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

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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Remaining Useful Life Prediction Method for Multi-Component System Considering Maintenance:Subsea Christmas Tree System as A Case Study

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China Ocean Engineering 2024年第2期38卷 198-209页

作者： WU qi-bing CAI Bao-ping FAN Hong-yan WANG Guan-nan rao Xi GE Weifeng shao Xiao-yan LIU Yong-hong CNOOC Safety Technology Services Co. Ltd.Tianjin 300456China College of Mechanical and Electronic Engineering China University of PetroleumQingdao 266580China CNOOC EnerTech Safety&Environmental Protection BranchTianjin 300456China

Maintenance is an important technical measure to maintain and restore the performance status of equipment and ensure the safety of the production process in industrial production,and is an indispensable part of prediction and health ***,most of the existing remaining useful life(RUL)prediction methods assume that there is no maintenance or only perfect maintenance during the whole life cycle;thus,the predicted RUL value of the system is obviously lower than its actual operating *** complex environment of the system further increases the difficulty of maintenance,and its maintenance nodes and maintenance degree are limited by the construction period and working conditions,which increases the difficulty of RUL *** RUL prediction method for a multi-omponent system based on the Wiener process considering maintenance is *** performance degradation model of components is established by a dynamic Bayesian network as the initial model,which solves the uncertainty of insufficient data *** on the experience of experts,the degree of degradation is divided according to Poisson process simulation random failure,and different maintenance strategies are used to estimate a variety of condition maintenance *** example of a subsea tree system is given to verify the effectiveness of the proposed method.

关键词： remaining useful life Wiener process dynamic Bayesian networks maintenance subsea Christmas tree system

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An M-VCUT level set-based data-driven model of microstructures and optimization of two-scale structures

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Frontiers of Mechanical Engineering 2024年第4期19卷 73-86页

作者： Minjie shao Tielin SHI qi XIA State Key Laboratory of Intelligent Manufacturing Equipment and Technology Huazhong University of Science and TechnologyWuhan 430074China

The optimization of two-scale structures can adapt to the different needs of materials in various regions by reasonably arranging different microstructures at the macro scale,thereby considerably improving structural ***,a multiple variable cutting(M-VCUT)level set-based data-driven model of microstructures is presented,and a method based on this model is proposed for the optimal design of two-scale *** geometry of the microstructure is described using the M-VCUT level set method,and the effective mechanical properties of microstructures are computed by the homogenization ***,a database of microstructures containing their geometric and mechanical parameters is *** two sets of parameters are adopted as input and output datasets,and a mapping relationship between the two datasets is established to build the data-driven model of *** the optimization of two-scale structures,the data-driven model is used for macroscale finite element and sensitivity *** efficiency of the analysis and optimization of two-scale structures is improved because the computational costs of invoking such a data-driven model are much smaller than those of homogenization.

关键词： two-scale structure structural optimization M-VCUT level set homogenization radial basis function data-driven

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To control false positives in genome-wide interaction assay:an conditional entropy-based approach

To control false positives in genome-wide interaction assay:...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xiao-Yu Zuo shao-qi rao School of Public Health Sun Yat-Sen University Institute of Medical Systems Biology and School of Public Health Guangdong Medical College

Background:Genome-wide analysis of gene-gene interactions has been recognized as a powerful and reasonable way to identify the missing heritability underlying complex disease that are undetectable in current single-point association ***,several data mining methods of model free in nature for detecting non-linear dependence between genetic loci have been developed,but most of them suffer from the risk of inflated false positive error(type 1 error) rate in testing the interaction hypothesis,which is particularly salient when the main effects at one or both loci are large. Methods:In this report,we propose to use two conditional entropy-based metrics to control this inflated false positive error rate,induced by the large main effects at the loci. We elucidate the mathematical relationship between the conditional mutual information and interaction metric in the context of relative ***,we evaluate the performance of these metrics for identifying interaction effects under different disease models,through extensive simulations and real data applications. Results:Our results demonstrate that unconditional mutual information,although more powerful in detecting interactions,is very sensitive to main effects,particularly in additive interaction *** comparison,the conditional mutual information metrics based on either genotype or haplotype can maintain the controlled false positive error rate without substantial loss of power for detecting gene-gene interactions in a wide range of disease models. Conclusions:In conclusion,we recommend to use the conventional unconditioned data mining metrics to identify "joint effect" of two genetic loci,followed by the use of conditional mutual information for purpose of detecting genuine "interaction effect",in the genome-wide interaction assay.

关键词： genome-wide interaction assay conditional mutual information false positive main effect

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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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A Two-stage Pathway-based Association Analysis Highlighting the Importance of DNA Repair Pathways in Nasopharyngeal Carcinoma

A Two-stage Pathway-based Association Analysis Highlighting ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Ke Liu Yan Liu shao-qi rao Department of Biomedical Engineering Zhongshan School of MedicineSun Yat-Sen University Institution of Medical Systems Biology and School of Public Health Guangdong Medical College

Background:Nasopharyngeal Carcinoma(NPC) is one of the highest mortal malignancies around the world,and its etiology involves a number of sophisticated biological *** repair related pathways are widely recognized as essential components in the etiology of NPC,yet few studies have systematically evaluated their *** this study, we proposed to use a two-stage association analysis for systematically assessing the relevance of DNA repair pathways with NPC. Methods:755 NPC cases and 755 controls of Cantonese population were recruited by Sun Yat-Sen University Cancer Center(SYSUCC).A total of 676 SNPs for 88 genes belonging to seven DNA repair related pathways were *** preprocessing the data based on Hardy-Weinberg equilibrium test,minor allele frequency and missing rate,587 SNPs were remained for subsequent *** avoid missing genes with moderate to small effects, we applied a two-stage approach that combines Fisher’s combination test and hypergeometric test to summarize the gene- and pathway-level association signals,respectively. Results:In the first stage,24 DNA repair related genes were identified associated with NPC(a=0.05),of which 17 genes were missed by the traditional single-SNP association *** the second stage,we found that two DNA repair pathways,Nucleotide Excision Repair(NER:P=0.0026) and Mismatch Repair(MMR,P= 0.0068) are significantly associated with NPC,in which association between MMR and NPC has not been reported previously. Conclusions:Our study demonstrates that the proposed two-stage approach,geneand pathway-level analysis,is able to capture genes with moderate to small effect,hence increasing the power to identify disease-relevant pathways.

关键词： Nasopharyngeal Carcinoma(NPC) DNA repair pathway pathway-based analysis

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Novel medium entropy perovskite oxide Sr(FeCoNiMo)_(1/4)O_(3−δ)for zinc-air battery cathode

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Journal of Energy Chemistry 2024年第9期96卷 669-678页

作者： Kaixin Li Juntao Gao Xu Han qi shao Zhe Lü School of Physics Harbin Institute of TechnologyHarbin 150001HeilongjiangChina Heilongjiang Provincial Key Laboratory of Advanced Quantum Functional Materials and Sensor Components Harbin 150001HeilongjiangChina

It is widely recognized that the development of ZABs is impeded by the kinetic bottleneck of oxygen evolution reaction(OER)and oxygen reduction reaction(ORR).The application of conformational entropy strategy to oxides often involves introducing multiple elements with different properties,thereby providing outstanding bifunctional catalytic activity for OER/***,the possible underlying catalytic pathways and potential interactions between various components are still poorly *** paper presents an excellent medium-entropy perovskite oxide,Sr(FeCoNiMo)_(1/4)O_(3−δ)(lower overpotential of 301 mV at 10 mA cm^(−2)).Zinc-air batteries employing it as a cathode catalyst demonstrate excellent round-trip efficiency(62%).By combining theoretical calculation with experiments,we aim to establish the link between the electronic structure of perovskite oxides with different elemental compositions and their OER *** reveals that the conformational entropy strategy can simultaneously shift the O 2p-band center and metal d-band center of perovskite oxide towards the vicinity of the Fermi energy level,thereby triggering a more favorable lattice oxygen-participated mechanism(LOM)during the OER *** outcomes of this work provide crucial insights into the role of conformational entropy strategies in oxygen catalysis and offer potential avenues for constructing efficient and stable electrocatalysts.

关键词： Sr(FeCoNiMo)_(1/4)O_(3−δ) Bifunctional catalyst Medium entropy LOM Rechargeable zinc-air batteries

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Statistical power of three model-free metrics for detecting gene-gene interactions

Statistical power of three model-free metrics for detecting ...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Su-Fen qi Liang-Chang Xiu shao-qi rao Yuan-Lin Ding Institute of Medical Systems Biology and School of Public Health Guangdong Medical College

Background:It is increasingly recognized that gene-gene interaction is an important genetic component for complex *** several metrics for detecting gene-gene interactions have been developed,there is dearth of knowledge regarding their statistical power under different scenarios of *** study thus aimed at systematic evaluation of the merits of three data mining metrics for detecting gene-gene interactions under various genetic models. Methods:In this article,we compared three different metrics of non-linear dependence between two genetic loci for detecting gene-gene *** three metrics were two-loci Fst,mutual information and linkage disequilibrium,*** generated case-control data by using simulation software genomeSIMLA based on 17 genetic models(including both epistatic and multiplicative interaction models).For each model,two different sets of disease allele frequencies and five different interaction effects were *** statistical power was computed from 500 simulated datasets. Results:In eight epistatic models,except for the model of recessive versus recessive, two-loci Fst and mutual information had higher statistical power than the linkagedisequilibrium based *** nine multiplicative models,two-loci Fst and mutual information also had higher statistical power. Conclusions:The evolution-based metric,Fst,and information-based metric, mutual information,are more powerful and robust statistic for detecting both epistatic and multiplicative gene-gene interactions.

关键词： Models of gene-gene interactions Evolutionary theory Case-control design

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Highly Differentiated Target Detection under Extremely Low-Light Conditions Based on Improved YOLOX Model

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Computer Modeling in Engineering & Sciences 2024年第8期140卷 1507-1537页

作者： Haijian shao Suqin Lei Chenxu Yan Xing Deng Yunsong qi School of Computer Jiangsu University of Science and TechnologyZhenjiang212003China Department of Electrical and Computer Engineering University of NevadaLas VegasNV89154USA Zhejiang Geely Automobile Research Institute Ningbo315336China

This paper expounds upon a novel target detection methodology distinguished by its elevated discriminatory efficacy,specifically tailored for environments characterized by markedly low luminance *** methodologies struggle with the challenges posed by luminosity fluctuations,especially in settings characterized by diminished radiance,further exacerbated by the utilization of suboptimal imaging *** envisioned approach mandates a departure from the conventional YOLOX model,which exhibits inadequacies in mitigating these *** enhance the efficacy of this approach in low-light conditions,the dehazing algorithm undergoes refinement,effecting a discerning regulation of the transmission rate at the pixel level,reducing it to values below 0.5,thereby resulting in an augmentation of image ***,the coiflet wavelet transform is employed to discern and isolate high-discriminatory attributes by dismantling low-frequency image attributes and extracting high-frequency attributes across divergent *** utilization of CycleGAN serves to elevate the features of low-light imagery across an array of stylistic *** computational methodologies are then employed to amalgamate and conflate intricate attributes originating from images characterized by distinct stylistic orientations,thereby augmenting the model’s erudition *** validation conducted on the PASCAL VOC and MS COCO 2017 datasets substantiates pronounced *** refined low-light enhancement algorithm yields a discernible 5.9%augmentation in the target detection evaluation index when compared to the original *** Average Precision(mAP)undergoes enhancements of 9.45%and 0.052%in low-light visual renditions relative to conventional YOLOX *** envisaged approach presents a myriad of advantages over prevailing benchmark methodologies in the realm of target detection within environments marked by an acute scarcity of lumi

关键词： Target detection extremely low-light wavelet transformation highly differentiated features YOLOX

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Correlation analysis of interstitial maturity and prognosis of colorectal cancer:Meta-analysis

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2816-2825页

作者： Zhen-Jun Liu Xu-Wen Zhang qi-qi Liu shao-Zhao Wang Department of Gastrointestinal Surgery Feicheng People's HospitalFeicheng 271600Shandong ProvinceChina Department of Hepatobiliary Surgery Feicheng People's HospitalFeicheng 271600Shandong ProvinceChina Department of Gastrointestinal Surgery Peking University Shenzhen HospitalShenzhen 518036Guangdong ProvinceChina Department of Anorectal Word Central Hospital Affiliated Shandong First Medical UniversityJinan 250013Shandong ProvinceChina

BACKGROUND To investigate the relationship between interstitial maturity and prognosis of colorectal *** To examine the correlation between interstitial maturity and the prognosis of colorectal *** The paper database PubMed,EMBASE,Cochranelibrary,Springerlink,CNKI,and Wanfang database were searched until December 2023."tumor stroma maturity""desmoplastic stroma reaction""desmoplastic reaction""stroma reaction""degree of stroma reaction""stroma classification""stroma density""colorectal cancer""colon cancer""rectal cancer""prognosis"were searched for the search *** system assessors independently screened the literature quality according to the inclusion exclusion criteria,Quality evaluation and data extraction were performed for the included literatures,and meta-analysis was performed for randomized control trials included at using Review Manager 5.2 *** Finally,data of 9849 patients with colorectal cancer from 19 cosets in 15 literatures were included,including 4339 patients with mature type(control group),3048 patients with intermediate type(intermediate group)and 2456 patients with immature type(immature group).The results of meta-analysis showed:Relapse-free survival[hazard ratio(HR)=2.66,95%confidence interval(CI):2.30-3.08;P<0.00001],disease-free survival(HR=3.68,95%CI:2.33-5.81;P<0.00001)and overall survival(HR=1.70,95%CI:1.53-1.87;P<0.00001)were significantly lower than those in mature group(control group);relapse-free survival(HR=1.36,95%CI:1.17-1.59;P<0.0001)and disease-free survival rate(HR=1.85,95%CI:1.53-2.24;P<0.0001)was significantly lower than the mature group(control group).CONCLUSION There is the correlation between tumor interstitial maturity and survival prognosis of colorectal cancer,and different degrees of tumor interstitial maturity have a certain impact on the quality of life of colorectal cancer patients.

关键词： Colorectal tumor Survival prognosis Tumor interstitial maturity Systematic review Meta-analysis

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