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Value of a newly sequenced bacterial genome

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World Journal of Biological Chemistry 2014年第2期5卷 161-168页

作者： Eudes GV Barbosa Flavia F Aburjaile Rommel TJ Ramos Adriana R Carneiro Yves Le Loir Jan Baumbach Anderson Miyoshi artur Silva Vasco Azevedo Laboratório de Genética Celular e Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte 31270-901 MG Brazil Department of Mathematics and Computer Science University of Southern Denmark5230 Odense Denmark INRA UMR1253 Science et Technologie du Lait et de l’uf F-35042 Rennes France Laboratório de Polimorfismo de DNA Instituto de Ciências Biológicas Univeridade Federal do Pará Belém 66075-110 Brazil

Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

关键词： Next-generation sequencing Drafts Prokaryotic genomes Computational tools Omics

Fields奖得主artur Avila访谈录

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数学译林 2021年第3期40卷 258-261页

作者： Ulf Persson artur Avila 崔鸿飞(译) 杨小舟(校) 瑞典哥德堡Chalmers理工大学不详

Ulf Persson(以下简写为“UP”):我的标准问题是:您对您获得Fields(菲尔兹)奖感到惊讶吗?它将对您的生活有何影响?artur Avila(以下简写为“AA”):我当然没想到会拿到奖牌.事实上,我认为它更有可能发生在海得拉巴.现在,我知道Maryam Mir... 详细信息

Ulf Persson(以下简写为“UP”):我的标准问题是:您对您获得Fields(菲尔兹)奖感到惊讶吗?它将对您的生活有何影响?artur Avila(以下简写为“AA”):我当然没想到会拿到奖牌.事实上,我认为它更有可能发生在海得拉巴.现在,我知道Maryam Mirzakhani被考虑了.我认为在这种情况下我更不可能被授予Fields奖.

关键词：海得拉巴奖牌访谈录

Improving ITS sequence data for identification of plant pathogenic fungi

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Fungal Diversity 2014年第4期67卷 11-19页

作者： R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad Bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna Friberg Tobias Guldberg Froslev Bettina Halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov Department of Biological and Environmental Sciences University of GothenburgBox 46140530 GothenburgSweden Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Plant Systematics and Geography Faculty of BiologyUniversity of WarsawAl.Ujazdowskie 400-478 WarsawPoland Department of Organismal Biology Uppsala UniversityNorbyvagen 18D75236 UppsalaSweden Institute of Ecology and Earth Sciences University of TartuLai 40Tartu 51005Estonia Microbial Evolution Research Group University of OsloBlindernveien 310371 OsloNorway Institute of Biological Sciences University of Malaya50603 Kuala LumpurMalaysia Department of Biology CESAMUniversity of Aveiro3810-193 AveiroPortugal School of Plant Sciences The University of Arizona1140 E South Campus DriveForbes 303TucsonAZ 85721USA Laboratory of Environmental Microbiology Institute of Microbiology ASCRVídeňská108314220 Prague 4Czech Republic Department of Infectious Diseases Institute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGuldhedsgatan 1041346 GoteborgSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden University of California at Berkeley 321 Koshland Hall University of CaliforniaBerkeleyCA 94720-3102USA Agriculture and Forestry Sciences Beijing 100097China Institute of Forestry and Rural Engineering Estonian University of Life SciencesKreutzwaldi551014 TartuEstonia Natural History Museum of Denmark Øster Voldgade 5-71350 København KDenmark Institute for Genomics and Bioinformatics Graz University of Technology8010 GrazAustria Core Facility Bioinformatics Austrian Centre of Industrial Biotechnology8010 GrazAustria Forest Soils and Biogeochemistry Swiss Federal Research Institute WSLZuercherstrasse 1118903 BirmensdorfSwitzerland Molecular Ecology Institute for Sustainability SciencesAgroscopeReckenholzstrasse 191

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human *** taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro *** a result,species identification is frequently ***(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular ***,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi *** we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological *** results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://***),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related *** present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.

关键词： Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation

Fungal diversity notes 1611-1716: taxonomic and phylogenetic contributions on fungal genera and species emphasis in south China

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Fungal Diversity 2023年第5期122卷 161-403页

作者： Indunil C.Senanayake Walter Rossi Marco Leonardi Alex Weir Mark McHugh Kunhiraman C.Rajeshkumar Rajnish K.Verma Samantha C.Karunarathna Saowaluck Tibpromma Nikhil Ashtekar Sreejith K.Ashtamoorthy Sanjay Raveendran Gurmeet Kour Aishwarya Singh Saúl De la Peña-Lastra Antonio Mateos Miroslav Kolařík Vladimír Antonín HanaŠevčíková Fernando Esteve-Raventós Ellen Larsson Fermín Pancorbo Gabriel Moreno Alberto Altés Yolanda Turégano Tian-Ye Du Li Lu Qi-Rui Li Ji-Chuan Kang Sugantha Gunaseelan Kezhocuyi Kezo Malarvizhi Kaliyaperumal Jizhen Fu Milan C.Samarakoon Yusufjon Gafforov Shakhnoza Teshaboeva Pradeep C.Kunjan Arya Chamaparambath Adam Flakus Javier Etayo Pamela Rodriguez-Flakus Mikhail P.Zhurbenko Nimali Ide Silva Danushka S.Tennakoon KPDeepna Latha Patinjareveettil Manimohan KNAnil Raj Mark S.Calabon Abdollah Ahmadpour Zeinab Heidarian Zahra Alavi Fatemeh Alavi Youbert Ghosta Razmig Azizi Mei Luo Min-Ping Zhao Nuwan D.Kularathnage Li Hua Yun-Hui Yang Chun-Fang Liao Hai-Jun Zhao Anis S.Lestari Subashini C.Jayasiri Feng-Ming Yu Lei Lei Jian-Wei Liu Omid Karimi Song-Ming Tang Ya-Ru Sun Yong Wang Ming Zeng Zin H.Htet Benedetto T.Linaldeddu artur Alves Alan J.L.Phillips Carlo Bregant Lucio Montecchio AndréDe Kesel Vincent P.Hustad Andrew N.Miller Anna G.Fedosova Viktor Kučera Mubashar Raza Muzammil Hussain Yan-Peng Chen Vinodhini Thiyagaraja Deecksha Gomdola Achala R.Rathnayaka Asha J.Dissanayake Nakarin Suwannarach Sinang Hongsanan Sajeewa S.N.Maharachchikumbura Lakmali S.Dissanayake Nalin N.Wijayawardene Rungtiwa Phookamsak Saisamorn Lumyong E.B.Gareth Jones Neelamanie Yapa Dhanushka N.Wanasinghe Ning Xie Mingkwan Doilom Ishara S.Manawasinghe Jian-Kui(Jack)Liu Qi Zhao Biao Xu Kevin D.Hyde Jiage Song Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China Ministry of Agriculture and Rural AffairsZhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225GuangdongChina Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Guangdong Provincial Key Laboratory for Plant Epigenetics College of Life Science and OceanographyShenzhen University3688Nanhai AvenueNanshanShenzhen 518055GuangdongChina Sect.Environmental Sciences Department MeSVAUniversity of L’AquilaVia Vetoio67100 CoppitoAQItaly Department of Environmental Biology SUNY-ESF241 Illick Hall1 Forestry DriveSyracuseNY 13210USA National Fungal Culture Collection of India MACS Agharkar Research InstitutePuneMaharashtra 411004India Department of Plant Pathology Punjab Agricultural UniversityLudhianaPunjab 141004India Center for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujing 655011YunnanChina Department of Forest Ecology Kerala Forest Research InstitutePeechiThrissurKerala 680653India Department of Botany The American CollegeTallakkulamMaduraiTamil Nadu 625002India Department of Zoology Savitribai Phule Pune UniversityGaneshkhind RdGaneshkhindPuneMaharashtra 411007India University of Santiago de Compostela 15782 Santiago de CompostelaSpain Sociedad Micológica Extremeña C/Sagitario 1410001 CáceresSpain Institute of Microbiology of the Czech Academy of Sciences Vídeňská108314220 Prague 4Czech Republic Department of Botany Moravian MuseumZelnýtrh 665937 BrnoCzech Republic Department of Life Sciences(Botany Unit) University of Alcalá28805 Alcaláde HenaresMadridSpain Biological and Enviromental Sciences University of Gothemburgand Gothemburg Global Biodiversity CentreBox 46140530 GöteborgSweden Madrid Mycological Society Real Jardín BotánicoC/Claudio Moyano 128014 MadridSpain State Ke

This article is the 15th contribution in the Fungal Diversity Notes series,wherein 115 taxa from three phyla,nine classes,28 orders,48 families,and 64 genera are *** taxa described and illustrated in the present study include a new family,five new genera,61 new species,five new combinations,one synonym,one new variety and 31 records on new hosts or new geographical *** *** introduced and accommodated in *** new genera introduced in this study are Ageratinicola,Kevinia,Pseudomultiseptospora(Parabambusicolaceae),Marasmiellomycena,and Vizzinia(Porotheleaceae).Newly described species are Abrothallus altoandinus,Ageratinicola kunmingensis,Allocryptovalsa aceris,Allophoma yuccae,Apiospora cannae,***,***,Boeremia wisteriae,Calycina papaeana,Clypeo-coccum lichenostigmoides,Coniochaeta riskali-shoyakubovii,Cryphonectria kunmingensis,Diaporthe angustiapiculata,***,***,Diatrypella guangdongense,Dothiorella franceschinii,Endocalyx phoenicis,Epicoc-cum terminosporum,Fulvifomes karaiensis,***,Ganoderma ghatensis,Hysterobrevium baoshanense,Inocybe avellaneorosea,***,Jahnula oblonga,Kevinia lignicola,Kirschsteiniothelia guangdongensis,Laboulbenia caprina,***,***,***,***,***,***,***,***,Laccaria rubriporus,Lasiodiplodia morindae,Lyophyllum agnijum,Marasmiellomycena pseudoomphaliiformis,Melomastia beihaiensis,Nemania guangdongensis,Nigrograna thailandica,Nigrospora ficuum,Oxydothis chinensis,***,Petriella thailandica,Phaeoacremonium chinensis,Phialocephala chinensis,Phytophthora debattistii,Polyplosphaeria nigrospora,Pronectria loweniae,Seriascoma acutispora,Setoseptoria bambusae,Stictis anomianthi,Tarzetta tibetensis,Tarzetta urceolata,Tetraploa obpyriformis,Trichoglossum beninense,and Tricoderma *** provide an emendation for Urnula ailaoshanensis Agaricus duplocingulatoides *** i

关键词： Agaricomycetes Ascomycota Basidiomycota Dothideomycetes Eurotiomycetes Fungal diversity Geoglossomycetes Geographical distribution Host records Incertae sedis Laboulbeniomycetes Lecanoromycetes Leotiomycetes Novel taxa New combination Oomycota Peronosporea Pezizomycetes Phylogeny Sordariomycetes South Chinese fungi Taxonomy

Sub-percent precision measurement of neutrino oscillation parameters with JUNO

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Chinese Physics C 2022年第12期46卷 28-49页

作者： Angel Abusleme Thomas Adam Shakeel Ahmad Rizwan Ahmed Sebastiano Aiello Muhammad Akram Abid Aleem Fengpeng An Qi An Giuseppe Andronico Nikolay Anfimov Vito Antonelli Tatiana Antoshkina Burin Asavapibhop João Pedro Athayde Marcondes de André Didier Auguste Weidong Bai Nikita Balashov Wander Baldini Andrea Barresi Davide Basilico Eric Baussan Marco Bellato Antonio Bergnoli Thilo Birkenfeld Sylvie Blin David Blum Simon Blyth Anastasia Bolshakova Mathieu Bongrand Clément Bordereau Dominique Breton Augusto Brigatti Riccardo Brugnera Riccardo Bruno Antonio Budano Jose Busto Ilya Butorov Anatael Cabrera Barbara Caccianiga Hao Cai Xiao Cai Yanke Cai Zhiyan Cai Riccardo Callegari Antonio Cammi Agustin Campeny Chuanya Cao Guofu Cao Jun Cao Rossella Caruso Cédric Cerna Chi Chan Jinfan Chang Yun Chang Guoming Chen Pingping Chen Po-An Chen Shaomin Chen Xurong Chen Yixue Chen Yu Chen Zhiyuan Chen Zikang Chen Jie Cheng Yaping Cheng Yu Chin Cheng Alexey Chetverikov Davide Chiesa Pietro Chimenti Artem Chukanov Gérard Claverie Catia Clementi Barbara Clerbaux Selma Conforti Di Lorenzo Daniele Corti Flavio Dal Corso Olivia Dalager Christophe De La Taille Zhi Deng Ziyan Deng Wilfried Depnering Marco Diaz Xuefeng Ding Yayun Ding Bayu Dirgantara Sergey Dmitrievsky Tadeas Dohnal Dmitry Dolzhikov Georgy Donchenko Jianmeng Dong Evgeny Doroshkevich Marcos Dracos Frédéric Druillole Ran Du Shuxian Du Stefano Dusini Martin Dvorak Timo Enqvist Heike Enzmann Andrea Fabbri Donghua Fan Lei Fan Jian Fang Wenxing Fang Marco Fargetta Dmitry Fedoseev Zhengyong Fei Li-Cheng Feng Qichun Feng Richard Ford Amélie Fournier Haonan Gan Feng Gao Alberto Garfagnini Arsenii Gavrikov Marco Giammarchi Nunzio Giudice Maxim Gonchar Guanghua Gong Hui Gong Yuri Gornushkin Alexandre Göttel Marco Grassi Vasily Gromov Minghao Gu Xiaofei Gu Yu Gu Mengyun Guan Yuduo Guan Nunzio Guardone Cong Guo Jingyuan Guo Wanlei Guo Xinheng Guo Yuhang Guo Paul Hackspacher Caren Hagner Ran Han Yang Han Miao He Wei He Tobias Heinz Patrick Hellmuth Yuekun Heng Rafael Herrera YuenKeung Ho Yerevan Physics Institute YerevanArmenia UniversiéLibre de Bruxelles BrusselsBelgium Universidade Estadual de Londrina LondrinaBrazil Pontificia Universidade Catolica do Rio de Janeiro Rio de JaneiroBrazil Pontificia Universidad Católica de Chile SantiagoChile Universidad Tecnica Federico Santa Maria ValparaisoChile Beijing Institute of Spacecraft Environment Engineering BeijingChina Beijing Normal University BeijingChina China Institute of Atomic Energy BeijingChina Institute of High Energy Physics BeijingChina North China Electric Power University BeijingChina School of Physics Peking UniversityBeijingChina Tsinghua University BeijingChina University of Chinese Academy of Sciences BeijingChina Jilin University ChangchunChina College of Electronic Science and Engineering National University of Defense TechnologyChangshaChina Chongqing University ChongqingChina Dongguan University of Technology DongguanChina Jinan University GuangzhouChina Sun Yat-Sen University GuangzhouChina Harbin Institute of Technology HarbinChina University of Science and Technology of China HefeiChina The Radiochemistry and Nuclear Chemistry Group in University of South China HengyangChina Wuyi University JiangmenChina Shandong University JinanChinaand Key Laboratory of Particle Physics and Particle Irradiation of Ministry of EducationShandong UniversityQingdaoChina Institute of Modern Physics Chinese Academy of SciencesLanzhouChina Nanjing University NanjingChina Guangxi University NanningChina East China University of Science and Technology ShanghaiChina School of Physics and Astronomy Shanghai Jiao Tong UniversityShanghaiChina Tsung-Dao Lee Institute Shanghai Jiao Tong UniversityShanghaiChina Institute of Hydrogeology and Environmental Geology Chinese Academy of Geological SciencesShijiazhuangChina Nankai University TianjinChina Wuhan University WuhanChina Xi'an Jiaotong University Xi'anChina Xiamen University XiamenChina School of Physics and Microelectronics Zhengzhou UniversityZhengzhou

JUNO is a multi-purpose neutrino observatory under construction in the south of *** publication presents new sensitivity estimates for the measurement of the △m_(31)^(2),△m_(21)^(2),sin^(2)θ_(12),and sin^(2)θ_(13) oscillation parameters using reactor antineutrinos,which is one of the primary physics goals of the *** sensitivities are obtained using the best knowledge available to date on the location and overburden of the experimental site,the nuclear reactors in the surrounding area and beyond,the detector response uncertainties,and the reactor antineutrino spectral shape constraints expected from the TAO satellite *** is found that the △m_(21)^(2) and sin^(2)θ_(12) oscillation parameters will be determined to 0.5%precision or better in six years of data *** the same period,the △m_(31)^(2) parameter will be determined to about 0.2%precision for each mass ordering *** new precision represents approximately an order of magnitude improvement over existing constraints for these three parameters.

关键词： neutrino oscillation reactor antineutrino precision measurement JUNO