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Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models

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Chinese Journal of Cancer 2013年第4期32卷 186-194页

作者： Hongyan Wang Xiaobo Zhou Department of Radiology the Methodist Hospital Research Institute Department of Radiology Weill Cornell Medical College

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.

关键词： Epigenetics, histone modification, conditional random field, regulatory elements

Carbonate-induced enhancement of phenols degradation in CuS/peroxymonosulfate system: A clear correlation between this enhancement and electronic effects of phenols substituents

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Journal of Environmental Sciences 2023年第7期129卷 139-151页

作者： xiaobo Wang Yu zhou Nan Wang Jindong Zhang Lihua Zhu College of Chemistry and Chemical Engineering Huazhong University of Science and TechnologyWuhan 430074China College of Chemistry and Chemical Engineering Hubei Polytechnic UniversityHuangshi 435003China

This study investigated the enhancement effects of dissolved carbonates on the peroxymonosulfate-based advanced oxidation process with CuS as a catalyst.It was found that the added CO_(3)^(2−)increased both the catalytic activity and the stability of the catalyst.Under optimized reaction conditions in the presence of CO_(3)^(2−),the degradation removal of 4-methylphenol(4-MP)within 2 min reached 100%,and this was maintained in consecutivemulti-cycle experiments.The degradation rate constant of 4-MP was 2.159 min^(−1),being 685%greater than that in the absence of CO_(3)^(2−)(0.315 min−1).The comparison of dominated active species and 4-MP degradation pathways in both CO_(3)^(2−)-free and CO_(3)^(2−)-containing systems suggested thatmore CO_(3)·^(−)/^(1)O_(2) was produced in the case of CO_(3)^(2−)deducing an electron transfer medium,which tending to react with electron-richmoieties.Meanwhile,Characterization by X-ray photoelectron spectroscopic and cyclic voltammetrymeasurement verified CO_(3)^(2−)enabled the effective reduction of Cu^(2+)to Cu^(+).By investigating the degradation of 11 phenolics with different substituents,the dependence of degradation kinetic rate constant of the phenolics on their chemical structures indicated that there was a good linear relationship between the Hammett constantsσp of the aromatic phenolics and the logarithm of k in the CO_(3)^(2−)-containing system.This work provides a new strategy for efficient removal of electron-rich moieties under the driving of carbonate being widely present in actual water bodies.

关键词： Carbonates Enhancement Catalytic degradation Phenolic pollutants Electronic effects

From plant immunity to crop disease resistance

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Journal of Genetics and Genomics 2022年第8期49卷 693-703页

作者： Yan Zhao xiaobo Zhu Xuewei Chen Jian-Min zhou State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural University at WenjiangChengduSichuan 611130China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China Hainan Yazhou Bay Seed Laboratory SanyaHainan 572025China

Plant diseases caused by diverse pathogens lead to a serious reduction in crop yield and threaten food security worldwide.Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases.In the last decade,our understanding of plant immunity at both molecular and genomic levels has improved greatly.Combined with advances in biotechnologies,particularly clustered regularly interspaced short palindromic repeat(CRISPR)/Cas9-based genome editing,we can now rapidly identify new resistance genes and engineer disease-resistance crop plants like never before.In this review,we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants.We also discuss existing challenges in this field and suggest directions for future studies.

关键词： Plant immunity Disease resistance Resistance genes Molecular breeding Genetic engineering Crops

Sensor Fault Diagnosis and Tolerant Control Based on Belief Rule Base for Complex System

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Journal of Systems Science & Complexity 2023年第3期36卷 1002-1023页

作者： FENG Zhichao zhou Zhijie BAN Xiaojun HU Changhua ZHANG xiaobo Rocket Force University of Engineering Xi'an 710025China Harbin Institute of Technology Harbin 150001China

This paper develops a new fault diagnosis and tolerant control framework of sensor failure(SFDTC)for complex system such as rockets and missiles.The new framework aims to solve two problems:The lack of data and the multiple uncertainty of knowledge.In the SFDTC framework,two parts exist:The fault diagnosis model and the output reconstruction model.These two parts of the new framework are constructed based on the new developed belief rule base with power set(BRB-PS).The multiple uncertainty of knowledge can be addressed by the local ignorance and global ignorance in the new developed BRB-PS model.Then,the stability of the developed framework is proved by the output error of the BRB-PS model.For complex system,the sensor state is determined by many factors and experts cannot provide accurate knowledge.The multiple uncertain knowledge will reduce the performance of the initial SDFTC framework.Therefore,in the SFDTC framework,to handle the influence of the uncertainty of expert knowledge and improve the framework performance,a new optimization model with two optimization goals is developed to ensure the smallest output uncertainty and the highest accuracy simultaneously.A case study is conducted to illustrate the effectiveness of the developed framework.

关键词： Belief rule base fault diagnosis and tolerant control optimization model uncertainty

Thermal Transport across Polyethylene Chains

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Journal of Thermal Science 2022年第4期31卷 1061-1067页

作者： YANG Cong DUAN Xuhui zhou Jun LIU Jun LI xiaobo School of Energy and Power Engineering Huazhong University of Science and Technology Wuhan 430074China Department of Mechanical and Aerospace Engineering North Carolina State University Raleigh 27695USA NNU-SULI Thermal Energy Research Center&Center for Quantum Transport and Thermal Energy Science School of Physics and Technology Nanjing Normal Universityanjing 210023China

In polymers,heat could transfer efficiently along the long polymer chains;however due to the finite length of polymer chains,such heat eventually has to pass across the chain-chain boundary which is less effective in heat transfer.This paper investigated the thermal transport across polyethylene chains with molecular dynamics(MD)simulations.Thermal transport across two polymer chains overlapping with each other is studied with different chain length(75 nm,150 nm and 251 nm)and chain-chain overlapping length.The results show that with increasing overlapping length,the total thermal conductance across the two chains exhibits maximum value,which is due to the increasing thermal resistance along the chains and the decreasing inter-chain thermal boundary resistance.Mathematically,we show that the total thermal resistance can be decomposed into two terms.The coupling term related to the inter-chain thermal resistance tends to saturate even with long overlapping length.

关键词： phonon transport polymer polyethylene thermal resistance van der Waals interaction

Factors influencing methane diffusion behaviors in micro-nano coal pores: a comprehensive study

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Frontiers of Earth Science 2023年第1期17卷 71-86页

作者： Xianglong FANG Dameng LIU Yingfang zhou xiaobo LIU Yidong CAI School of Energy Resources China University of GeosciencesBeijing 100083China Coal Reservoir Laboratory of National Engineering Research Center of CBM Development&Utilization China University of GeosciencesBeijing 100083China School of Engineering Fraser Noble BuildingKing's CollegeUniversity of AberdeenAB243UE AberdeenUK Postdoctoral Workstation of Applied Technology Research Institute Northeast Petroleum UniversityDaqing 163318China

Gas diffusion in the coal matrix plays a significant role in forecasting the production performance of coalbed methane(CBM)wells.To better understand methane diffusion behavior,a systematic study was performed on various rank coals with vitrinite reflectance(Ro,m)ranging from 0.46%to 2.79%.Multiple experiments,including coal petrographic analysis,field emission scanning electron microscopy(FESEM),low-temperature N2 adsorption/desorption,and mercury intrusion porosimetry(MIP),were conducted to quantitatively characterize the multiscale micro-nano pore system in different rank coals,which showed that the pore structure of coals exhibited a multimodal pore size and volume distribution.Isothermal adsorption-diffusion experiments using the volumetric method were also performed to understand the methane diffusion characteristics in the micro-nano pores of the coal reservoir.The applicability of the multiporous diffusion model is verified,and methane diffusion in the multi-scale pores of coal reservoirs exhibits the characteristics of early fast diffusion,transitional diffusion in the medium term,and slow diffusion in the later period.In addition,the factors affecting methane diffusion in coals were systematically analyzed,and gray relational analysis(GRA)was employed to analyze and identify the importance of these factors on methane diffusion.The results show the impact ranking of factors,in order from the most important to the least:particle size>moisture>surface area>pore volume>pressure>coal rank>temperature in all of three diffusion stages.These findings are helpful for forecasting production performance and enhancing the production efficiency of CBM.

关键词： coalbed methane reservoir micro-characteristic diffusion coefficient grey relational analysis

The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 619-631页

作者： Sijia Wu Zhiwei Fan Pora Kim Liyu Huang Xiaobo Zhou School of Life Science and Technology Xidian UniversityXi’an 710071China West China School of Public Health and West China Fourth Hospital Sichuan UniversityChengdu 610040China Center for Computational Systems Medicine School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTX 77030USA

Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient.To fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas.For individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional annotations.Finally,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and miR-589-3p.These events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor genes.Our functional A-to-I RNA editing events(https://ccsm.***.edu/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect.

关键词： A-to-I RNA editing Cancer Protein recoding Alternative splicing MicroRNA regulation

Advanced oxidative degradation of sulfamethoxazole by using bowl-like FeCuS@Cu_(2)S@Fe^(0) catalyst to efficiently activate peroxymonosulfate

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Journal of Environmental Sciences 2023年第4期126卷 348-364页

作者： xiaobo Wang Yu zhou Sylvestre Ndayiragije Nan Wang Heqing Tang Lihua Zhu College of Chemistry and Chemical Engineering Huazhong University of Science and TechnologyWuhan 430074China College of Chemistry and Chemical Engineering Hubei Polytechnic UniversityHuangshi 435003China Key Laboratory of Catalysis and Materials Science of the State Ethnic Affairs Commission and Ministry of Education Hubei ProvinceCollege of Resources and Environmental ScienceSouth-Central University for NationalitiesWuhan 430074China

A novel hierarchical bowl-like FeCuS@Cu_(2)S@Fe^(0)nanohybrid catalyst(B-FeCuS@Cu_(2)S@Fe^(0))was synthesized for removing sulfamethoxazole(SMX) through catalytic activation of peroxymonosulfate(PMS). It was found that this catalyst exhibited excellently high catalytic activity. Under optimized reaction conditions, all the added SMX(12 mg/L) could be completely degraded within 5 min. The SMX degradation followed pseudo first order kinetics with a rate constant k of 0.89 min^(-1), being 1.38, 4.51, 8.99 and 35.6 times greater than that of other catalysts including Fe^(0)(0.644 min^(-1)in the very initial stage), bowl-like iron-doped CuS(B-FeCuS, 0.197 min^(-1)), bowl-like CuS(B-CuS, 0.099 min^(-1)) and Cu_(2)O(0.025 min^(-1)), respectively. During the degradation, several reactive oxygen species(·OH, SO_(4)·-and1O_(2)) were generated with ·OH as the main one as confirmed by electron paramagnetic resonance analysis. The SMX degradation in the present system included both radical and non-radical mediated processes. A possible mechanistic insight of the PMS activation by bowl Fe^(0)decorated CuS@Cu_(2)S-based catalyst was proposed according to X-ray photoelectron spectroscopic(XPS) analysis, and the degradation pathway of SMX was speculated by monitoring the degradation intermediates with liquid chromatography coupled with mass spectrometry(LC-MS).

关键词： Sulfamethoxazole Peroxymonosulfate Sulfide catalyst Degradation Reactive oxygen species

周晓波教授运用升清降浊法治疗脾胃病医案撷萃

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天津中医药 2020年第1期37卷 79-82页

作者：孙文恺周晓波南京中医药大学附属医院

总结周晓波教授运用升清降浊法治疗脾胃病的经验。作者通过跟师侍诊,整理资料,查阅相关文献,结合典型病案探讨其用药特色。周晓波教授治疗脾胃病以健脾益中,升降并用为核心,升法中补气升阳,配伍风药,降法中以降气为主,同治兼证,升降法... 详细信息

总结周晓波教授运用升清降浊法治疗脾胃病的经验。作者通过跟师侍诊,整理资料,查阅相关文献,结合典型病案探讨其用药特色。周晓波教授治疗脾胃病以健脾益中,升降并用为核心,升法中补气升阳,配伍风药,降法中以降气为主,同治兼证,升降法中擅用药对,注重疏肝宣肺,取得良好疗效。周晓波教授运用升清降浊法治疗脾胃病经验值得借鉴。

关键词：升清降浊名医经验脾胃病周晓波