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Biological origin and depositional environment of crude oils in the Qiongdongnan Basin: Insights from molecular biomarkers and whole oil carbon isotope

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Petroleum Science 2024年第5期21卷 3029-3046页

作者： Zi-Ming Zhang Du-Jie Hou Xiong cheng da-ye chen Gang Liang Xia-Ze Yan Wei-He chen School of Energy Resources China University of Geosciences Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism Ministry of Education Beijing Key Laboratory of Unconventional Natural Gas Geological Evaluation and Development Engineering China Coal Research Institute Exploration and Development Resource Institute Hainan Branch of China National Offshore Oil Corporation

Molecular biomarker and whole oil carbon isotope(δ13Coil) analyses were conducted on eleven typical crude oils from the Qiongdongnan Basin to investigate their biological sources and depositional environments. Saturated hydrocarbon biomarkers in most samples are characterized by angiosperm-derived compounds, with aromatic compounds dominated by the naphthalene, phenanthrene, biphenyl, and fluorene series. The related source rocks of these oils were mainly deposited under oxic condition, but a subanoxic-suboxic and enclosed water column condition in the Central Depression during *** identification of simonellite and related compounds in the aromatic fractions provides reliable evidence for the input of coniferous gymnosperms. Cadalene may also have a potential association with gymnosperms since it shows a strong positive correlation with simonellite. Evidence from density, nalkanes, short-chain alkylbenzenes and secondary brine inclusions indicates that the unique crude oil B13-1 may have suffered from thermal alteration. These crude oils（excluding B13-1） can be classified into four types based on the δ13Coilvalues and molecular biomarkers. Type A oil（solely S34-3） is characterized by non-angiosperm plants, with minor dinoflagellates and increasing contribution from conifer gymnosperms than others. Type B oils（L17-2, L18-1, L25-1, and L25-1W） show heavy δ13Coil（-24 ‰to-25 ‰） and mixed contributions from both angiosperms and marine algae, with the marine algae contribution increasing. Type C oils（L13-2 and B21-1） share similar biological sources with Type B, but the moderately δ13Coil（-25‰ to-26‰） and high level of terrestrial biomarkers suggesting a predominant contribution of angiosperms. Type D oils（Y13-1a, Y13-1b, and Y13-4） possess the lightestδ13Coil（mainly below-26‰） and are primarily derived from angiosperms, with mangrove vegetation playing an important role. Spearman correlation analysis among 14 source biomarker parameters withδ13Coiland geologica

关键词： Gas chromatography-mass spectrometry Molecular biomarker Simonellite Biological source Depositional environment

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Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP data

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Genomics, Proteomics & Bioinformatics 2016年第6期14卷 349-356页

作者： Xiang Zhao Yi-Zhao Luan Xiaoyu Zuo ye-da chen Jiheng Qin Lv Jin Yiqing Tan Meihua Lin Naizun Zhang Yan Liang Shao-Qi Rao Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology School of Public HealthGuangdong Medical CollegeDongguan 523808China School of Life Sciences Sun Yat-sen UniversityGuangzhou 510080China Department of Medical Statistics and Epidemiology School of Public HealthSun Yat-sen UniversityGuangzhou 510080China Maoming People's Hospital Maoming 525000China

Coronary artery disease （CAD） is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism （SNP） profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium （WTCCC） SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene-gene interactions involved in these susceptible pathways with their protein protein interaction （PPI） knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer＇s disease, non-alcoholic fatty liver disease, and Huntington＇s disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer＇s disease. These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer＇s disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.

关键词： Coronary artery disease Genome-wide SNP profiling Risk pathway Functional module Genetic network

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Pathway-based Analysis Tools for Complex Diseases: A Review

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Genomics, Proteomics & Bioinformatics 2014年第5期12卷 210-220页

作者： Lv Jin Xiao-Yu Zuo Wei-Yang Su Xiao-Lei Zhao Man-Qiong Yuan Li-Zhen Han Xiang Zhao ye-da chen Shao-Qi Rao Institute for Medical Systems Biology and Department of Medical Statistics and Epidemiology School of Public HealthGuangdong Medical College Department of Medical Statistics and Epidemiology School of Public Health Sun Yat-Sen University Community Health Service Management Center of Panyu District Department of Statistical Sciences School of Mathematics and Computational Science Sun Yat-Sen University

Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehen- sive understanding of the molecular mechanisms underlying complex diseases. Extensive studies uti- lizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available path- way-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are dis- cussed. This review will provide a useful guide to dissect complex diseases.

关键词： Complex disease Pathway-based analysisAlgorithms Software and databases

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Netrin-1 signaling pathway mechanisms in neurodegenerative diseases

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Neural Regeneration Research 2025年第4期20卷 960-972页

作者： Kedong Zhu Hualong Wang Keqiang ye Guiqin chen Zhaohui Zhang Department of Neurology Renmin Hospital of Wuhan UniversityWuhanHubei ProvinceChina Department of Neurology The First Hospital of Hebei Medical UniversityBrain Aging and Cognitive Neuroscience Laboratory of Heibei ProvinceShijiazhuangHebei ProvinceChina Faculty of Life and Health Sciences Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong ProvinceChina

Netrin-1 and its receptors play crucial roles in inducing axonal growth and neuronal migration during neuronal *** profound impacts then extend into adulthood to encompass the maintenance of neuronal survival and synaptic *** amounts of evidence highlight several key points:(1)Diminished Netrin-1 levels exacerbate pathological progression in animal models of Alzheimer’s disease and Parkinson’s disease,and potentially,similar alterations occur in humans.(2)Genetic mutations of Netrin-1 receptors increase an individuals’susceptibility to neurodegenerative disorders.(3)Therapeutic approaches targeting Netrin-1 and its receptors offer the benefits of enhancing memory and motor function.(4)Netrin-1 and its receptors show genetic and epigenetic alterations in a variety of *** findings provide compelling evidence that Netrin-1 and its receptors are crucial targets in neurodegenerative *** a comprehensive review of Netrin-1 signaling pathways,our objective is to uncover potential therapeutic avenues for neurodegenerative disorders.

关键词： Alzheimer’s disease axon guidance colorectal cancer Netrin-1 receptors Netrin-1 signaling pathways Netrin-1 neurodegenerative diseases neuron survival Parkinson’s disease UNC5C

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Targeted gene sequencing and bioinformatics analysis of patients with gallbladder neuroendocrine carcinoma:A case report

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World Journal of Gastrointestinal Oncology 2025年第1期17卷 239-251页

作者： Yun-Chuan Yang Zhi-Tao chen da-Long Wan Hui Tang Mu-Lin Liu Department of Medical College Jinan UniversityGuangzhou 510000Guangdong ProvinceChina Department of General Surgery The First Affiliated Hospital of Bengbu Medical UniversityBengbu 233000Anhui ProvinceChina Department of Hepatobiliary Surgery Shulan(Hangzhou)Hospital Affiliated to Zhejiang Shuren University Shulan International Medical CollegeHangzhou 310022Zhejiang ProvinceChina Department of Hepatobiliary and Pancreatic Surgery The First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou 310003Zhejiang ProvinceChina Department of Pathology The First Affiliated Hospital of Medical School of Zhejiang UniversityHangzhou 310000Zhejiang ProvinceChina

BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor *** its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain *** SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and *** gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder *** mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated *** Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and *** results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder *** Gallbladder NEC requires standardized *** with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.

关键词： Gallbladder neuroendocrine carcinoma Targeted-gene sequencing Bioinformatics analysis case report Immunocytochemistry Case report

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Insight Into the Separation-of-Variable Methods for the Closed-Form Solutions of Free Vibration of Rectangular Thin Plates

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 329-355页

作者： Yufeng Xing ye Yuan Gen Li Institute of Solid Mechanics Beihang University(BUAA)Beijing100191China

The separation-of-variable(SOV)methods,such as the improved SOV method,the variational SOV method,and the extended SOV method,have been proposed by the present authors and coworkers to obtain the closed-form analytical solutions for free vibration and eigenbuckling of rectangular plates and circular cylindrical *** taking the free vibration of rectangular thin plates as an example,this work presents the theoretical framework of the SOV methods in an instructive way,and the bisection–based solution procedures for a group of nonlinear eigenvalue ***,the explicit equations of nodal lines of the SOV methods are presented,and the relations of nodal line patterns and frequency orders are *** is concluded that the highly accurate SOV methods have the same accuracy for all frequencies,the mode shapes about repeated frequencies can also be precisely captured,and the SOV methods do not have the problem of missing roots as well.

关键词： Separation-of-variable method Rayleigh quotient nodal line eigenvalue equation bisection method

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Peripheral mitochondrial DNA as a neuroinflammatory biomarker for major depressive disorder

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Neural Regeneration Research 2025年第6期20卷 1541-1554页

作者： Jinmei ye Cong Duan Jiaxin Han Jinrong chen Ning Sun Yuan Li Tifei Yuan daihui Peng Division of Mood Disorder Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina Department of Psychiatry First Hospital of Shanxi Medical UniversityTaiyuanShanxi ProvinceChina Shanghai Key Laboratory of Psychotic Disorders Brain Health InstituteNational Center for Mental DisordersShanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghaiChina Co-Innovation Center of Neuroregeneration Nantong UniversityNantongJiangsu ProvinceChina

In the pathogenesis of major depressive disorder, chronic stress-related neuroinflammation hinders favorable prognosis and antidepressant response. Mitochondrial DNA may be an inflammatory trigger, after its release from stress-induced dysfunctional central nervous system mitochondria into peripheral circulation. This evidence supports the potential use of peripheral mitochondrial DNA as a neuroinflammatory biomarker for the diagnosis and treatment of major depressive disorder. Herein, we critically review the neuroinflammation theory in major depressive disorder, providing compelling evidence that mitochondrial DNA release acts as a critical biological substrate, and that it constitutes the neuroinflammatory disease pathway. After its release, mitochondrial DNA can be carried in the exosomes and transported to extracellular spaces in the central nervous system and peripheral circulation. Detectable exosomes render encaged mitochondrial DNA relatively stable. This mitochondrial DNA in peripheral circulation can thus be directly detected in clinical practice. These characteristics illustrate the potential for mitochondrial DNA to serve as an innovative clinical biomarker and molecular treatment target for major depressive disorder. This review also highlights the future potential value of clinical applications combining mitochondrial DNA with a panel of other biomarkers, to improve diagnostic precision in major depressive disorder.

关键词： biomarker cytokine exosomes inflammasome major depressive disorder microglia mitochondrial DNA mitochondrial dysfunction neuroinflammation Toll-like receptor

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Inhibiting SHP2 reduces glycolysis, promotes microglial M1 polarization, and alleviates secondary inflammation following spinal cord injury in a mouse model

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Neural Regeneration Research 2025年第3期20卷 858-872页

作者： Xintian Ding Chun chen Heng Zhao Bin dai Lei ye Tao Song Shuai Huang Jia Wang Tao You Department of Orthopedics The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui ProvinceChina Department of Orthopedics Provincial Hospital Affiliated to Anhui Medical UniversityHefeiAnhui ProvinceChina

Reducing the secondary inflammatory response, which is partly mediated by microglia, is a key focus in the treatment of spinal cord injury. Src homology 2-containing protein tyrosine phosphatase 2(SHP2), encoded by PTPN11, is widely expressed in the human body and plays a role in inflammation through various mechanisms. Therefore, SHP2 is considered a potential target for the treatment of inflammation-related diseases. However, its role in secondary inflammation after spinal cord injury remains unclear. In this study, SHP2 was found to be abundantly expressed in microglia at the site of spinal cord injury. Inhibition of SHP2 expression using siRNA and SHP2 inhibitors attenuated the microglial inflammatory response in an in vitro lipopolysaccharide-induced model of inflammation. Notably, after treatment with SHP2 inhibitors, mice with spinal cord injury exhibited significantly improved hind limb locomotor function and reduced residual urine volume in the bladder. Subsequent in vitro experiments showed that, in microglia stimulated with lipopolysaccharide, inhibiting SHP2 expression promoted M2 polarization and inhibited M1 polarization. Finally, a co-culture experiment was conducted to assess the effect of microglia treated with SHP2 inhibitors on neuronal cells. The results demonstrated that inflammatory factors produced by microglia promoted neuronal apoptosis, while inhibiting SHP2 expression mitigated these effects. Collectively, our findings suggest that SHP2 enhances secondary inflammation and neuronal damage subsequent to spinal cord injury by modulating microglial phenotype. Therefore, inhibiting SHP2 alleviates the inflammatory response in mice with spinal cord injury and promotes functional recovery postinjury.

关键词： apoptosis glycolysis inflammatory response microglia neurons polarization spinal cord injury Src homology 2-containing protein tyrosine phosphatase 2

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双阳极电子枪测量系统研制与实验

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原子能科学技术 2016年第11期50卷 2075-2080页

作者：尚风雷李骥尚雷陆业明陈大潮王远远孙振标中国科学技术大学国家同步辐射实验室安徽合肥230029

为测量双阳极电子枪的输出束流品质,设计了一套完善的测量系统。使用该测量系统对双阳极电子枪进行测量。实验结果表明,增加中间电极可提高电子枪输出束流流强并改善横向聚焦。

关键词：电子枪测量装置束斑尺寸测量阴栅组件

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Overexpression of low-density lipoprotein receptor prevents neurotoxic polarization of astrocytes via inhibiting NLRP3 inflammasome activation in experimental ischemic stroke

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Neural Regeneration Research 2025年第2期20卷 491-502页

作者： Shuai Feng Juanji Li Tingting Liu Shiqi Huang Xiangliang chen Shen Liu Junshan Zhou Hongdong Zhao ye Hong Department of Neurology Nanjing First HospitalNanjing Medical UniversityNanjingJiangsu ProvinceChina Department of Neurology Nanjing Jinling HospitalAffiliated Hospital of Medical SchoolNanjing UniversityNanjingJiangsu ProvinceChina

Neurotoxic astrocytes are a promising therapeutic target for the attenuation of cerebral ischemia/reperfusion ***-density lipoprotein receptor,a classic cholesterol regulatory receptor,has been found to inhibit NLR family pyrin domain containing protein 3(NLRP3)inflammasome activation in neurons following ischemic stroke and to suppress the activation of microglia and astrocytes in individuals with Alzheimer’s ***,little is known about the effects of low-density lipoprotein receptor on astrocytic activation in ischemic *** address this issue in the present study,we examined the mechanisms by which low-density lipoprotein receptor regulates astrocytic polarization in ischemic stroke ***,we examined low-density lipoprotein receptor expression in astrocytes via immunofluorescence staining and western blotting *** observed significant downregulation of low-density lipoprotein receptor following middle cerebral artery occlusion reperfusion and oxygen-glucose deprivation/***,we induced the astrocyte-specific overexpression of low-density lipoprotein receptor using astrocyte-specific adeno-associated ***-density lipoprotein receptor overexpression in astrocytes improved neurological outcomes in middle cerebral artery occlusion mice and reversed neurotoxic astrocytes to create a neuroprotective ***,we found that the overexpression of low-density lipoprotein receptor inhibited NLRP3 inflammasome activation in oxygen-glucose deprivation/reoxygenation injured astrocytes and that the addition of nigericin,an NLRP3 agonist,restored the neurotoxic astrocyte *** findings suggest that low-density lipoprotein receptor could inhibit the NLRP3-meidiated neurotoxic polarization of astrocytes and that increasing low-density lipoprotein receptor in astrocytes might represent a novel strategy for treating cerebral ischemic stroke.

关键词： inflammation ischemia/reperfusion injury ischemic stroke low-density lipoprotein receptor neuroprotective astrocytes neurotoxic astrocytes NLRP3 inflammasome polarization

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