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kLDM:Inferring Multiple Metagenomic Association Networks Based on the Variation of Environmental Factors

Genomics, Proteomics & Bioinformatics 2021年第5期19卷 834-847页

作者： Yuqing Yang Xin Wang Kaikun Xie congmin zhu Ning Chen Ting Chen Department of Computer Science and Technology and Institute of Artificial Intelligence Tsinghua UniversityBeijing 100084China Sogou Inc. Beijing 100084China Department of Bioinformatics Key Laboratory of Ministry of Education for Gastrointestinal CancerSchool of Basic Medical SciencesFujian Medical UniversityFuzhou 350122China Peking Union Medical College Chinese Academy of Medical ScienceBeijing 100005China Department of Ultrasound Peking Union Medical College HospitalBeijing 100005China Beijing National Research Center for Information Science and Technology Beijing 100084China State Key Laboratory of Networking and Switching Technology Beijing University of Posts and TelecommunicationsBeijing 100876China

Identification of significant biological relationships or patterns is central to many metagenomic studies.Methods that estimate association networks have been proposed for this purpose;however,they assume that associations are static,neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors(EFs),which can result in inaccurate estimations.Therefore,in this study,we propose a computational model,called the k-Lognormal-Dirichlet-Multinomial(kLDM)model,which estimates multiple association networks that correspond to specific environmental conditions,and simultaneously infers microbe-microbe and EF-microbe associations for each network.The effectiveness of the kLDM model was demonstrated on synthetic data,a colorectal cancer(CRC)dataset,the Tara Oceans dataset,and the American Gut Project dataset.The results revealed that the widely-used Spearman’s rank correlation coefficient method performed much worse than the other methods,indicating the importance of separating samples by environmental conditions.Cancer fecal samples were then compared with cancer-free samples,and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria,especially five CRC-associated operational taxonomic units,indicating gut microbe translocation in cancer patients.Some EF-dependent associations were then found within a marine eukaryotic community.Finally,the gut microbial heterogeneity of inflammatory bowel disease patients was detected.These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems.The kLDM program,R,and Python scripts,together with all experimental datasets,are accessible at https://***/tinglab/kLDM.git.

关键词： Metagenomics Association inference Environmental condition Bayesian model Clustering

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Constructing a Boolean implication network to study the interactions between environmental factors and OTUs

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Frontiers of Electrical and Electronic Engineering in China 2014年第4期9卷 127-141页

作者： congmin zhu Rui Jiang Ting Chen MOE Key Laboratory of Bioinformatics and Bioinformatics Division Center for Synthetic & Systems Biology TNLIST/ Department of Automation Tsinghua University Beijing 100084 China Computational and Molecular Biology Program University of Southern California Loa Angles CA 90089 USA

Mining relationships between microbes and the environment they live in are crucial to understand the intrinsic mechanisms that govern cycles of carbon, nitrogen and energy in a microbial community. Building upon next- generation sequencing technology, the selective capture of 16S rRNA genes has enabled the study of co-occurrence patterns of microbial species from the viewpoint of complex networks, yielding successful descriptions of phenomena exhibited in a microbial community. However, since the effects of such environmental factors as temperature or soil conditions on microbes are complex, reliance on the analysis of co-occurrence networks alone cannot elucidate such complicated effects underlying microbial communities. In this study, we apply a statistical method, which is called Boolean implications for metagenomic studies （BIMS） for extracting Boolean implications （IF-THEN relationships） to capture the effects of environmental factors on microbial species based on 16S rRNA sequencing data. We first demonstrate the power and effectiveness of BIMS through comprehensive simulation studies and then apply it to a 16S rRNA sequencing dataset of real marine microbes. Based on a total of 6,514 pairwise relationships identified at a low false discovery rate （FDR） of 0.01, we construct a Boolean implication network between operational taxonomic units （OTUs） and environmental factors. Relationships in this network are supported by literature, and, most importantly, they bring biological insights into the effects of environmental factors on microbes. We next apply BIMS to detect three-way relationships and show the possibility of using this strategy to explain more complex relationships within a microbial community.

关键词： Boolean implication metagenome marine OTUs environmental factors

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基于碰撞位特征值的RFID标签识别算法研究

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现代信息科技 2024年第3期8卷 176-181页

作者：付钰朱弘旭刘鑫文聪敏广东科学技术职业学院计算机工程技术学院(人工智能学院) 广东珠海519090 陆军装甲兵学院士官学校吉林长春130000

“万物智联”网络中系统感知层将部署海量标签,为快速获取粘贴标签的物品信息,设计一种基于特征值策略的标签防碰撞算法,结合电子标签ID识别码的二进制特性和异或运算,可准确地推断出任意两位碰撞位,以此消除对无效节点的查询,加快查询... 详细信息

“万物智联”网络中系统感知层将部署海量标签,为快速获取粘贴标签的物品信息,设计一种基于特征值策略的标签防碰撞算法,结合电子标签ID识别码的二进制特性和异或运算,可准确地推断出任意两位碰撞位,以此消除对无效节点的查询,加快查询进程。仿真实验结果表明,所提算法可有效减少空闲时隙和总查询次数,提高系统效率,当标签数量为20000时,算法的系统效率达0.43,对比经典的查询树算法提高了24%,总查询次数减少了10905。

关键词：射频识别标签防碰撞特征值树算法

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Synthesis of Biphasic Defective TiO2-x/Reduced Graphene Oxide Nanocomposites with Highly Enhanced Photocatalytic Activity

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Chemical Research in Chinese Universities 2018年第2期34卷 158-163页

作者： GAO Guiqi zhu Qing CHONG Hanbao ZHENG Jun FAN congmin LI Guang Center of Modern Experimental Technology Anhui University Hefei 230601 F. R. China School of Physics and Material Science Anhui University Hefei 230601 R R. China College of Materials and Chemistry & Chemical Engineering Chengdu University of Technology Chengdu 610059 P. R. China

Biphasic defective TiO2-x/reduced graphene oxide（RGO） nanocomposites were synthesized by simple hydrothermal reactions. Compared with TiO2-x and commercial P25, TiO2-x/RGO shows much better photocatalytic activity and excellent stability in pollutants degradation, which could be ascribed to Ti^3＋ centers complexed with RGO and the synergetic effect between the two phases. The study reveals a new route for the synthesis of mixed-phase defective TiO2-x/carbon material nanocomposites for photocatalytic applications.

关键词： Defective biphasic TiO2-x Graphene sheet Photocatalysis Reduced graphene oxide

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静液压传动车辆的复合控制

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农业机械学报 2005年第4期36卷 26-29页

作者：朱从民西安理工大学机械与精密仪器工程学院

针对柴油机为动力的静液压传动车辆设计了由两个模糊控制器、一个模糊自适应PI控制器和一个PID控制器组成的复合控制系统,并利用柴油机外特性曲线对柴油机工况进行优化,使柴油机根据静液压系统的功率需求自动进行调速,解决了使用中柴油... 详细信息

针对柴油机为动力的静液压传动车辆设计了由两个模糊控制器、一个模糊自适应PI控制器和一个PID控制器组成的复合控制系统,并利用柴油机外特性曲线对柴油机工况进行优化,使柴油机根据静液压系统的功率需求自动进行调速,解决了使用中柴油机过载保护,利用柴油机转速补偿车速和静液压传动系统的时变非线性控制等问题。

关键词：传动车辆静液压传动系统复合控制系统 PID控制器模糊控制器 PI控制器模糊自适应外特性曲线静液压系统非线性控制柴油机转速车辆设计过载保护匹配性能控制特性控制方式动力仿真

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A multicenter retrospective cohort study of ketogenic diet therapy in 481 children with infantile spasms

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Acta Epileptologica 2022年第1期5卷 42-49页

作者： Yuanzhen Ye Dan Sun Hua Li Jianmin Zhong Rong Luo Baomin Li Dengna zhu Dan Li Shaoping Huang Yuwu Jiang Nong Xiao Yucai Chen Yuqin Zhang Mei Yu Xiaoyun Shen Li Gao Guo Zheng congmin Zhao Baoqiang Yuan Jianxiang Liao Jiong Qin CAAE KD group Shenzhen Children's Hospital Shenzhen 518038China Wuhan Children's Hospital Wuhan 430019China Guangdong 999 Brain Hospital Guangzhou 510515China Jiangxi Provincial Children's Hospital Nanchang 330006China West China Second University Hospital Sichuan UniversityChengdu 610044China Qilu Hospital of Shandong University Jinan 250063China Third Affiliated Hospital Zhengzhou UniversityZhengzhou 450015China The Second Affiliated Hospital of Xi’an Jiaotong University Xian 710004China Peking University First Hospital Beijing 100034China Children's Hospital of Chongqing Medical University Chongqing 400015China Children^Hospital of Shanghai Shanghai 20006China Tianjin Children's Hospital Tianjing 300134China Henan Provincial People's Hospital Zhengzhou 451161China Nanjing Children's Hospital Nanjing 210008China Xinqiao Hospital Army Medical UniversityChongqing 400037China The Affiliated Hospital of Xuzhou Medical University Xuzhou 221004China Peking University Peopled Hospital Beijing 100044China

Background:Ketogenic diet(KD)therapy is one of the main treatments for drug-resistant epilepsy.However,the KD therapy has been applied in only a small number of infantile spasm cases.In this large multicenter study,we investigated the efficacy of KD therapy in the treatment of infantile spasms.Methods:In this retrospective,multicenter cohort study,clinical data from main epilepsy centers were analyzed.Patients were classified into different groups according to age,type of drug and whether glucocorticoid was used before initiation of KD.Results:From October 2014 to March 2020,481 patients(308 males and 173 females)with infantile spasms were treated with the KD therapy.The age of the patients ranged from 2 months to 20 years,with a mean age of 1 year and 10 months.The number of anti-seizure medications(ASMs)used before KD initiation ranged 0-6,with a median of 3.In different time from initiation(1,3,6,and 12 months),the rates of seizure freedom after KD were 6.9,11.6;16.0 and 16.8%,respectively(x^(2)=27.1772,P0.05).Two hundred and eighteen patients(45.3%)failed to respond to c

关键词： Epilepsy Infantile spasms Ketogenic diet Adverse events Effectiveness rate West syndrome Multicenter study Retrospective Cohort

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Corrosion and Electrochemical Behavior of 316L Stainless Steel in Sulfate-reducing and Iron-oxidizing Bacteria Solutions

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Chinese Journal of Chemical Engineering 2006年第6X期14卷 829-834页

作者：胥聪敏张耀亨程光旭朱文胜 Department of Chemical Engineering Xi'an Jiaotong University Research and Technology Center of Lanzhou Oil Refinery Factory PetroChina Company Ltd.

Corrosion and electrochemical behavior of 316L stainless steel was investigated in the presence of aerobic iron-oxidizing bacteria IOB and anaerobic sulfate-reducing bacteria SRB isolated from cooling water systems in an oil refinery using electrochemical measurement, scanning electron microscopy SEM and energy dispersive atom X-ray analysisEDAX. The results show the corrosion potential and pitting potential of 316L stainless steel decrease distinctly in the presence of bacteria, in comparison with those observed in sterile medium under the same exposure time. SEM morphologies have shown that 316L stainless steel reveals no signs of pitting attack in the sterile medium. However, micrometer-scale corrosion pits were observed on 316L stainless steel sur- face in the presence of bacteria. The presence of SRB leads to higher corrosion rates than IOB. The interactions between the stainless steel surface, abiotic corrosion products, and bacterial cells and their metabolic products in- creased the corrosion damage degree of the passive film and accelerated pitting propagation.

关键词： sulfate-reducing bacteria SRB iron-oxidizing bacteria IOB 316L stainless steel pitting corrosion ele

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D-氨基酸驱散生物膜的行为与作用机理研究

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材料导报 2023年第1期37卷 239-245页

作者：胥聪敏高豪然朱文胜杨兴陈月清王文渊西安石油大学材料科学与工程学院西安710065 中海油常州涂料化工研究院有限公司江苏常州213000

为了明确D-氨基酸增强杀菌剂的生物膜驱散效果及杀菌机理,采用不同D-氨基酸与传统杀菌剂三丁基正十四烷基氯化膦(TTPC)、四羟甲基硫酸磷(THPS)以及抗菌肽组成复配杀菌剂,通过失重实验、电化学测试、表面分析等手段研究了复配杀菌剂对碳... 详细信息

为了明确D-氨基酸增强杀菌剂的生物膜驱散效果及杀菌机理,采用不同D-氨基酸与传统杀菌剂三丁基正十四烷基氯化膦(TTPC)、四羟甲基硫酸磷(THPS)以及抗菌肽组成复配杀菌剂,通过失重实验、电化学测试、表面分析等手段研究了复配杀菌剂对碳钢表面上的硫酸盐还原菌(SRB)、铁氧化菌(IOB)、SRB+IOB混合菌的杀菌缓蚀效果,明确了D-氨基酸驱散生物膜的行为与作用机理。结果表明:SRB和IOB发生协同作用,在碳钢试样表面形成致密的生物膜,其不仅提供了适合SRB生长的厌氧环境,还对SRB起到一定的保护作用,导致SRB+IOB混合菌造成的腐蚀最为严重,而D-氨基酸释放出的生物膜分散信号因子可改变细菌细胞壁肽聚糖成分以及调节细胞基因表达方式,通过其与细菌蛋白质结合来抑制生物膜形成,并使已有生物膜主动从碳钢表面分散脱落,破坏SRB与IOB所构成的氧浓差环境,在很大程度上抑制了因细菌所产生的胞外聚合物(EPS)导致的金属腐蚀加剧,进而使得杀菌剂能更好地杀灭生物膜下的细菌,对混合菌生物膜中SRB和IOB的杀菌率分别高达100%、82.60%,表明D-氨基酸通过驱散生物膜行为对杀菌剂起到了很好的杀菌增强效果。

关键词： D-氨基酸混合菌生物膜硫酸盐还原菌(SRB) 铁氧化菌(IOB) 碳钢杀菌增强效果

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医用冷敷贴缓解海姆泊芬光动力治疗鲜红斑痣术后灼痛及恢复皮肤稳态的疗效观察

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中华皮肤科杂志 2022年第9期55卷 784-789页

作者：祝贺吴英英杨蓉娅王聪敏敖俊红解放军总医院第七医学中心皮肤科北京100700 解放军医学院北京100853

目的观察医用冷敷贴缓解海姆泊芬光动力治疗鲜红斑痣术后灼痛及修复皮肤稳态的疗效。方法收集2019年11月至2021年4月解放军总医院第七医学中心皮肤科符合纳排标准的面中部鲜红斑痣患者40例,随机分为试验组和对照组,每组20例。接受海姆... 详细信息

目的观察医用冷敷贴缓解海姆泊芬光动力治疗鲜红斑痣术后灼痛及修复皮肤稳态的疗效。方法收集2019年11月至2021年4月解放军总医院第七医学中心皮肤科符合纳排标准的面中部鲜红斑痣患者40例,随机分为试验组和对照组,每组20例。接受海姆泊芬光动力治疗后,试验组术后即刻治疗部位使用医用冷敷贴1 h,之后每日敷贴1 h,连续使用3 d;对照组无特殊处理,自然恢复。分别于术后即刻与0.5、1、12 h进行疼痛指数(NRS)评分。于术前10 min,术后即刻与30 min、1 h检测皮肤表面温度。于术前10 min,术后即刻与24、48、72 h检测经皮水分丢失(TEWL)和角质层含水量(WCSC)。统计两组术后1、2、3周结痂率。治疗前后不同时间点观察指标的比较采用两因素重复测量方差分析,组间和组内比较采用Bonferroni或Sidak's检验。结果术前试验组与对照组年龄、性别构成及TEWL、WCSC差异均无统计学意义(P>0.05)。术后即刻,试验组与对照组NRS评分差异无统计学意义(8.00±1.17、8.20±1.06,F=0.30,P=0.592);术后0.5、1 h时试验组NRS评分(6.25±1.29、4.80±0.77)均低于对照组(7.15±0.99、6.50±0.69,均P<0.05)。术后即刻试验组与对照组皮肤表面温度分别升高至(35.211±1.333)℃和(35.637±0.832)℃,两组差异无统计学意义(P=0.062);术后30、60 min时试验组分别为(29.11±1.59)℃、(32.46±1.07)℃,均低于对照组[(35.01±0.91)、(34.86±0.74)℃,F=212.63、100.20,P<0.001]。术后48、72 h时试验组TEWL分别为(12.44±0.67)、(10.85±0.81)g·h^(-1)·m^(-2),均低于对照组[(14.61±0.34)、(14.93±0.24)g·h^(-1)·m^(-2),F=195.87、520.54,P<0.001],而WCSC分别为(57.83±9.29)、(52.64±8.09)AU,均高于对照组[(43.87±4.82)、(38.68±5.33)AU,F=24.41、49.22,P<0.001]。试验组术后1周有3例结痂,对照组为6例,两组结痂率差异无统计学意义(P=0.451)。结论海姆泊芬光动力治疗鲜红斑痣术后应用医用冷敷贴可降低表皮温度,发挥镇痛作用,缩短术后疼痛时间,同时促进皮肤通透屏障功能的恢复。

关键词：葡萄酒色痣光化学疗法医用冷敷贴疼痛皮肤稳态

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行波激励下大跨越输电线路纵向地震响应分析

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南方电网技术 2021年第12期15卷 72-77页

作者：杨军永朱从民朱瑞元国网山东省电力公司莱芜供电公司济南271100 电力规划总院有限公司北京100120

为更加贴近输电线路实际路径状况,深入理解大档距、大高差、非一致激励下输电线路地震响应,选取某±500 kV直流输电线路大跨越段,利用“四塔三线”精细化有限元模型开展了地震动响应分析,结果表明:导地线显著降低铁塔固有频率;跨越塔受... 详细信息

为更加贴近输电线路实际路径状况,深入理解大档距、大高差、非一致激励下输电线路地震响应,选取某±500 kV直流输电线路大跨越段,利用“四塔三线”精细化有限元模型开展了地震动响应分析,结果表明:导地线显著降低铁塔固有频率;跨越塔受导地线约束明显,塔顶位移峰值较小;地线支架、横担和塔身主材应力均在弹性范围内;跨越档导线张力峰值远高于设计值,但仍然小于拉断力,且张力值与锚塔横担长度大小有一定相关性;行波激励对位移响应有一定的影响,但无规律可循,行波激励对杆件应力和导线张力的影响很小。

关键词：大跨越塔线体系地震响应行波激励

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