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Covering Your Bases： Inheritance of DNA Methylation in Plant Genomes

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Molecular Plant 2014年第3期7卷 472-480页

作者： Chad E. Niederhuth robert J. schmitz Department of Genetics University of Georgia Athens GA 30602 USA

Cytosine methylation is an important base modification that is inherited across mitotic and meiotic cell divisions in plant genomes. Heritable methylation variants can contribute to within-species phenotypic variation. Few methylation variants were known until recently, making it possible to begin to address major unanswered questions： the extent of natural methylation variation within plant genomes, its effects on phenotypic variation, its degree of depend- ence on genotype, and how it fits into an evolutionary context. Techniques like whole-genome bisulfite sequencing （WGBS） make it possible to determine cytosine methylation states at single-base resolution across entire genomes and populations. Application of this method to natural and novel experimental populations is revealing answers to these long-standing questions about the role of DNA methylation in plant genomes.

关键词： DNA methylation epigenetics epiallele whole-genome bisulfite sequencing.

Crop Epigenomics： Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

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Molecular Plant 2015年第6期8卷 860-870页

作者： Lexiang Ji Drexel A. Neumann robert J. schmitz Department of Genetics University of Georgia Athens GA 30602 USA Institute of Bioinformatics University of Georgia Athens GA 30602 USA These authors contributed equally to this article.

DNA methylation is a key chromatin modification in plant genomes that is meiotically and mitotically her- itable, and at times is associated with gene expression and morphological variation. Benefiting from the increased availability of high-quality reference genome assemblies and methods to profile single-base res- olution DNA methylation states, DNA methylomes for many crop species are available. These efforts are making it possible to begin answering crucial questions, including understanding the role of DNA methyl- ation in developmental processes, its role in crop species evolution, and whether DNA methylation is dynamically altered and heritable in response to changes in the environment. These genome-wide maps provide evidence for the existence of silent epialleles in plant genomes which, once identified, can be tar- geted for reactivation leading to phenotypic variation.

关键词： epigenomics DNA methylation whole-genome bisulfite sequencing (WGBS) crops comparativegenomics

A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

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Plant Communications 2022年第4期3卷 72-82页

作者： Xiaoyu Tu Alexandre P.Marand robert J.schmitz Silin Zhong Joint Center for Single Cell Biology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Collaborative Innovation Center of Agri-Seeds School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Department of Genetics University of GeorgiaAthensGA 30602USA State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina

Understanding how cis-regulatory elements facilitate gene expression is a key question in *** advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal ***,the high equipment and reagent costs of commercial systems limit their applications for many *** this study,we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized *** generated chromatin accessibility profiles for 13576 root nuclei with an average of 12784 unique Tn5 integrations per *** of the single-cell assay for transposaseaccessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription,chromatin,and cis-regulatory *** with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin *** anticipate that,by removing cost,instrumentation,and other technical obstacles,this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.

关键词： combinatorial indexing single-cell ATAC-seq epigenome

Way to grow:in search of genes that makes plants stand out in a crowd

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Way to grow:in search of genes that makes plants stand out i...

Predicting the coefficient of friction in a sliding contact by applying machine learning to acoustic emission data

2013全国植物生物学大会

作者： LI Lin Ullas PEDMALE robert schmitz Kazumasa NITO Benjamin COLE Joseph ECKER Joanne CHORY State Key Laboratory of Genetic Engineering and Institute of Plant Biology School of Life SciencesFudan University Plant Biology Laboratory The Salk Institute for Biological StudiesLa JollaCA 92037USA

Plants sense neighbor proximity as a decrease in the red to far-red ratio of incoming light,which triggers a series of developmental responses known collectively as the "shade avoidance syndrome"(SAS).In Arabidopsis thalianu,phytochrome B is the major sensor of shade light,but to date phytochrome excitation has not been linked directly to a growth response. We show that the bHLH transcription factor,PIF7,previously shown to interact with phytochrome B,accumulates in its dephosphorylated form in shade,allowing it to bind to the promoters of a subset of auxin biosynthetic genes and increase their *** new auxin is required for changes in growth in the shade,our studies link directly the perception of a light quality signal to a rapid growth *** are also working on a most shade induced gene PIL1 and find PIL1 protein accumulates after shade treatment and PIL1 overexpression attenuates expression of many shade-induced ***,PIL1 protein represses PIL1 expression to form a self-limiting feedback ***,PIL1 is a negative regulator of the shade-induced transcriptional response in Arabidopsis.

关键词： shade avoidance response hypocotyl elongation bHLH transcription factor Arabidopsis thaliana

来源： cnki会议评论

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Friction 2024年第6期12卷 1299-1321页

作者： robert GUTIERREZ Tianshi FANG robert MAINWARING Tom REDDYHOFF Tribology Group Department of Mechanical EngineeringImperial College LondonExhibition RoadLondon SW72AZUK Shell Global Solutions(US)Inc.Shell Technology Center Houston 3333 Highway 6 SouthHoustonTX 77082USA Shell International Petroleum Company Limited Shell CentreYork RoadLondon SE17NAUK

It is increasingly important to monitor sliding interfaces within machines,since this is where both energy is lost,and failures *** emission(AE)techniques offer a way to monitor contacts remotely without requiring transparent or electrically conductive ***,acoustic data from sliding contacts is notoriously complex and difficult to ***,we simultaneously measure coefficient of friction(with a conventional force transducer)and acoustic emission(with a piezoelectric sensor and high acquisition rate digitizer)produced by a steel‒steel rubbing *** data is then used to train machine learning(ML)algorithms(e.g.,Gaussian process regression(GPR)and support vector machine(SVM))to correlated acoustic emission with *** training requires the dense AE data to first be reduced in size and a range of processing techniques are assessed for this(e.g.,down-sampling,averaging,fast Fourier transforms(FFTs),histograms).Next,fresh,unseen AE data is given to the trained model and the resulting friction predictions are compared with the directly measured *** is excellent agreement between the measured and predicted friction when the GPR model is used on AE histogram data,with root mean square(RMS)errors as low as 0.03 and Pearson correlation coefficients reaching ***,predictions remain accurate despite changes in test conditions such as normal load,reciprocating frequency,and stroke *** paves the way for remote,acoustic measurements of friction in inaccessible locations within machinery to increase mechanical efficiency and avoid costly failure/needless maintenance.

关键词： acoustic emission condition monitoring friction machine learning Gaussian process regression support vector machine

A general mirror equivalence theorem for coset vertex operator algebras

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Science China Mathematics 2024年第10期67卷 2237-2282页

作者： robert McRae Yau Mathematical Sciences Center Tsinghua UniversityBeijing 100084China

We prove a general mirror duality theorem for a subalgebra U of a simple conformal vertex algebra A and its commutant V=ComA(U).Specifically,we assume that A≌■_(i∈I)U_(i)■V_(i) as a U■V-module,where the U-modules Uiare simple and distinct and are objects of a semisimple braided ribbon category of Umodules,and the V-modules Viare semisimple and contained in a(not necessarily rigid) braided tensor category of *** also assume U=ComA(V).Under these conditions,we construct a braid-reversed tensor equivalence τ:u_(A)→v_(A),where u_(A)is the semisimple category of U-modules with simple objects Ui,i∈I,and v_(A)is the category of V-modules whose objects are finite direct sums of *** particular,the V-modules Viare simple and distinct,and v_(A)is a rigid tensor *** an application,we find a rigid semisimple tensor subcategory of modules for the Virasoro algebra at central charge 13+6p+6p^(-1),p∈Z_(≥2), which is braided tensor equivalent to an abelian 3-cocycle twist of the category of finite-dimensional ***,the Virasoro vertex operator algebra at central charge 13+6p+6p^(-1)is the PSL_(2)(C)-fixed-point subalgebra of a simple conformal vertex algebra w(-p),analogous to the realization of the Virasoro vertex operator algebra at central charge 13-6p-6p^(-1)as the PSL_(2)(C)-fixed-point subalgebra of the triplet algebra W(p).

关键词： vertex operator algebras coset conformal eld theory braid-reversed tensor equivalence Virasoro algebra

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Necrotic enteritis and antibiotic-free production of broiler chickens:Challenges in testing and using alternative products

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Animal Nutrition 2024年第1期16卷 288-298页

作者： robert J.Moore School of Science RMIT University

The global trend towards raising broiler chickens without the use of in-feed antibiotics(IFAs) means that there is an ongoing need to develop alternative treatments capable of delivering the benefits that IFAs previously provided. IFAs supported the productivity performance of chickens and played a key role in maintaining their health. Necrotic enteritis(NE) is an important disease of broilers that affects health,productivity, and welfare, and was previously well controlled by IFAs. However, with the reduction in IFA use, NE is resurgent in some countries. Vaccines and various feed additives, including pre-, pro-, and postbiotics, phytobiotics, fatty acids, and phage therapies have been introduced as alternative methods of NE control. While some of these feed additives have specific activity against the NE pathogen, Clostridium perfringens, most have the more general goal of reinforcing gut health. Extensive reviews of the effects of many of these feed additives on gut health have been published recently. Hence, rather than cover previously well reviewed areas of research this review focuses on the challenges and pitfalls in undertaking experimental assessment of alternative NE treatments and translating laboratory research to real world commercial production settings. The review is based on the author's particular experience,reading, thoughts, and analysis of the available information and inevitably presents a particular understanding that is likely to be at odds with others thinking on these issues. It is put forward to stimulate thinking and discussion on the issues covered.

关键词： Necrotic enteritis Clostridium perfringens Vaccines Feed additive Farm management

利用虚拟许用值计算计算加快航空CFRP材料开发和认证

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纤维复合材料 2019年第4期36卷 53-56页

作者：杜伟卓 robert schmitz Joe Sharp Pierre Yves Lavertu Anthony Cheruet 华敏翰尊国际广场中国上海市200050 Axis园区比利时圣吉贝尔B-1435蒙

在轻量化解决方案的研究中,CFRP的使用在过去几十年中急剧增加,目前约占新型商用飞机所用材料的50%。然而,设计师们仍然面临着加速引入新材料体系以用于实际应用的挑战。主要挑战之一是缩短材料认证时间,然而材料认证时间仅依赖于实验... 详细信息

在轻量化解决方案的研究中,CFRP的使用在过去几十年中急剧增加,目前约占新型商用飞机所用材料的50%。然而,设计师们仍然面临着加速引入新材料体系以用于实际应用的挑战。主要挑战之一是缩短材料认证时间,然而材料认证时间仅依赖于实验程序。从全球范围来看,以数字形式进行材料定义和认证来满足平台要求的方法成为一种趋势。这种方法可以过用高级仿真取代手工测试来降低新材料的成本和开发时间。本文提出并加以描述一个全面的仿真方法。此方法能够定义一个完整的测试矩阵,以便生成给定材料系统的B基准许用值。该方法的实施必须考虑几个方面。第一个方面涉及材料建模以及强度和失效行为。这种建模方式结合了通过平均场均质化推导出的细观力学模型与从材料本构和微观结构描述和渐进失效中得出非线性复合属性。第二个方面考虑需要定义的测试矩阵,此方面可以涵盖铺层定义、待仿真测试类型和环境条件。有限元模型将按照相应条件生成。最后一个方面考虑了在不确定性定量方法下由参数分散度导致的材料敏感性。平均场均质化提供了一种方法,用于从材料属性(硬度和强度组成特性)、制造过程(纤维分数、空隙)和测试条件的变化(纤维方向不对中)来研究复合材料分散度的来源。具体的复合材料试片示例将说明此流程,可以在UD或woven增强聚合物的完整虚拟测试后生成B基准许用值。该过程完全集成于DIGIMAT软件包中。

关键词： CFRP Digimat 平均场均质化虚拟测试 B-basis许用值

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A detailed rock density model of the Hong Kong territories

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Geodesy and Geodynamics 2024年第1期15卷 75-81页

作者： Albertini Nsiah Ababio robert Tenzer Department of Land Surveying and Geo-Informatics Hong Kong Polytechnic UniversityHong KongChina

We used the geological map and published rock density measurements to compile the digital rock density model for the Hong Kong *** then estimated the average density for the whole *** to our result,the rock density values in Hong Kong vary from 2101 to 2681 kg·m^(-3).These density values are typically smaller than the average density of 2670 kg·m^(-3),often adopted to represent the average density of the upper continental crust in physical geodesy and gravimetric geophysics *** finding reflects that the geological configuration in Hong Kong is mainly formed by light volcanic formations and lava flows with overlying sedimentary deposits at many locations,while the percentage of heavier metamorphic rocks is very low(less than 1%).This product will improve the accuracy of a detailed geoid model and orthometric heights.

关键词： Density model Rock types Gravimetric modeling Hong Kong

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