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Integrative modeling of transmitted and de novo variants identifies novel risk genes for congenital heart disease

Quantitative Biology 2021年第2期9卷 216-227页

作者： Mo Li Xue Zeng Chentian Jin Sheng Chih Jin Weilai Dong Martina Brueckner Richard Lifton Qiongshi Lu hongyu zhao Department of Biostatistics Yale School of Public HealthNew HavenCT 06510USA Department of Genetics Yale UniversityNew HavenCT 06510USA Department of Molecular Cellular&Developmental BiologyYale UniversityCT 06510USA Department of Genetics Washington University School of MedicineSt LouisMO 63110USA Department of Pediatrics Yale UniversityNew HavenCT 06510USA Laboratory of Human Genetics and Genomics Rockefeller UniversityNew YorkNY 10065USA Department of Biostatistics and Medical Informatics University of Wisconsin-MadisonMadisonWl 53792USA Program of Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06510USA

Background:Whole-exome sequencing(WES)studies have identified multiple genes enriched for de novo mutations(DNMs)in congenital heart disease(CHD)***,risk gene identification based on DNMs alone remains statistically challenging due to heterogenous etiology of CHD and low mutation rate in each ***:In this manuscript,we introduce a hierarchical Bayesian framework for gene-level association test which jointly analyzes de novo and rare transmitted *** integrative modeling of multiple types of genetic variants,gene-level annotations,and reference data from large population cohorts,our method accurately characterizes the expected frequencies of both de novo and transmitted variants and shows improved statistical power compared to analyses based on DNMs ***:Applied to WES data of 2,645 CHD proband-parent trios,our method identified 15 significant genes,half of which are novel,leading to new insights into the genetic bases of ***:These results showcase the power of integrative analysis of transmitted and de novo variants for disease gene discovery.

关键词： rare variants gene-level association test congenital heart disease de novo mutation

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Tuning Active Metal Atomic Spacing by Filling of Light Atoms and Resulting Reversed Hydrogen Adsorption-Distance Relationship for Efficient Catalysis

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Nano-Micro Letters 2023年第10期15卷 151-162页

作者： Ding Chen Ruihu Lu Ruohan Yu hongyu zhao Dulan Wu Youtao Yao Kesong Yu Jiawei Zhu Pengxia Ji Zonghua Pu Zongkui Kou Jun Yu Jinsong Wu Shichun Mu State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070People’s Republic of China NRC(Nanostructure Research Centre) Wuhan University of TechnologyWuhan 430070People’s Republic of China

Precisely tuning the spacing of the active centers on the atomic scale is of great significance to improve the catalytic activity and deepen the understanding of the catalytic mechanism,but still remains a ***,we develop a strategy to dilute catalytically active metal interatomic spacing(d_(M-M))with light atoms and discover the unusual adsorption *** example,by elevating the content of boron as interstitial atoms,the atomic spacing of osmium(d_(Os-Os))gradually increases from 2.73 to 2.96?.More importantly,we find that,with the increase in dOs-Os,the hydrogen adsorption-distance relationship is reversed via downshifting d-band states,which breaks the traditional cognition,thereby optimizing the H adsorption and H_2O dissociation on the electrode surface during the catalytic process;this finally leads to a nearly linear increase in hydrogen evolution reaction ***,the maximum dOs-Os of 2.96?presents the optimal HER activity(8 mV@10 mA cm^(-2))in alkaline media as well as suppressed O adsorption and thus promoted *** is believed that this novel atomic-level distance modulation strategy of catalytic sites and the reversed hydrogen adsorption-distance relationship can shew new insights for optimal design of highly efficient catalysts.

关键词： Electrocatalysis DFT calculation Interstitial filling Hydrogen evolution Structure–activity relationships

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Magnetically driven microrobots moving in a flow:a review

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Frontiers of Information Technology & Electronic Engineering 2023年第11期24卷 1520-1540页

作者： Jiamiao MIAO Xiaopu WANG Yan ZHOU Min YE hongyu zhao Ruoyu XU Huihuan QIAN School of Science and Engineering the Chinese University of Hong Kong(Shenzhen)Shenzhen 518172China Shenzhen Institute of Artificial Intelligence and Robotics for Society(AIRS) Shenzhen 518129China

Magnetically driven microrobots hold great potential to perform specific tasks more locally and less invasively in the human *** reach the lesion area in vivo,microrobots should usually be navigated in flowing blood,which is much more complex than static ***,it is more challenging to design a corresponding precise control scheme.A considerable amount of work has been done regarding control of magnetic microrobots in a flow and the corresponding *** this paper,we review and summarize the state-of-the-art research progress concerning magnetic microrobots in blood flow,including the establishment of flow systems,dynamics modeling of motion,and control *** addition,current challenges and limitations are *** hope this work can shed light on the efficient control of microrobots in complex flow environments and accelerate the study of microrobots for clinical use.

关键词： Microrobot Flow Dynamics modeling Control

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Bashang Village: Alleviating Poverty through Red Tourism

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China Today 2018年第9期67卷 62-63页

作者： JIN LUYAO zhao hongyu HUAN YU 不详

THE Jinggang Mountain is the cradle of the Chinese *** years ago,a revolutionary base was set up in the *** then,the spark of the Chinese revolution had been originating from here to all across the country.

关键词： Bashang Village

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Network Module Identification with Its Applications in Biological Networks

Network Module Identification with Its Applications in Biolo...

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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：张淑芹 hongyu zhao Center for Computational Systems Biology School of Mathematical SciencesFudan University Division of Biostatistics Yale School of Public Health

Background:Module(community) structure is a common and important property of many types of networks such as social networks and biological *** classes of algorithms have been proposed for module structure detection and identification,including clustering techniques,modularity optimization,and other *** these methods,the modularity optimization method has attracted great attention and much related research has been ***,the existing modularity optimization method does not perform well in the presence of unbalanced module structures. Methods:In this paper,we first propose a new metric to better characterize the module structure than other metrics in this *** metric is based on the average degrees in and between the subnetworks(modules).The model is formulated as an optimization problem. We then develop an algorithm for the module structure identification based on this metric. Results:We apply the proposed method to synthetic network data sets and the gene co- expression networks constructed from the real gene expression data for yeast and the different tissues of a large sample of morbidly obese *** method shows better performance than the existing popular methods in our *** also identifies more modules with significantly better enrichment of functionally related genes in the real *** differences of the identified modules across the different tissues are also discussed. Conclusions:We propose a novel method for module identification in networks,which can capture the important module *** method can be applied as a general method to assist in the analysis of biological networks.

关键词： Gene co-expression network Module identification Optimization problem

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The R5Y5 sequence's affinity to histones in vitro

The R5Y5 sequence's affinity to histones in vitro

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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：蔡禄 hongyu zhao Rong Chai School of Mathematics Physics and Biological EngineeringInner Mongolia University of Science and Technology

Background:Nucleosome positioning plays an important role in regulation of the gene activity in eukaryotic *** sequence is believed to be one of the major factors affecting the nucleosome positioning and sequence-dependent nucleosome positioning is largely dependent on DNA deformability *** of basic binary periodical patterns was well established:in purine/pyrimidine alphabet YRRRRRYYYYYR by theoretical calculation model,but its validity need to be further verified. Methods:One of chemical synthetic R5Y5 sequences version was cloned into multiple cloning sites of *** then the sequence was labeled by biotin and purified after PCR. A salt dialysis method in vitro was employed to assembly nucleosome and in which 601 sequences was used as control. Results:The sequence has strong nucleosome formation ability in the 1.2 ratio of octamer to *** in the 0.8 ratio it has low affinity to ***,its stability to assembly nucleosome is not as high as 601. Conclusions:The R5Y5 sequence’s ability to assembly nucleosome was perhaps strong in vitro and the result was the basic to further investigate the sequence-dependent of nucleosome positioning.

关键词： nucleosome positioning R5Y5 DNA sequence epigenetic

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Toll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function

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Cellular & Molecular Immunology 2021年第2期18卷 328-338页

作者： Juan Huang Jian Peng James Alexander Pearson Georgios Efthimiou Youjia Hu Ningwen Tai Yanpeng Xing Luyao Zhang Jianlei Gu Jianping Jiang hongyu zhao Zhiguang Zhou F.Susan Wong Li Wen National Clinical Research Center for Metabolic Diseases Key Laboratory of Diabetes Immunology(Central South University)Ministry of Educationand Department of Metabolism and EndocrinologyThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina Section of Endocrinology Department of Internal MedicineSchool of MedicineYale UniversityNew HavenCTUSA Division of Infection and Immunity School of MedicineCardiff UniversityCardiffUK Department of Microbiology University of HullHullUK Department of Gastrointestinal Surgery of the First Hospital of Jilin University ChangchunJilinChina Department of Biostatistics Data Science&GeneticsYale School of Public HealthNew HavenCTUSA

Innate immunity mediated by Toll-like receptors(TLRs),which can recognize pathogen molecular patterns,plays a critical role in type 1 diabetes ***7 is a pattern recognition receptor that senses single-stranded RNAs from viruses and host tissue cells;however,its role in type 1 diabetes development remains *** our study,we discovered that Tlr7-deficient(Tlr7^(−/−))nonobese diabetic(NOD)mice,a model of human type 1 diabetes,exhibited a significantly delayed onset and reduced incidence of type 1 diabetes compared with Tlr7-sufficient(Tlr7^(+/+))NOD *** investigations showed that Tlr7 deficiency significantly altered B-cell differentiation and immunoglobulin ***,Tlr7^(−/−)NOD B cells were found to suppress diabetogenic CD4^(+)T-cell responses and protect immunodeficient NOD mice from developing diabetes induced by diabetogenic T *** addition,we found that Tlr7 deficiency suppressed the antigen-presenting functions of B cells and inhibited cytotoxic CD8^(+)T-cell activation by downregulating the expression of both nonclassical and classical MHC class I(MHC-I)molecules on B *** data suggest that TLR7 contributes to type 1 diabetes development by regulating B-cell functions and subsequent interactions with T ***,therapeutically targeting TLR7 may prove beneficial for disease protection.

关键词： Type 1 diabetes Toll-like receptor 7 B cell

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The roles of electrons in the electronic structures and optical properties of graphyne

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Chinese Science Bulletin 2012年第23期57卷 3080-3085页

作者： HE XiuJie TAN Jie BU HongXia ZHANG hongyu zhao MingWen School of Physics and State Key Laboratory of Crystal Materials Shandong University Jinan 250100 China

The electronic structures and optical properties of graphyne consisting of sp-and sp 2-hybridized carbon atoms are studied using first-principles calculations.A tight-binding model of the 2p z orbitals are proposed to describe the electronic bands near the Fermi *** results show that the natural band gap of graphyne originates from the inhomogeneous bindings between differently-hybridized carbon *** interlayer interactions of bulk graphyne narrow the band gap to 0.16 eV and result in redshift of the optical spectral peaks as compared to single-layered graphyne.

关键词： graphyne electronic structure tight-binding model first—principles calculation

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基于代价敏感方法的智能制造故障诊断

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计算机集成制造系统 2019年第9期25卷 2180-2187页

作者：赵宏宇沈江安邦天津大学管理与经济学部

在设备故障诊断过程中,数据集中正负分类样本数量相差较为悬殊等数据不平衡问题会导致诊断准确率降低。为减少由于正负类样本不均衡而导致的误判,提高设备故障诊断准确率,提出一种代价敏感方法。该方法借助Boosting方法,通过多次概率采... 详细信息

在设备故障诊断过程中,数据集中正负分类样本数量相差较为悬殊等数据不平衡问题会导致诊断准确率降低。为减少由于正负类样本不均衡而导致的误判,提高设备故障诊断准确率,提出一种代价敏感方法。该方法借助Boosting方法,通过多次概率采样生成多个模型,并确定每个模型的权重。其中采样的概率取决于代价调整值,所提方法在每一个迭代过程中根据上一次迭代的结果对代价调整值进行调整。通过实验,并与其他方法进行对比,结果表明与采用固定的代价敏感值及非代价敏感方法相比,提出的方法具有更好的表现。

关键词：故障诊断代价敏感方法非均衡数据集智能制造

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采用轨道复合绝缘技术的城市轨道交通杂散电流防护研究

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腐蚀与防护 2023年第4期44卷 94-99页

作者：赵宏宇青岛地铁运营有限公司青岛266001

针对地铁走行兼牵引回流作用的轨道对地形成杂散电流的问题,提出了一种提升轨道对地绝缘性能以降低杂散电流分布的绝缘技术。通过实验室试验和仿真手段检验了该技术的可靠性和稳定性。结果表明:轨道复合绝缘技术可明显减轻扣件结构体电... 详细信息

针对地铁走行兼牵引回流作用的轨道对地形成杂散电流的问题,提出了一种提升轨道对地绝缘性能以降低杂散电流分布的绝缘技术。通过实验室试验和仿真手段检验了该技术的可靠性和稳定性。结果表明:轨道复合绝缘技术可明显减轻扣件结构体电阻及表面电阻降低对轨道结构绝缘性能的负面影响,有效提升轨道对地绝缘性能。

关键词：杂散电流轨道结构对地电阻绝缘试验复合绝缘有限元仿真

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