, Shanghai, 200072, People’s Republic of ChinaCorrespondence: Chun WangDepartment of Oncology, Liyang People’s Hospital, 70 Jianshe Road, Liyang, Jiangsu, 213300, People’s Republic of ChinaEmail zlkwangchun@163.comObjective: Anal canal cancer is a rare malignancy with increasing incidence in recent times. This study aimed to develop two nomograms to predict the overall survival (OS) and cancer-specific survival (CSS) of patients with anal canal cancer.Methods: Information of patients with anal canal cancer from 2004 to 2015 was extracted from the surveillance, epidemiology, and end results (SEER) database. Cox analysis was used to select the risk factors for prognosis, and nomograms were constructed using the R software. The C-index, area under the curve (AUC) of time-dependent receiver operating characteristic (ROC) curves, calibration plot and decision curve analysis (DCA) were used to assess the clinical utility of the nomograms.Results: A total of 2458 patients with malignant tumours of the anal canal were screened out. Sex, age, marital status, histological type, grade, tumour size, AJCC stage, SEER stage and chemotherapy were independent prognostic factors for OS, whereas sex, age, race, histological type, grade, tumour size, AJCC stage, SEER stage and radiotherapy were independent prognostic factors for CSS. In the training cohort, the C-index value for OS nomogram was 0.73 (95% CI, 0.69– 0.77), and the AUC values that predicted the 1-, 3- and 5-year survival rates were 0.764, 0.758 and 0.760, respectively, whereas the C-index value for CSS nomogram model was 0.74 (95% CI, 0.69– 0.79), and the AUC values were 0.763, 0.769 and 0.763, respectively. The calibration plot and DCA curves demonstrated good prediction performance of the model in both the training and validation cohorts.Conclusion: The established nomogram is a visualisation tool that can effectively predict the OS and CSS of patients with anal canal cancer.Keywords: anal canal cancer, cancer specific survival, nomogram, overall survival, prognosis
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- 2021
10. Tackling Health Inequity One Text at a Time
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Sarilla, G., primary, Atak, E., additional, Fernandez-Rodriguez, E., additional, Menjivar, E., additional, Shu, C., additional, Dixit, D., additional, Ge, D., additional, Baldospin, S., additional, Nagella, N., additional, and Hussain, S., additional
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- 2024
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11. A Wake-up Call for Medical Students' Sleep Education
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Ge, D., primary, Shah, V.P., additional, Kim, D., additional, Fayngersh, A., additional, Wong, K., additional, and Jobanputra, A.M., additional
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- 2024
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12. Reaching the Underserved for Cancer Screening: Digitally
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Manfra, A., primary, Ge, D., additional, Sarilla, G., additional, Akat, E., additional, Andrews, T., additional, Menjivar, E., additional, Fernandez-Rodriguez, E., additional, Shu, C., additional, Natarajan, A., additional, Ariwoola, A., additional, AL-Khateeb, M., additional, and Hussain, S., additional
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- 2024
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13. Paeonol and glycyrrhizic acid in combination ameliorate the recurrent nitroglycerin-induced migraine-like phenotype in rats by regulating the GABBR2/TRPM8/PRKACA/TRPV1 pathway.
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Zhang Y, Ge F, Luo Y, Ji X, Liu Z, Qiu Y, Hou J, Zhou R, Zhao C, Xu Q, Zhang S, Yu X, Wang C, Ge D, Meng F, and Tao X
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- Animals, Male, Rats, Disease Models, Animal, Drug Therapy, Combination, Phenotype, Protein Kinase C-alpha metabolism, Protein Kinase C-alpha genetics, Rats, Sprague-Dawley, Receptors, GABA metabolism, Receptors, GABA genetics, Signal Transduction drug effects, Acetophenones pharmacology, Glycyrrhizic Acid pharmacology, Glycyrrhizic Acid therapeutic use, Migraine Disorders drug therapy, Migraine Disorders chemically induced, Migraine Disorders metabolism, Nitroglycerin toxicity, Nitroglycerin pharmacology, TRPM Cation Channels metabolism, TRPM Cation Channels genetics, TRPV Cation Channels metabolism, TRPV Cation Channels genetics
- Abstract
Ethnopharmacological Relevance: Paeonol (PAE) and glycyrrhizic acid (GLY) are predominate components of 14 blood-entering ones of Piantongtang No. 1, which is a traditional Chinese medicine prescription for chronic migraine with minimal side effects. Both paeonol and glycyrrhizic acid exhibit analgesic, neuroprotective and anti-inflammatory properties individually. Our previous research has highlighted their combined effect (PAE + GLY) in ameliorating migraine symptoms. However, there are not yet any studies exploring the mechanism of action of PAE + GLY in the treatment of migraine., Aim of the Study: This research aimed to determine the mechanism of PAE + GLY in ameliorating the recurrent nitroglycerin-induced migraine-like phenotype in rats., Materials and Methods: Using a nitroglycerin-induced migraine model via subcutaneous injection in the neck, we evaluated the effect of PAE + GLY on migraine-like symptoms. Behavioural tests and biomarkers analysis were employed, alongside transcriptome sequencing (RNA-seq). Mechanistic insights were further verified utilising reverse transcription quantitative PCR (RT-qPCR), Western blot (WB), ELISA and immunofluorescence (IF) techniques., Results: Following treatment with PAE + GLY, hyperalgesia threshold and 5-hydroxytryptamine (5-HT) levels increased, and migraine-like head scratching, histamine and calcitonin gene-related peptide (CGRP) levels were reduced. RNA-Seq experiments revealed that PAE + GLY upregulated the expression of Glutamate decarboxylase 2 (GAD2) and γ-aminobutyric acid type B receptor subunit 2 (GABBR2) genes. This upregulation activated the GABAergic synapse pathway, effectively inhibiting migraine attacks. Further validation demonstrated an increase in γ-aminobutyric acid (GABA) content in cerebrospinal fluid post PAE + GLY treatment, coupled with increased expression of dural GAD2, GABBR2 and transient receptor potential channel M8 (TRPM8). Consequently, this inhibited the expression of dural cAMP-dependent protein kinase catalytic subunit alpha (PRKACA) and transient receptor potential channel type 1 (TRPV1), subsequently downregulating p-ERK1/2, p-AKT1, IL-1β and TNF-α., Conclusions: Our findings underscore that PAE + GLY ameliorates inflammatory hyperalgesia migraine by upregulating inhibitory neurotransmitters and modulating the GABBR2/TRPM8/PRKACA/TRPV1 pathway., Competing Interests: Declaration of competing interest There are no conflicts of interest to declare, and all the authors have approved this manuscript for publication., (Copyright © 2024. Published by Elsevier B.V.)
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- 2024
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14. The Pivotal Role of Heavy Terpenes and Anthropogenic Interactions in New Particle Formation on the Southeastern Qinghai-Tibet Plateau.
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Liu Y, Nie W, Qi X, Li Y, Xu T, Liu C, Ge D, Chen L, Niu G, Wang J, Yang L, Wang L, Zhu C, Wang J, Zhang Y, Liu T, Zha Q, Yan C, Ye C, Zhang G, Hu R, Huang RJ, Chi X, Zhu T, and Ding A
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- Tibet, Aerosols, Atmosphere chemistry, Air Pollutants, Environmental Monitoring, Particulate Matter, Terpenes
- Abstract
Aerosol particles originating from the Qinghai-Tibet Plateau (QTP) readily reach the free troposphere, potentially affecting global radiation and climate. Although new particle formation (NPF) is frequently observed at such high altitudes, its precursors and their underlying chemistry remain poorly understood. This study presents direct observational evidence of anthropogenic influences on biogenic NPF on the southeastern QTP, near the Himalayas. The mean particle nucleation rate ( J
1.7 ) is 2.6 cm-3 s-1 , exceeding the kinetic limit of sulfuric acid (SA) nucleation (mean SA: 2.4 × 105 cm-3 ). NPF is predominantly driven by highly oxygenated organic molecules (HOMs), possibly facilitated by low SA levels. We identified 1538 ultralow-volatility HOMs driving particle nucleation and 764 extremely low-volatility HOMs powering initial particle growth, with mean total concentrations of 1.5 × 106 and 3.7 × 106 cm-3 , respectively. These HOMs are formed by atmospheric oxidation of biogenic precursors, unexpectedly including sesquiterpenes and diterpenes alongside the commonly recognized monoterpenes. Counterintuitively, over half of HOMs are organic nitrates, mainly produced by interacting with anthropogenic NOx via RO2 +NO terminations or NO3 -initiated oxidations. These findings advance our understanding of NPF mechanisms in this climate-sensitive region and underscore the importance of heavy terpene and NOx -influenced chemistry in assessing anthropogenic-biogenic interactions with climate feedbacks.- Published
- 2024
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15. SGFCCDA: Scale Graph Convolutional Networks and Feature Convolution for circRNA-Disease Association Prediction.
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Shang J, Zhao L, He X, Meng X, Zhang L, Ge D, Li F, and Liu JX
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- Humans, Algorithms, RNA, Circular genetics, Neural Networks, Computer, Computational Biology methods
- Abstract
Circular RNAs (circRNAs) have emerged as a novel class of non-coding RNAs with regulatory roles in disease pathogenesis. Computational models aimed at predicting circRNA-disease associations offer valuable insights into disease mechanisms, thereby enabling the development of innovative diagnostic and therapeutic approaches while reducing the reliance on costly wet experiments. In this study, SGFCCDA is proposed for predicting potential circRNA-disease associations based on scale graph convolutional networks and feature convolution. Specifically, SGFCCDA integrates multiple measures of circRNA and disease similarity and combines known association information to construct a heterogeneous network. This network is then explored by scale graph convolutional networks to capture both topological and attribute information. Additionally, convolutional neural networks are employed to further learn the features and obtain higher-order feature representations containing richer information about nodes. The Hadamard product is utilized to effectively combine circRNA features with disease features, and a multilayer perceptron is applied to predict the association between each pair of circRNA and disease. Five-fold cross validation experiments conducted on the CircR2Disease dataset demonstrate the accurate prediction capabilities of SGFCCDA in identifying potential circRNA-disease associations. Furthermore, case studies provide further confirmation of SGFCCDA's ability to identify disease-associated circRNAs.
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- 2024
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16. Developing Cell-Membrane-Associated Liposomes for Liver Diseases.
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Ge D, An R, Xue L, Qiu M, Zhu Y, Wen G, Shi Y, Ren H, Li W, and Wang J
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- Humans, Animals, Liposomes chemistry, Liver Diseases drug therapy, Liver Diseases metabolism, Cell Membrane metabolism, Cell Membrane chemistry, Drug Delivery Systems
- Abstract
Over the past decade, a marked escalation in the prevalence of hepatic pathologies has been observed, adversely impacting the quality of life for many. The predominant therapeutic strategy for liver diseases has been pharmacological intervention; however, its efficacy is often constrained. Currently, liposomes are tiny structures that can deliver drugs directly to targeted areas, enhancing their effectiveness. Specifically, cell membrane-associated liposomes have gained significant attention. Despite this, there is still much to learn about the binding mechanism of this type of liposome. Thus, this review comprehensively summarizes relevant information on cell membrane-associated liposomes, including their clinical applications and future development directions. First, we will briefly introduce the composition and types of cell membrane-associated liposomes. We will provide an overview of their structure and discuss the various types of liposomes associated with cell membranes. Second, we will thoroughly discuss various strategies of drug delivery using these liposomes. Lastly, we will discuss the application and clinical challenges associated with using cell membrane-associated liposomes in treating liver diseases. We will explore their potential benefits while also addressing the obstacles that need to be overcome. Furthermore, we will provide prospects for future development in this field. In summary, this review underscores the promise of cell membrane-associated liposomes in enhancing liver disease treatment and highlights the need for further research to optimize their utilization. In summary, this review underscores the promise of cell membrane-associated liposomes in enhancing liver disease treatment and highlights the need for further research to optimize their utilization.
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- 2024
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17. DMHANT: DropMessage Hypergraph Attention Network for Information Propagation Prediction.
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Ouyang Q, Chen H, Liu S, Pu L, Ge D, and Fan K
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Predicting propagation cascades is crucial for understanding information propagation in social networks. Existing methods always focus on structure or order of infected users in a single cascade sequence, ignoring the global dependencies of cascades and users, which is insufficient to characterize their dynamic interaction preferences. Moreover, existing methods are poor at addressing the problem of model robustness. To address these issues, we propose a predication model named DropMessage Hypergraph Attention Networks, which constructs a hypergraph based on the cascade sequence. Specifically, to dynamically obtain user preferences, we divide the diffusion hypergraph into multiple subgraphs according to the time stamps, develop hypergraph attention networks to explicitly learn complete interactions, and adopt a gated fusion strategy to connect them for user cascade prediction. In addition, a new drop immediately method DropMessage is added to increase the robustness of the model. Experimental results on three real-world datasets indicate that proposed model significantly outperforms the most advanced information propagation prediction model in both MAP@k and Hits@K metrics, and the experiment also proves that the model achieves more significant prediction performance than the existing model under data perturbation.
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- 2024
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18. An easy-to-use anesthetic strategy for mitigating postoperative complications following laparoscopic colorectal surgery.
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Li H, Li Y, Sun Y, Ge D, Zheng Z, Tang W, Zheng H, and Yan T
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- 2024
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19. Respiratory pathogen analysis in pediatric inpatients unraveled the infection pattern of Mycoplasma pneumoniae post the COVID-19 pandemic.
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Chen Q, Xu R, Gu Y, Peng J, Ma C, Su D, Liu S, Ge D, Yang Y, and Ning W
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- Humans, Child, Child, Preschool, China epidemiology, Female, Male, Infant, Adolescent, Inpatients statistics & numerical data, SARS-CoV-2, Pandemics, Hospitalization statistics & numerical data, COVID-19 epidemiology, Pneumonia, Mycoplasma epidemiology, Mycoplasma pneumoniae isolation & purification, Respiratory Tract Infections epidemiology, Respiratory Tract Infections microbiology, Coinfection epidemiology
- Abstract
Background: To counteract the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) were implemented globally, exerting a profound influence on a wide spectrum of infectious diseases, encompassing respiratory tract infections (RTIs). Subsequent to the easing of NPIs, China experienced a significant outbreak of Mycoplasma pneumoniae (MP)., Methods: Over a decade from 2015 to 2024, our study scrutinized 12 common infectious diseases among pediatric children. Etiologically diagnostic data and clinical outcome metrics of children with RTIs, tested for 13 pathogens, were analyzed to evaluate changes during and after the pandemic compared to pre-pandemic periods, with a notable emphasis on age profile and coinfection patterns of MP., Results: Among 57,471 hospitalized children, 23,178 were diagnosed with infectious diseases. Under NPIs, most respiratory infections declined compared to pre-pandemic levels, rebounding by 69.64% in 2023. While the infection rate of common respiratory pathogens decreased, cases of respiratory syncytial virus increased during the period of extensive NPI implementation. In 2023, pediatric intensive care unit durations for these pathogens increased, suggesting greater severity of illness compared to 2019. MP exhibited the highest infection rate (31.38% average), with a notable outbreak post-pandemic due to severity increase in <3 year olds and rise among older children. NPIs reduced MP coinfections and mitigated their severity, while exerting a significant influence on bacterial coinfections with MP over the span of 5 years, in contrast to their impact on viral pathogens., Conclusion: NPIs effectively curb transmission of respiratory infections by most pathogens, resulting in increased average age of MP infections and altered patterns of coinfection post-pandemic., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Chen, Xu, Gu, Peng, Ma, Su, Liu, Ge, Yang and Ning.)
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- 2024
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20. An investigation of γ radiation detection with a CMOS imaging sensor.
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Lin J, Wang F, Wang J, Xu Z, Yang M, Hong B, Yong N, Xia D, Ge D, and Shen S
- Abstract
In this study, a feasibility of γ radiation detection using complementary metal-oxide semiconductor (CMOS) image sensors with a neural network algorithm to extract the γ rays interacted pixels has been investigated. The responses characteristics of the CMOS imaging sensor to γ-ray is studied by placed in a γ fields produced by standard
60 Co or137 Cs isotope sources. The supported preview frame rate of the CMOS image sensor is 25 fps, establishing the functional relationship between the gray level histograms and the dose rate through the neural network, the high energy γ-ray from60 Co and137 Cs source radiation dose rate in µSv/h level can be detected using the CMOS imaging sensor. The results show that the proposed method can effectively identify the number of photon particles which detected by the radiation monitoring system based on CMOS image sensor, and infer that the CMOS imaging sensor with a radiation signal extraction algorithm can be used as a dose warner for radiation protection purpose., (© 2024. The Author(s).)- Published
- 2024
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21. Identification and Characterization of Four Novel Viruses in Balclutha incisa .
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Xiao J, Yang G, Liu R, and Ge D
- Abstract
Balclutha incisa (Cicadellidae: Deltocephalinae), a leafhopper prevalent in tropical and temperate regions, is notably abundant in grasses and rice. The virome of B. incisa was investigated using deep transcriptome sequencing, leading to the first identification of four viruses belonging to the families Aliusviridae , Iflaviridae , and Totiviridae in B. incisa . These viruses have been provisionally named B. incisa ollusvirus 1 (BiOV1), B. incisa ollusvirus 2 (BiOV2), B. incisa iflavirus 1 (BiIV1), and B. incisa totivirus 1 (BiTV1). The complete genome sequences of these viruses were obtained through rapid amplification of cDNA ends (RACE). BiOV1 has a linear genome of 15,125 nucleotides (nt), while BiOV2 possesses a circular genome of 14,853 nt. The BiIV1 genome, excluding the poly(A) tail, is 10,903 nt in length and encodes a single open reading frame (ORF) for a polyprotein consisting of 3194 amino acids (aa). The BiTV1 genome is 4357 nt long and contains two overlapping ORFs, with the viral RNA-dependent RNA polymerase (RdRp) translated via a -1 ribosomal frameshift. Phylogenetic and sequence identity analyses suggest that all these viruses are novel members of their respective families. This study significantly expands our understanding of the virome associated with B. incisa by reporting and characterizing these novel viruses.
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- 2024
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22. Protective and Damaging Mechanisms of Neuromelanin-Like Nanoparticles and Iron in Parkinson's Disease.
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Liu L, Wang T, Zhou H, Zheng J, Liu Q, Wang W, Liu X, Zhang X, Ge D, Shi W, and Sun Y
- Abstract
Parkinson's disease (PD) pathology speculates that neuromelanin (NM) and iron ions play a significant role in physiological and pathological conditions of PD. Because the difficult accessibility of NM has limited targeted research, synthetic melanin-like nanoparticles have been used to instead. In this report, the eumelanin and pheomelanin-like polydopamine (PDA) nanoparticles are prepared that can be used to simulate natural NM with or without chelating iron ion and studied the redox effects in vitro and in vivo on neuronal cells and PD. The synthetic pheomelanin-like PDA nanoparticles have much stronger redox activity than eumelanin-like PDA nanoparticles without or with iron ion. They can protect neurons by scavenging reactive oxygen species (ROS), while cause neuronal cell death and PD due to excessive binding of iron ions. This work provides new evidence for the relationship among two structural components of NM and iron in PD as well as displays the different effects on the roles of eumelanin and pheomelanin in redox activity under physiological or pathological conditions, which provide a new effective choice for cellular and animal models of PD and offer theoretical guidance for targeted treatment and mechanism research on PD., (© 2024 Wiley‐VCH GmbH.)
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- 2024
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23. Puerarin alleviates apoptosis and inflammation in kidney stone cells via the PI3K/AKT pathway: Network pharmacology and experimental verification.
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Xu Y, Liang H, Mao X, Song Z, Shen X, Ge D, Chen Y, Hou B, and Hao Z
- Subjects
- Animals, Humans, Mice, Molecular Docking Simulation, Male, Cell Line, Oxidative Stress drug effects, Calcium Oxalate metabolism, Calcium Oxalate chemistry, Disease Models, Animal, Epithelial Cells drug effects, Epithelial Cells metabolism, Epithelial Cells pathology, Kidney Tubules pathology, Kidney Tubules drug effects, Kidney Tubules metabolism, Isoflavones pharmacology, Isoflavones therapeutic use, Isoflavones chemistry, Apoptosis drug effects, Proto-Oncogene Proteins c-akt metabolism, Phosphatidylinositol 3-Kinases metabolism, Kidney Calculi drug therapy, Kidney Calculi pathology, Kidney Calculi metabolism, Signal Transduction drug effects, Network Pharmacology, Inflammation drug therapy, Inflammation pathology, Inflammation metabolism
- Abstract
Puerarin(PUE), an isoflavonoid extracted from Pueraria root, has anti-apoptotic effects. The objective of this research is to examine the impact of PUE on renal apoptosis and inflammation resulting from renal calculi and to elucidate its mechanism. The approach of network pharmacology and molecular docking was employed to discover potential targets and pathways of PUE. An animal model of calcium oxalate crystal deposition by intraperitoneal injection of glyoxylate and a model of COM-induced human renal tubular epithelial cells (HK2) were used to investigate the pharmacological mechanisms of PUE against apoptosis and inflammation. We used haematoxylin-eosin (H&E) and Periodic Acid-Schiff staining (PAS) to assess the effect of PUE on crystal deposition and damage. The mechanism of PUE was elucidated and validated using Western blotting, histology and immunohistochemical staining. Network pharmacology findings indicated that the PI3K/AKT pathway plays a crucial role in PUE. We experimentally demonstrate that PUE alleviated COM-induced changes in apoptotic proteins, increased inflammatory indicators and changes in oxidative stress-related indicators in HK2 cells by activating the PI3K/AKT pathway, reduced serum creatinine and urea nitrogen levels in mice caused by CaOx, alleviated crystal deposition and damage, and alleviated apoptosis, oxidative stress and inflammation. Puerarin attenuates renal apoptosis and inflammation caused by kidney stones through the PI3K/AKT pathway., (© 2024 The Author(s). Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.)
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- 2024
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24. Preparation of a New Hexafluorobutanol-Farnesol Based Supramolecular Solvent and Its Application in Microextraction of Sudan Dyes From Beverage and Water Samples.
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Li Q, Liu H, Wang Y, Huang X, Huang Y, Weng Z, Ge D, and Wang Y
- Subjects
- Chromatography, High Pressure Liquid, Naphthols analysis, Naphthols chemistry, Liquid Phase Microextraction, Solvents chemistry, Beverages analysis, Coloring Agents analysis, Coloring Agents isolation & purification, Coloring Agents chemistry, Water Pollutants, Chemical analysis, Water Pollutants, Chemical isolation & purification, Azo Compounds analysis
- Abstract
In this work, a new supramolecular solvent (SUPRAS) was prepared for the first time using hexafluorobutanol (HFB) and farnesol (FO). FO acts as an amphiphile and HFB as a coacervation inducer and density regulator. The method of dispersive liquid-liquid microextraction followed by high-performance liquid chromatography, supported by a vortex technique, was established using the prepared SUPRAS for the determination of Sudan dyes in aqueous samples. The extraction parameters, including FO content, HFB content, vortex time, salt addition, and solution pH, were thoroughly investigated and optimized. Under the optimized conditions, the linearity range is 10-750 ng/mL for Sudan I, and 10-1000 ng/mL for Sudan III and Sudan IV, respectively. The limits of detection for Sudan dyes were in the range of 0.8-3.1 ng/mL. The inter- and intra-day relative standard deviations for Sudan dyes were in the range of 1.3%-4.1% and 0.2%-2.6%, respectively. Finally, the proposed method was applied to the determination of Sudan dyes in beverage and river water samples with recoveries ranging from 93.9% to 122.1%. Compared to conventional techniques for the extraction of Sudan dyes in real samples, the proposed method is simpler, faster, and more environmentally friendly., (© 2024 Wiley‐VCH GmbH.)
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- 2024
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25. Gram-negative microflora dysbiosis facilitates tumor progression and immune evasion by activating CCL3/CCL5-CCR1-MAPK-PD-L1 pathway in esophageal squamous cell carcinoma.
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Yang H, Cai J, Huang XL, Zhan C, Lu C, Gu J, Ma T, Zhang H, Cheng T, Xu F, and Ge D
- Abstract
Gram-negative micro-flora dysbiosis occurs in multiple digestive tumors and is found to be the dominant micro-flora in esophageal squamous cell carcinoma (ESCC) micro-environment. The continuous stimulation of G- bacterium metabolites may cause tumorigenesis and reshape the micro-immune environment in ESCC. However, the mechanism of G- bacilli causing immune evasion in ESCC remains underexplored. We identified CC Chemokine receptor 1 (CCR1) as a tumor-indicating gene in ESCC. Interestingly, expression levels of CCR1 and PD-L1 were mutually up regulated after G- bacilli metabolites lipopolysaccharide (LPS) stimulation. Firstly, we found CCR1 high expression level to be associated with poor overall survival in ESCC. Importantly, we found that high level expression of CCR1 up-regulated PD-L1 expression by activating MAPK phosphorylation in ESCC and induced tumor malignant behavior. Finally, we found that T cells exhaustion and cytotoxicity suppression were associated with CCR1 expression in ESCC, which were decreased after CCR1 inhibiting. Our work identifies CCR1 as a potential immune check point regulator of PD-L1 and may cause T cell exhaustion and cytotoxicity suppression in ESCC micro-environment and highlights the potential value of CCR1 as therapeutic target of immunotherapy. Implications: The esophageal microbial environment and its metabolites significantly affect the outcome of immunotherapy for ESCC.
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- 2024
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26. Development of a TLR-Based Model That Can Predict Prognosis, Tumor Microenvironment, and Drug Response for Esophageal Squamous Cell Carcinoma.
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Cheng T, Huang X, Yang H, Gu J, Lu C, Zhan C, Xu F, and Ge D
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- Humans, Prognosis, Female, Gene Expression Regulation, Neoplastic, Male, Biomarkers, Tumor genetics, Fluorouracil pharmacology, Fluorouracil therapeutic use, Antineoplastic Agents therapeutic use, Antineoplastic Agents pharmacology, Middle Aged, Tumor Microenvironment, Esophageal Neoplasms genetics, Esophageal Neoplasms pathology, Esophageal Neoplasms drug therapy, Esophageal Squamous Cell Carcinoma genetics, Esophageal Squamous Cell Carcinoma pathology, Esophageal Squamous Cell Carcinoma drug therapy, Toll-Like Receptors genetics, Toll-Like Receptors metabolism
- Abstract
The toll-like receptor (TLR) family is an important class of proteins involved in the immune response. However, little is known about the association between TLRs and Esophageal squamous cell cancer (ESCC). We explored differentially expressed genes (DEGs) between ESCC and esophagus tissues in TCGA and GTEx database. By taking the intersection with TLR gene set and using univariate Cox analysis and multivariate Cox regression analysis to discriminate the hub genes, we created a TLR-prognostic model. Our model separated patients with ESCC into high- and low-risk score (RS) groups. Prognostic analysis was performed with Kaplan-Meier curves. The two groups were also compared regarding tumor immune microenvironment and drug sensitivity. Six hub genes (including CD36, LGR4, MAP2K3, NINJ1, PIK3R1, and TRAF3) were screened to construct a TLR-prognostic model. High-RS group had a worse survival (p < 0.01), lower immune checkpoint expression (p < 0.05), immune cell abundance (p < 0.05) and decreased sensitivity to Epirubicin (p < 0.001), 5-fluorouracil (p < 0.0001), Sorafenib (p < 0.01) and Oxaliplatin (p < 0.05). We constructed a TLR-based model, which could be used to assess the prognosis of patients with ESCC, provide new insights into drug treatment for ESCC patients and investigate the TME and drug response., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2024
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27. Stiff gel-protected fiber-shaped supercapacitors based on CNFA/silk composite fiber with superhigh interference-resistant ability as self-powered temperature sensor.
- Author
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Chen L, Gong R, Ge D, Yang L, Hu Z, and Yu HY
- Subjects
- Biosensing Techniques methods, Electric Capacitance, Wearable Electronic Devices, Temperature, Silk chemistry
- Abstract
The development of self-powered sensors with interference-resistant detection is a priority area of research for the next generation of wearable electronic devices. Nevertheless, the presence of multiple stimuli in the actual environment will result in crosstalk with the sensor, thereby hindering the ability to obtain an accurate response to a singular stimulus. Here, we present a self-powered sensor composed of silk-based conductive composite fibers (CNFA@ESF), which is capable of energy storage and sensing. The fabricated CNFA@ESF exhibits excellent mechanical performance, as well as flexibility that can withstand various deformations. The CNFA@ESF provides a good areal capacitance (44.44 mF cm
-2 ), high-rate capability, and excellent cycle stability (91 % for 5000 cycles). In addition, CNFA@ESF also shows good sensing performance for multiple signals including strain, temperature, and humidity. It was observed that the assembly of the symmetrical device with a stiff hydrogel surface layer for protection enabled the real-time, interference-free monitoring of temperature signals. Also, the CNFA@ESF can be woven into fabrics and integrated with a solar cell to form a self-powered sensor system, which has been proven to convert and store solar energy to power electronic watches, indicating its huge potential for future wearable electronics., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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28. Proposal for a New Method for Evaluating Polymer-Modified Bitumen Fatigue and Self-Restoration Performances Considering the Whole Damage Characteristic Curve.
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Lv S, Ge D, Cao S, Liu D, Zhang W, Li CH, and Cabrera MB
- Abstract
Fatigue performance and self-repairing activity of asphalt binders are two properties that highly influence the fatigue cracking response of asphalt pavement. There are still numerous gaps in knowledge to fill linked with these two characteristics. For instance, current parameters fail to accommodate these two bitumen phenomena fully. This study aims to propose a new procedure to address this issue utilizing the linear amplitude sweep (LAS) test, LAS with rest period (RP) (LASH) test, and simplified viscoelastic continuum damage (S-VECD) model. This research work used four different types of asphalt binders: neat asphalt (NA), self-healing thermoplastic polyurethane (STPU)-modified bitumen (STPB), self-healing poly (dimethyl siloxane) crosslinked with urea bond (IPA1w)-modified bitumen (IPAB), and styrene-butadiene-styrene (SBS)-modified bitumen (SBSB). Before the testing process, all the materials were subjected to short-term and long-term aging. The new procedure showed a superior capacity to analyze and accommodate all bitumen fatigue performances and self-repairing activities compared to the current method. Another finding proved that asphalt binders with a higher self-restoration behavior failed to show a better fatigue performance. Moreover, the higher fatigue performance increments produced by STPU and IPA1w in NA concerning the control bitumen were 123.7% and 143.7%, respectively. Those values were obtained with 1.0% STPU and 0.5% IPA1w in NA. A breakthrough finding demonstrated that asphalt binder fatigue response is augmented when the RP was applied at a higher damage intensity ( S ) value. STPB and IPAB reached their highest increments of fatigue response, containing 1.0% of STPU and 0.5% of IPA1w, respectively. Those augmentations were 207.54% and 232.64%, respectively.
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- 2024
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29. De novo genome of thick-tailed pygmy jerboa Salpingotus crassicauda, Cardiocraniinae, Dipodidae.
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Cheng J, Zhang Y, Xia L, Yang F, Ge D, Peng X, and Yang Q
- Subjects
- Animals, Rodentia genetics, Rodentia classification, Phylogeny, Molecular Sequence Annotation, RNA, Transfer genetics, Genome, Mitochondrial, Genome
- Abstract
Pygmy jerboas are one of the smallest taxa of rodents. They exhibit distinctly different morphological and biological characteristics from other subfamilies, such as more restricted distribution, species richness, reproductive ability, and population size. Agricultural expansion and the development of new energy projects in recent years lead to sharp decline of their natural populations. Here, we assembled and annotated the first reference genome for the subfamily Cardiocraniinae using Illunima and Nanopore sequencing from the thick-tailed pygmy jerboa, Salpingotus crassicauda. The final genome is 2.44 Gb in size, with a contig N50 length of 13.71 Mb and a BUSCO completeness of 96.35%. A total of 23,344 protein-coding genes were annotated in the final genome. We also determined the mitochondrial genome of this species and annotated 13 protein-coding genes, 22 tRNAs, and 2 rRNA. These genomic assemblies provide resources in studying phylogeny and adaptive evolution of Dipodidae, as well as implementing conservation management of jerboas., (© 2024. The Author(s).)
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- 2024
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30. pscAdapt: pre-trained domain adaptation network based on structural similarity for cell type annotation in single cell RNA-seq data.
- Author
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Zhao Y, Shang J, Qin B, Zhang L, He X, Ge D, Ren Q, and Liu JX
- Abstract
Cell type annotation refers to the process of categorizing and labeling cells to identify their specific cell types, which is crucial for understanding cell functions and biological processes. Although many methods have been developed for automated cell type annotation, they often encounter challenges such as batch effects due to variations in data distribution across platforms and species, thereby compromising their performance. To address batch effects, in this study, a pre-trained domain adaptation model based on structural similarity, named pscAdapt, is proposed for cell type annotation. Specifically, a pre-trained strategy is employed to initialize model parameters to learn the data distribution of source domain. This strategy is also combined with an adversarial learning strategy to train the domain adaptation network for achieving domain level alignment and reducing domain discrepancy. Furthermore, to better distinguish different types of cells, a structural similarity loss is designed, aiming to shorten distances between cells of the same type and increase distances between cells of different types in feature space, thus achieving cell level alignment and enhancing the discriminability of cell types. Comprehensive experiments were conducted on simulated datasets, cross-platforms datasets and cross-species datasets to validate the effectiveness of pscAdapt, results of which demonstrate that pscAdapt outperforms several popular cell type annotation methods. The source code of pscAdapt is available online at https://github.com/CDMBlab/pscAdapt.
- Published
- 2024
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31. Applications of plant-derived extracellular vesicles in medicine.
- Author
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Zhu Y, Zhao J, Ding H, Qiu M, Xue L, Ge D, Wen G, Ren H, Li P, and Wang J
- Abstract
Plant-derived extracellular vesicles (EVs) are promising therapeutic agents owing to their natural abundance, accessibility, and unique biological properties. This review provides a comprehensive exploration of the therapeutic potential of plant-derived EVs and emphasizes their anti-inflammatory, antimicrobial, and tumor-inhibitory effects. Here, we discussed the advancements in isolation and purification techniques, such as ultracentrifugation and size-exclusion chromatography, which are critical for maintaining the functional integrity of these nanovesicles. Next, we investigated the diverse administration routes of EVs and carefully weighed their respective advantages and challenges related to bioavailability and patient compliance. Moreover, we elucidated the multifaceted mechanisms of action of plant-derived EVs, including their roles in anti-inflammation, antioxidation, antitumor activity, and modulation of gut microbiota. We also discussed the impact of EVs on specific diseases such as cancer and inflammatory bowel disease, highlighting the importance of addressing current challenges related to production scalability, regulatory compliance, and immunogenicity. Finally, we proposed future research directions for optimizing EV extraction and developing targeted delivery systems. Through these efforts, we envision the seamless integration of plant-derived EVs into mainstream medicine, offering safe and potent therapeutic alternatives across various medical disciplines., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.)
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- 2024
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32. Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.
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Du P, Zhu K, Wang M, Sun Z, Tan J, Sun B, Sun B, Wang P, He G, Xiong J, Huang Z, Meng H, Sun C, Xie S, Wang B, Ge D, Ma Y, Sheng P, Ren X, Tao Y, Xu Y, Qin X, Allen E, Zhang B, Chang X, Wang K, Bao H, Yu Y, Wang L, Ma X, Du Z, Guo J, Yang X, Wang R, Ma H, Li D, Pan Y, Li B, Zhang Y, Zheng X, Han S, Jin L, Chen G, Li H, Wang CC, and Wen S
- Subjects
- Humans, China, History, Ancient, DNA, Ancient analysis, Human Migration history, Rivers, Genetics, Population, Archaeology, Genetic Variation, Genomics, Genome, Human
- Abstract
The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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33. The Chinese version of the tendency to stigmatize epidemic diseases scale: a translation and validation study.
- Author
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Wang X, Wang Y, Ge Y, Liu Y, Niu R, Guo Z, and Ge D
- Abstract
Objective: To translate the Tendency to Stigmatize Epidemics Diseases Scale (TSEDS) into Chinese and to evaluate its psychometric properties., Methods: Translation and cross-cultural adaptation using the Brislin translation model, and pre-testing to form a Chinese version of TSEDS. A total of 434 adults participated in the study and the TSEDS were measured using the critical ratio method, Pearson correlation analysis, retest reliability, content validity, structural validity, and concurrent validity., Results: The Chinese version of the TSEDS scale contains 27 items in 5 dimensions, including structural stigma, perceived stigma, organizational stigma, internalized stigma, and social stigma. The average content validity index of the scale was 0.975. The goodness of fit index (χ2/df= 1.981, RMSEA = 0.067, CFI= 0.930, IFI = 0.931, TLI = 0.922) indicated a good model fit. The Cronbach's alpha coefficient was 0.962 and the dimensionality ranged from 0.882 to 0.928. The retest reliability was 0.912., Conclusion: The Chinese version of TSEDS has good reliability and validity, which can be used to assess the epidemiological stigma tendency of Chinese adults., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wang, Wang, Ge, Liu, Niu, Guo and Ge.)
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- 2024
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34. The Impact of Driving Pressure-Guided Positive End-Expiratory Pressure Ventilation on Cerebral Blood Flow and Pulmonary Function in Patients Undergoing Laparoscopic Radical Prostatectomy.
- Author
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Ge D, Luo Z, Bu X, Chen B, and Leng X
- Subjects
- Humans, Male, Retrospective Studies, Middle Aged, Aged, Lung blood supply, Respiratory Function Tests, Prostatectomy methods, Positive-Pressure Respiration methods, Laparoscopy, Cerebrovascular Circulation physiology
- Abstract
Purpose: To examine the impact of driving pressure-guided positive end-expiratory pressure ventilation on cerebral blood flow and pulmonary function in patients undergoing laparoscopic radical prostatectomy., Methods: A retrospective analysis was conducted on clinical data from patients who underwent laparoscopic radical prostatectomy at our hospital between June 2022 and June 2023. The patients were divided into two groups, namely the conventional ventilation group and the driving pressure-guided positive end-expiratory pressure ventilation group. Measurements and analyses were performed on cerebral blood flow, neurological status, and pulmonary function parameters., Results: A total of 105 patients were included in this single-centre retrospective study, with 51 patients in the conventional ventilation group and 54 patients in the driving pressure-guided positive end-expiratory pressure ventilation group. The driving pressure-guided positive end-expiratory pressure ventilation group demonstrated significantly higher cerebral blood flow, cerebral autoregulation index, cerebrovascular resistance, and cerebral oxygen saturation compared to the conventional ventilation group ( p < 0.05). Additionally, patients in the driving pressure-guided positive end-expiratory pressure ventilation group exhibited improved neurological outcomes, a higher partial pressure of oxygen/fraction of inspired oxygen ratio, increased lung compliance, decreased peak expiratory flow, elevated respiratory rate, and a lower lung injury score compared to the conventional ventilation group ( p < 0.05)., Conclusions: The findings suggest that driving pressure-guided positive end-expiratory pressure ventilation might positively influence cerebral blood flow and pulmonary function parameters in patients undergoing laparoscopic radical prostatectomy., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s).)
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- 2024
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35. Experimental study of intramodal XPM reduction by intramodal dispersion in weakly coupled FMF.
- Author
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Zuo M, Qiao G, Yang Y, Long C, Ge D, Wang D, Li Y, Chen Z, Zhang D, Li H, and Li J
- Abstract
The understanding of nonlinear propagation effects in low-crosstalk few-mode fiber is crucial for a weakly coupled mode-division multiplexed system. In this Letter, we report the first, to the best of our knowledge, experimental verification of the advantage of intramodal dispersion on mitigating intramodal cross-phase modulation in a weakly coupled few-mode fiber transmission. The experimental system is established over a 70-km multiple-ring-core few-mode fiber accommodating 6 linearly polarized modes, based on which the influences of intramodal cross-phase modulation on transmission performances of each linearly polarized mode are evaluated. Experimental results show that the intramodal cross-phase modulation of degenerate linearly polarized modes with much larger intramodal dispersion values are significantly weaker than those of non-degenerate linearly polarized modes, in which the maximum suppression of intramodal cross-phase modulation noise is up to 9.7 dB. We believe that this work would be beneficial to practical applications of weakly coupled mode-division multiplexing technologies.
- Published
- 2024
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36. Discovery of a first-in-class protein degrader for the c-ros oncogene 1 (ROS1).
- Author
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Yang J, Wu Y, Zhu Q, Qu X, Ou H, Liu H, Wei Y, Ge D, Lu C, Jiang B, and Song X
- Subjects
- Humans, Animals, Molecular Structure, Mice, Structure-Activity Relationship, Apoptosis drug effects, Drug Screening Assays, Antitumor, Dose-Response Relationship, Drug, Proteolysis drug effects, Molecular Docking Simulation, Cell Line, Tumor, Protein Kinase Inhibitors pharmacology, Protein Kinase Inhibitors chemistry, Protein Kinase Inhibitors chemical synthesis, Mice, Nude, Proto-Oncogene Proteins antagonists & inhibitors, Proto-Oncogene Proteins metabolism, Antineoplastic Agents pharmacology, Antineoplastic Agents chemistry, Antineoplastic Agents chemical synthesis, Cell Proliferation drug effects, Protein-Tyrosine Kinases antagonists & inhibitors, Protein-Tyrosine Kinases metabolism, Drug Discovery
- Abstract
The c-ros oncogene 1 (ROS1), an oncogenic driver, is known to induce non-small cell lung cancer (NSCLC) when overactivated, particularly through the formation of fusion proteins. Traditional targeted therapies focus on inhibiting ROS1 activity with ROS 1 inhibitors to manage cancer progression. However, a new strategy involving the design of protein degraders offers a more potent approach by completely degrading ROS1 fusion oncoproteins, thereby effectively blocking their kinase activity and enhancing anti-tumour potential. Utilizing PROteolysis-TArgeting Chimera (PROTAC) technology and informed by molecular docking and rational design, we report the first ROS1-specific PROTAC, SIAIS039. This degrader effectively targets multiple ROS1 fusion oncoproteins (CD74-ROS1, SDC4-ROS1 and SLC34A2-ROS1) in engineered Ba/F3 cells and HCC78 cells, demonstrating anti-tumour effects against ROS1 fusion-driven cancer cells. It suppresses cell proliferation, induces cell cycle arrest, and apoptosis, and inhibits clonogenicity. The anti-tumour efficacy of SIAIS039 surpasses two approved drugs, crizotinib and entrectinib, and matches that of the top inhibitors, including lorlatinib and taletrectinib. Mechanistic studies confirm that the degradation induced by 039 requires the participation of ROS1 ligands and E3 ubiquitin ligases, and involves the proteasome and ubiquitination. In addition, 039 exhibited excellent oral bioavailability in a mouse xenograft model, highlighting its potential for clinical application. In conclusion, our study presents a promising and novel therapeutic strategy for ROS1 fusion-positive NSCLC by targeting ROS1 fusion oncoproteins for degradation, laying the foundation for the development of further PROTAC and offering hope for patients with ROS1 fusion-positive NSCLC., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
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37. Associations between social isolation, perceived ageism and subjective well-being among rural Chinese older adults: A cross-sectional study.
- Author
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Wang X, Wang Y, Zhang F, Ge D, and Guo Z
- Subjects
- Humans, Male, Cross-Sectional Studies, Female, Aged, Surveys and Questionnaires, China, Perception, Aged, 80 and over, East Asian People, Ageism psychology, Rural Population, Social Isolation psychology
- Abstract
Objective: This study aimed to investigate the relationship between social isolation, perceived ageism and subjective well-being among rural Chinese older adults and its mechanisms of action., Methods: A total of 403 rural resident older adults were surveyed from March to April 2024. Data were collected using the General Information Questionnaire, the General Alienation Scale (GAS), the Perceived Ageism Questionnaire (PAQ), and the Memorial University of Newfoundland Scale of Happiness (MUNSH). SPSS 27.0 and PROCESS macro were used to analyze the data., Results: Pearson correlation analysis revealed a significant negative correlation (p<0.01) between subjective well-being and social isolation (r = -0.720) and perceived ageism (r = -0.661) among rural older adults. Perceived ageism partially mediated the effect between social isolation and subjective well-being in rural older adults, and the mediating effect accounted for 29.9 % of the total effect (p<0.001)., Conclusion: Social isolation can reduce the subjective well-being of rural older adults through perceived ageism., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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38. Solvated Electrons Generated on the Surface of Na-SPHI for Boosting Visible Light Photocatalytic Hydrogen Evolution with Ultra-High AQE.
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Li Y, Ge D, Zhang H, Shangguan L, Mou Z, Xia F, Sun J, Liu X, Su Y, and Lei W
- Abstract
Enhancing the utilization of visible-light-active semiconductors with an excellent apparent quantum efficiency (AQE) remains a significant and challenging goal in the realm of photocatalytic water splitting. In this study, a fully condensed sulfur-doped poly(heptazine imide) metalized with Na (Na-SPHI) is synthesized by an ionothermal method by using eutectic NaCl/LiCl mixture as the ionic solvent. Comprehensive characterizations of the obtained Na-SPHI reveal several advantageous features, including heightened light absorption, facilitated exciton dissociation, and expedited charge transfer. More importantly, solvated electron, powerful reducing agents, can be generated on the surface of Na-SPHI upon irradiation with visible light. Benefiting from above advantage, the Na-SPHI exhibits an excellent H
2 evolution rate of 571.8 µmol·h-1 under visible light illumination and a super-high AQE of 61.7% at 420 nm. This research emphasizes the significance of the solvated electron on the surface of photocatalyst in overcoming the challenges associated with visible light-driven photocatalysis, showcasing its potential application in photocatalytic water splitting., (© 2024 Wiley‐VCH GmbH.)- Published
- 2024
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39. Fufang Zhenshu Tiaozhi capsule enhances bone formation and safeguards against glucocorticoid-induced osteoporosis through innovative Mekk2-mediated β-catenin deubiquitination.
- Author
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Hong G, Tang L, Zhou T, Xie Y, Wang J, Ge D, Dong Q, and Sun P
- Subjects
- Animals, Mice, Ubiquitination drug effects, Capsules, Dexamethasone pharmacology, Cell Differentiation drug effects, Osteoporosis metabolism, Osteoporosis chemically induced, Osteoporosis pathology, Osteogenesis drug effects, beta Catenin metabolism, Glucocorticoids pharmacology, Osteoblasts metabolism, Osteoblasts drug effects, MAP Kinase Kinase Kinase 2 metabolism, Mice, Knockout, Drugs, Chinese Herbal pharmacology
- Abstract
Introduction: Bone homeostasis depends on the regulation of β-catenin in osteoblasts. Glucocorticoids (GCs) are known to diminish β-catenin activity via Wnt pathway signaling, leading to osteoporosis. Conversely, activating β-catenin in osteoblasts through mitogen-activated protein kinase kinase kinase 2 (Mekk2) offers an innovative approach to combat GC-induced osteoporosis (GIOP). Fufang Zhenshu Tiaozhi (FTZ) capsules have shown effectiveness in treating GIOP, but the mechanisms behind this are still unclear., Materials and Methods: In this study, Mekk2 knockout mice (Mekk2
-/- ) was generated by CRISPR/Cas9. These mice were then subjected to Alcian Blue-Alizarin Red staining and immunofluorescence to assess their bone and cartilage development. To establish models of GIOP, both Mekk2-/- and wild-type (WT) mice were treated with dexamethasone (DXMS) and subsequently given FTZ capsules. We analyzed the resulting phenotypic changes in these mice using Micro-CT scans and histomorphological studies. Primary osteoblasts, isolated from both Mekk2-/- and WT mice, underwent qRT-PCR to measure key osteogenesis markers, including Runx2, Sp7, Bgalp, Col1a1 and Alp. Cells were then exposed to treatments with either FTZ or Wnt3a and the phosphorylation levels of β-catenin and Mekk2, along with the protein expression of Runx2, were evaluated using Western blotting and immunoprecipitation. Additionally, C3H10T1/2 cells transfected with TOPflash-luciferase and Renilla luciferase reporters were treated with FTZ and Wnt3a to measure β-catenin activity., Results: In our study, administering FTZ in vivo effectively prevented bone loss typically induced by GCs. However, it's important to note that this protective effect was substantially reduced in mice lacking Mekk2. Additionally, FTZ showed a significant ability to enhance osteogenic differentiation in primary osteoblasts, doing so by altering the expression of Mekk2. Intriguingly, the impact of FTZ on Mekk2 appears to function through a pathway separate from the traditional Wnt signaling route. Furthermore, our findings indicate that FTZ also promotes the deubiquitination of β-catenin, contributing further to its positive effects on bone health., Conclusions: This study suggests that FTZ plays a significant role in protecting bone mass in cases of GIOP. The mechanism through which FTZ confers this benefit involves the activation of Mekk2/β-catenin signaling pathways, which represents a promising alternative strategy to counteract the deleterious effects of GIOP by augmenting osteoblastogenesis., (© 2024. The Japanese Society Bone and Mineral Research.)- Published
- 2024
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40. Mendelian randomization study of urolithiasis: exploration of risk factors using human blood metabolites.
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Hu D, Pan J, Deng A, Ge D, Yao R, Hou B, and Hao Z
- Subjects
- Humans, Molecular Epidemiology, Dehydroepiandrosterone Sulfate blood, Glycerol blood, Mendelian Randomization Analysis, Urolithiasis blood
- Abstract
Background: Urolithiasis is a highly prevalent global disease closely associated with metabolic factors; however, the causal relationship between blood metabolites and urolithiasis remains poorly understood., Method: In our study, we employed a bi-directional two-sample Mendelian randomization (MR) analysis to investigate the causal associations between urolithiasis and metabolites. The random-effects inverse-variance weighted (IVW) estimation method was utilized as the primary approach, complemented by several other estimators including MR-Egger, weighted median, colocalization and MR-PRESSO. Furthermore, the study included replication and meta-analysis. Finally, we conducted metabolic pathway analysis to elucidate potential metabolic pathways., Results: After conducting multiple tests for correction, glycerol might contribute to the urolithiasis and dehydroisoandrosterone sulfate (DHEA-S) might inhibit this process. Furthermore, several blood metabolites had shown potential associations with a causal relationship. Among the protective metabolites were lipids (dehydroisoandrosterone sulfate and 1-stearoylglycerol (1-monostearin)), amino acids (isobutyrylcarnitine and 2-aminobutyrate), a keto acid (acetoacetate) and a carbohydrate (mannose). The risk metabolites included lipids (1-palmitoylglycerophosphoethanolamine, glycerol and cortisone), a carbohydrate (erythronate), a peptide (pro-hydroxy-pro) and a fatty acid (eicosenoate). In reverse MR analysis, urolithiasis demonstrated a statistically significant causal relationship with butyrylcarnitine, 3-methyl-2-oxobutyrate, scyllo-inositol, leucylleucine and leucylalanine. However, it was worth noting that none of the blood metabolites exhibited statistical significance after multiple corrections. Additionally, we identified one metabolic pathway associated with urolithiasis., Conclusion: The results we obtained demonstrate the causal relevance between two metabolites and urolithiasis, as well as identify one metabolic pathway potentially associated with its development. Given the high prevalence of urolithiasis, further investigations are encouraged to elucidate the mechanisms of these metabolites and explore novel therapeutic strategies., (© 2024. The Author(s).)
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- 2024
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41. Combining (CH 2 O) n and (NH 4 ) 2 CO 3 as a Formamidine Equivalent for "Four-in-One" Synthesis of Fluoroalkylated 2- H -Pyrimidines.
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Han W, Ren YY, Tang MY, Ji YF, Ge D, Ma M, Shen ZL, and Chu XQ
- Abstract
Multicomponent reactions hold the potential to maximize the synthetic efficiency in the preparation of diverse and complex molecular scaffolds. An unprecedented formal [3+1+1+1] annulation approach for the one-step synthesis of fluoroalkylated 2- H -pyrimidines commencing from perfluoroalkyl alkenes, paraformaldehyde, and ammonium carbonate is described. By harnessing readily accessible (CH
2 O)n and cheap (NH4 )2 CO3 as a formamidine surrogate, this method effectively replaces traditionally preformed amidines with a pyrimidine assembly. The multicomponent reaction proceeds in a step-economical, operationally simple, metal-free, and additive-free manner, featuring a broad substrate scope, excellent functional group compatibility, and scalability. The potential for the synthetic elaboration of the obtained 2- H -pyrimidine is further demonstrated in the alkylation and vinylation of its C2 position.- Published
- 2024
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42. Approaches for Positioning the Active Medium in Hybrid Nanoplasmonics. Focus on Plasmon-Assisted Photopolymerization.
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Chen M, Marguet S, Issa A, Jradi S, Couteau C, Fiorini-Debuisschert C, Douillard L, Soppera O, Ge D, Plain J, Zhou X, Dang C, Béal J, Kostcheev S, Déturche R, Xu T, Wei B, and Bachelot R
- Abstract
Over the past 20 years, hybrid plasmonics for nanoemitters of light or for nanoabsorbers, based on weak or strong coupling between metallic nanocavities and active media (emissive or absorbing entities), have given rise to important research efforts. One of the main current challenges is the control of the nanoscale spatial distribution and associated symmetry of the active medium in the vicinity of the metallic nanoparticles. In this review, we first recall the main principles of weak and strong coupling by stressing the importance of controlling the spatial distribution of the active medium and present the main approaches developed for achieving this control. Nine different approaches are identified. We then focus our attention on one of them based on plasmonic photopolymerization and discuss the flexibility of this approach in terms of control of the spatial symmetry of the hybrid nanosystem metal-polymer nanoemitters and the resulting polarization dependence of the light emission. The different approaches are analyzed and compared with each other, and some future perspectives and challenges are finally discussed., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)
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- 2024
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43. Discovery and Genomic Analysis of Three Novel Viruses in the Order Mononegavirales in Leafhoppers.
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Xiao J, Nie B, Chen ME, Ge D, and Liu R
- Subjects
- Animals, RNA, Viral genetics, High-Throughput Nucleotide Sequencing, Transcriptome, Genome, Viral, Phylogeny, Mononegavirales genetics, Mononegavirales classification, Rhabdoviridae genetics, Rhabdoviridae classification, Hemiptera virology, Genomics methods
- Abstract
Leafhoppers are economically important pests and may serve as vectors for pathogenic viruses that cause substantial crop damage. In this study, using deep transcriptome sequencing, we identified three novel viruses within the order Mononegavirales , including two viruses belonging to the family Rhabdoviridae and one to the family Lispiviridae . The complete genome sequences were obtained via the rapid amplification of cDNA ends and tentatively named Recilia dorsalis rhabdovirus 1 (RdRV1, 14,251 nucleotides, nt), Nephotettix virescens rhabdovirus 1 (NvRV1, 13,726 nt), and Nephotettix virescens lispivirus 1 (NvLV1, 14,055 nt). The results of a phylogenetic analysis and sequence identity comparison suggest that RdRV1 and NvRV1 represent novel species within the family Rhabdoviridae , while NvLV1 is a new virus belonging to the family Lispiviridae . As negative-sense single-strand RNA viruses, RdRV1 and NvRV1 contain the conserved transcription termination signal and intergenic trinucleotides in the non-transcribed region. Intergenomic sequence and transcriptome profile analyses suggested that all these genes were co-transcriptionally expressed in these viral genomes, facilitated by specific intergenic trinucleotides and putative transcription initiation sequences.
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- 2024
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44. An improved subtraction model applied in supercritical fluid chromatography to characterise polar stationary phases.
- Author
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Ge D, Lu J, Yu Z, Jin Y, Ke Y, Fu Q, and Liang X
- Subjects
- Models, Chemical, Benzene Derivatives chemistry, Silicon Dioxide chemistry, Chromatography, Supercritical Fluid methods, Hydrophobic and Hydrophilic Interactions
- Abstract
Herein, an improved subtraction model was proposed to characterise the polar stationary phases in supercritical fluid chromatography (SFC). Fifteen stationary phases were selected, including two types of aromatic columns, Waters Torus and Viridis series columns, as well as silica and amino columns. Ethylbenzene and Torus 1-AA were defined as the reference solute and column, respectively. Identifying the interaction with the maximum contribution to retention in SFC separation and using it as the initial term is a key step in modelling. The dipole, or induced dipole interaction (θ
' P), replaced the hydrophobic interaction (η' H) as the starting term. The improved model was expressed as logα=η' H+β' A+α' B+κ' C+θ' P+ε' E+σ' S, where the term ε' E indicated that anion exchange interaction was intentionally supplemented. A 7-step modelling process, including bidirectional fitting and residual analysis, was proposed. The obtained column parameters had reasonable physical significance, with the adjusted determination coefficient (R2 adj ) greater than 0.999 and the standard error (SE) less than 0.029. Methodological validation was further performed using the other four columns and 12 solutes that were not involved in the modelling. The result revealed good predictions of solutes' retention, as demonstrated by R2 adj from 0.9923 to 0.9979 and SE from 0.0636 to 0.1088. This study indicated the feasibility of using the improved subtraction model to characterise polar stationary phases in SFC, with the most crucial being the determination of an initial term, followed by the addition of a new descriptor and the selection of an appropriate reference column. The study expanded the application scope of the subtraction model in SFC, which will help gain an in-depth understanding of the SFC separation mechanism., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper, (Copyright © 2024. Published by Elsevier B.V.)- Published
- 2024
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45. Altered functional connectivity of primary olfactory cortex-hippocampus-frontal cortex in subjective cognitive decline during odor stimulation.
- Author
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Zhang X, Zhu Y, Lu J, Chen Q, Chen F, Long C, Xu X, Ge D, Bai Y, Liu D, Du S, Zhu Z, Mai X, Yang QX, and Zhang B
- Subjects
- Humans, Male, Female, Aged, Middle Aged, Olfactory Perception physiology, Nerve Net diagnostic imaging, Nerve Net physiopathology, Nerve Net physiology, Connectome, Odorants, Magnetic Resonance Imaging, Cognitive Dysfunction diagnostic imaging, Cognitive Dysfunction physiopathology, Cognitive Dysfunction etiology, Olfactory Cortex diagnostic imaging, Olfactory Cortex physiology, Olfactory Cortex physiopathology, Hippocampus diagnostic imaging, Hippocampus physiopathology, Frontal Lobe diagnostic imaging, Frontal Lobe physiopathology
- Abstract
Subjective cognitive decline (SCD) is a high-risk population in the preclinical stage of Alzheimer's disease (AD), and olfactory dysfunction is a risk factor for dementia progression. The present study aimed to explore the patterns of functional connectivity (FC) changes in the olfactory neural circuits during olfactory stimulation in SCD subjects. A total of 56 SCD subjects and 56 normal controls (NCs) were included. All subjects were assessed with a cognitive scale, an olfactory behavior test, and olfactory task-based functional magnetic resonance imaging scanning. The FC differences in olfactory neural circuits between the two groups were analyzed by the generalized psychophysiological interaction. Additionally, we calculated and compared the activation of brain regions within the olfactory neural circuits during odor stimulation, the volumetric differences in brain regions showing FC differences between groups, and the correlations between neuroimaging indicators and olfactory behavioral and cognitive scale scores. During odor stimulation, the FC between the bilateral primary olfactory cortex (bPOC) and the right hippocampus in the SCD group was significantly reduced; while the FC between the right hippocampus and the right frontal cortex was significantly increased in the SCD group. The bPOC of all subjects showed significant activation, but no significant difference in activation between groups was found. No significant differences were observed in the volume of the brain regions within the olfactory neural circuits or in olfactory behavior between groups. The volume of the bPOC and right frontal cortex was significantly positively correlated with olfactory identification, and the volume of the right frontal cortex and right hippocampus was significantly correlated with cognitive functions. Furthermore, a significant correlation between the activation of bPOC and the olfactory threshold was found in the whole cohort. These results suggested that while the structure of the olfactory neural circuits and olfactory behavior in SCD subjects remained stable, there were significant changes observed in the FC of the olfactory neural circuits (specifically, the POC-hippocampus-frontal cortex neural circuits) during odor stimulation. These findings highlight the potential of FC alterations as sensitive imaging markers for identifying high-risk individuals in the early stage of AD., (© 2024 The Author(s). Human Brain Mapping published by Wiley Periodicals LLC.)
- Published
- 2024
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46. Mitochondrial dysfunction in kidney stones and relief of kidney stones after reducing mtROS.
- Author
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Xu Y, Li G, Ge D, Chen Y, Hou B, and Hao Z
- Subjects
- Humans, Animals, Mice, Male, Female, Mice, Inbred C57BL, Middle Aged, Disease Models, Animal, Kidney pathology, Kidney metabolism, Adult, Organophosphorus Compounds, Piperidines, Kidney Calculi blood, Kidney Calculi etiology, DNA, Mitochondrial genetics, Mitochondria metabolism, Calcium Oxalate metabolism, Reactive Oxygen Species metabolism
- Abstract
Mitochondria are essential organelles because they generate the energy required for cellular functions. Kidney stones, as one of the most common urological diseases, have garnered significant attention. In this study, we first collected peripheral venous blood from patients with kidney stones and used qRT-PCR to detect mitochondrial DNA (mtDNA) copy number as a means of assessing mitochondrial function in these patients. Subsequently, through Western blotting, qPCR, immunofluorescence, immunohistochemistry, and transmission electron microscopy, we examined whether calcium oxalate crystals could cause mitochondrial dysfunction in the kidney in both in vitro and in vivo. We then examined the intersection of the DEGs obtained by transcriptome sequencing of the mouse kidney stone model with mitochondria-related genes, and performed KEGG and GO analyses on the intersecting genes. Finally, we administered the mitochondrial ROS scavenger Mito-Tempo in vivo and observed its effects. Our findings revealed that patients with kidney stones had a reduced mtDNA copy number in their peripheral venous blood compared to the control group, suggesting mitochondrial dysfunction in this population. This conclusion was further validated through in vitro and in vivo experiments. Enrichment analyses revealed that the intersecting genes were closely related to metabolism. We observed that after mitochondrial function was preserved, the deposition of calcium oxalate crystals decreased, and the kidney damage and inflammation caused by them were also alleviated. Our research indicates that kidney stones can cause mitochondrial dysfunction. After clearing mtROS, the damage and inflammation caused by kidney stones are reversed, providing new insights into the prevention and treatment of kidney stones., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
- Published
- 2024
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47. HTB50-2 Inhibits Growth and Migration of Triple-negative Breast Cancer via FOSL2/FOXC1 Signaling Axis and Subsequent Ferroptosis.
- Author
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Liu N, Yin WY, Duan WQ, Lyu YZ, Xie S, Fang L, Ji Y, Yang FY, and Ge D
- Abstract
Background: The manipulation of ferroptosis in cancer cells is a possible therapeutic technique that has been investigated for use in the treatment of cancer. Consequently, ferroptosis-inducing medications have recently received increased interest in cancer therapy. In this research, we assessed the anticancer efficacy of 14β-hydroxy- 3β-(β-D-Glucopyranosyloxy)-5α-bufa-20,22-dienolide (HTB50-2), a natural product derived from the plant Helleborus thibetanus Franch, in Triple-Negative Breast Cancer (TNBC). Moreover, we also studied its potential mechanisms., Methods: The biological effects of HTB50-2 in a series of breast cancer cell lines were analyzed using sulforhodamine B (SRB) and other methods. The migration ability was analyzed using three methods: wound healing assay, transwell assay, and Western blot. Meanwhile, the potential therapeutic value of HTB50-2 was evaluated in BALB/c mice by orthotopic transplantation. Transcriptome sequencing was conducted to explore the FOS-like antigen 2 (FOSL2) gene, and its role in ferroptosis was verified by Western blot and immunohistochemistry. The association of FOSL2 and ferroptosis-related genes was analyzed using NetworkAnalyst databases, and a TF-Gene interaction network was constructed., Results: Ferroptosis was found to be induced in TNBC cells by HTB50-2. Furthermore, HTB50-2 inhibited tumor development by inducing ferroptosis in TNBC in vivo. Mechanistically, we demonstrated that a transcription factor FOSL2 mediated ferroptosis by HTB50-2. Additionally, it was found that Forkhead box C1 (FOXC1) was regulated by FOSL2 and correlated with ferroptosis., Conclusion: Our data suggest that HTB50-2 exerts its anti-cancer properties by ferroptosis via FOSL2/FOXC1 signaling pathway. Hence, HTB50-2 has an important application potential in the treatment of TNBC., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
- Published
- 2024
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48. The role of lncRNAs related ceRNA regulatory network in multiple hippocampal pathological processes during the development of perioperative neurocognitive disorders.
- Author
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Zhou B, Zheng Y, Suo Z, Zhang M, Xu W, Wang L, Ge D, Qu Y, Wang Q, Zheng H, and Ni C
- Subjects
- Animals, Mice, Neurocognitive Disorders genetics, Neurocognitive Disorders metabolism, Neurocognitive Disorders pathology, Male, Perioperative Period, Sevoflurane, Mice, Inbred C57BL, RNA, Competitive Endogenous, RNA, Long Noncoding genetics, RNA, Long Noncoding metabolism, Hippocampus metabolism, Hippocampus pathology, MicroRNAs genetics, MicroRNAs metabolism, Gene Regulatory Networks, RNA, Messenger genetics, RNA, Messenger metabolism
- Abstract
Background: Perioperative neurocognitive disorders (PND) refer to neurocognitive abnormalities during perioperative period, which are a great challenge for elderly patients and associated with increased morbidity and mortality. Our studies showed that long non-coding RNAs (lncRNAs) regulate mitochondrial function and aging-related pathologies in the aged hippocampus after anesthesia, and lncRNAs are associated with multiple neurodegenerations. However, the regulatory role of lncRNAs in PND-related pathological processes remains unclear., Methods: A total of 18-month mice were assigned to control and surgery (PND) groups, mice in PND group received sevoflurane anesthesia and laparotomy. Cognitive function was assessed with fear conditioning test. Hippocampal RNAs were isolated for sequencing, lncRNA and microRNA libraries were constructed, mRNAs were identified, Gene Ontology (GO) analysis were performed, and lncRNA-microRNA-mRNA networks were established. qPCR was performed for gene expression verification., Results: A total of 312 differentially expressed (DE) lncRNAs, 340 DE-Transcripts of Uncertain Coding Potential (TUCPs), and 2,003 DEmRNAs were identified in the hippocampus between groups. The lncRNA-microRNA-mRNA competing endogenous RNA (ceRNA) network was constructed with 29 DElncRNAs, 90 microRNAs, 493 DEmRNAs, 148 lncRNA-microRNA interaction pairs, 794 microRNA-mRNA interaction pairs, and 110 lncRNA-mRNA co-expression pairs. 795 GO terms were obtained. Based on the frequencies of involved pathological processes, BP terms were divided into eight categories: neurological system alternation, neuronal development, metabolism alternation, immunity and neuroinflammation, apoptosis and autophagy, cellular communication, molecular modification, and behavior changes. LncRNA-microRNA-mRNA ceRNA networks in these pathological categories were constructed, and involved pathways and targeted genes were revealed. The top relevant lncRNAs in these ceRNA networks included RP23-65G6.4, RP24-396L14.1, RP23-251I16.2, XLOC_113622, RP24-496E14.1, etc ., and the top relevant mRNAs in these ceRNA networks included Dlg4 (synaptic function), Avp (lipophagy), Islr2 (synaptic function), Hcrt (regulation of awake behavior), Tnc (neurotransmitter uptake)., Conclusion: In summary, we have constructed the lncRNA-associated ceRNA network during PND development in mice, explored the role of lncRNAs in multiple pathological processes in the mouse hippocampus, and provided insights into the potential mechanisms and therapeutic gene targets for PND., Competing Interests: The authors declare that they have no competing interests., (© 2024 Zhou et al.)
- Published
- 2024
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49. Ultrasound-guided superior laryngeal nerve block: a randomized comparison between parasagittal and transverse approach.
- Author
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Shan T, Tan Q, Wu D, Bao H, Ge D, Han L, Su C, and Ju Y
- Subjects
- Humans, Female, Male, Middle Aged, Adult, Prospective Studies, Hoarseness prevention & control, Hoarseness etiology, Aged, Laryngeal Nerves, Ultrasonography, Interventional methods, Intubation, Intratracheal methods, Nerve Block methods
- Abstract
Background: Different approach ultrasound-guided superior laryngeal nerve block was used to aid awake intubation, but little is known which approach was superior. We aimed to compare the parasagittal and transverse approaches for ultrasound-guided superior laryngeal nerve block in adult patients undergoing awake intubation., Methods: Fifty patients with awake orotracheal intubation were randomized to receive either a parasagittal or transverse ultrasound-guided superior laryngeal nerve block. The primary outcome was patient's quality of airway anesthesia grade during insertion of the tube into the trachea. The patients' tube tolerance score after intubation, total procedure time, mean arterial pressure, heart rate, Ramsay sedation score at each time point, incidence of sore throat both 1 h and 24 h after extubation, and hoarseness before intubation, 1 h and 24 h after extubation were documented., Results: Patients' quality of airway anesthesia was significantly better in the parasagittal group than in the transverse group (median grade[IQR], 0 [0-1] vs. 1 [0-1], P = 0.036). Patients in the parasagittal approach group had better tube tolerance scores (median score [IQR],1[1-1] vs. 1 [1-1.5], P = 0.042) and shorter total procedure time (median time [IQR], 113 s [98.5-125.5] vs. 188 s [149.5-260], P < 0.001) than those in the transverse approach group. The incidence of sore throat 24 h after extubation was lower in the parasagittal group (8% vs. 36%, P = 0.041). Hoarseness occurred in more than half of the patients in parasagittal group before intubation (72% vs. 40%, P = 0.023)., Conclusions: Compared to the transverse approach, the ultrasound-guided parasagittal approach showed improved efficacy in terms of the quality of airway topical anesthesia and shorter total procedure time for superior laryngeal nerve block., Trial Registration: This prospective, randomized controlled trial was approved by the Ethics Committee of Nanjing First Hospital (KY20220425-014) and registered in the Chinese Clinical Trial Registry (19/6/2022, ChiCTR2200061287) prior to patient enrollment. Written informed consent was obtained from all participants in this trial., (© 2024. The Author(s).)
- Published
- 2024
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50. Injectable Self-Oxygenating Cardio-Protective and Tissue Adhesive Silk-Based Hydrogel for Alleviating Ischemia After Mi Injury.
- Author
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Hassan S, Rezaei Z, Luna E, Yilmaz-Aykut D, Lee MC, Perea AM, Jamaiyar A, Bassous N, Hirano M, Tourk FM, Choi C, Becker M, Yazdi I, Fan K, Avila-Ramirez AE, Ge D, Abdi R, Fisch S, Leijten J, Feinberg MW, Mandal BB, Liao R, and Shin SR
- Subjects
- Animals, Tissue Adhesives chemistry, Tissue Adhesives pharmacology, Injections, Cardiotonic Agents pharmacology, Cardiotonic Agents administration & dosage, Cardiotonic Agents chemistry, Chemokine CXCL12 administration & dosage, Chemokine CXCL12 pharmacology, Chemokine CXCL12 metabolism, Myocytes, Cardiac drug effects, Rats, Myocardial Infarction pathology, Myocardial Infarction drug therapy, Silk chemistry, Hydrogels chemistry, Oxygen chemistry
- Abstract
Myocardial infarction (MI) is a significant cardiovascular disease that restricts blood flow, resulting in massive cell death and leading to stiff and noncontractile fibrotic scar tissue formation. Recently, sustained oxygen release in the MI area has shown regeneration ability; however, improving its therapeutic efficiency for regenerative medicine remains challenging. Here, a combinatorial strategy for cardiac repair by developing cardioprotective and oxygenating hybrid hydrogels that locally sustain the release of stromal cell-derived factor-1 alpha (SDF) and oxygen for simultaneous activation of neovascularization at the infarct area is presented. A sustained release of oxygen and SDF from injectable, mechanically robust, and tissue-adhesive silk-based hybrid hydrogels is achieved. Enhanced endothelialization under normoxia and anoxia is observed. Furthermore, there is a marked improvement in vascularization that leads to an increment in cardiomyocyte survival by ≈30% and a reduction of the fibrotic scar formation in an MI animal rodent model. Improved left ventricular systolic and diastolic functions by ≈10% and 20%, respectively, with a ≈25% higher ejection fraction on day 7 are also observed. Therefore, local delivery of therapeutic oxygenating and cardioprotective hydrogels demonstrates beneficial effects on cardiac functional recovery for reparative therapy., (© 2024 Wiley‐VCH GmbH.)
- Published
- 2024
- Full Text
- View/download PDF
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