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Towards standardizing taxonomic ranks using divergence times-a case study for reconstruction of the Agaricus taxonomic system

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Fungal Diversity 2016年第3期78卷 239-292页

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li jean-marc moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in Fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada Department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S 3B2Canada Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunming 650201China INRA-UR1264 Mycologie et Sécuritédes AlimentsCS 2003233882 Villenave d’Ornon cedexFrance Avda.Padre Claret n°7 5°G09400 Aranda de DueroBurgosSpain

The recognition of taxonomic ranks in the Linnean classification system is largely *** authors have proposed the use of divergence time as a universally standardized ***(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial *** studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional *** this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and *** monophyletic groups were recognized,but most basal relationships were *** hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence *** times within the multi-gene phylogeny were estimated using BEAST *** on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic *** propose to segregate Agaricus into five subgenera and 20 *** Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are *** Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are *** Laeticolores is placed in the subgenus Minores and sections Rarolen

关键词： Agaricaceae Divergence times Multi-gene phylogenetics Systematics Taxonomy

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Bound and Resonating Multiquark Configurations

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Chinese Physics Letters 2024年第8期41卷 8-12页

作者： jean-marc Richard Institut de Physique des 2 Infinis de Lyon Université Claude Bernard(Lyon 1) CNRS-IN2P34 rue Enrico Fermi69622 VilleurbanneFrance

We review the predictions of quark models for multiquark configurations that are bound or resonant states,and compare different methods for estimating the properties of resonances.

关键词： quark Configuration resonant

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A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective

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Fungal Diversity 2017年第3期84卷 43-74页

作者： Rui-Lin Zhao Guo-Jie Li Santiago Sanchez-Ramirez Matt Stata Zhu-Liang Yang Gang Wu Yu-Cheng Dai Shuang-Hui He Bao-Kai Cui Jun-Liang Zhou Fang Wu Mao-Qiang He jean-marc moncalvo Kevin D.Hyde State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesChaoyang DistrictBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408China Department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S 3B2Canada Department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina

In this paper,we provide a phylogenetic overview of Basidiomycota and related phyla in relation to ten years of DNA based phylogenetic studies since the AFTOL publications in *** selected 529 species to address phylogenetic relationships of higher-level taxa using a maximumlikelihood framework and sequence data from six genes traditionally used in fungal molecular systematics(nrLSU,nrSSU,5.8S,tef1-a,rpb1 and rpb2).These species represent 18 classes,62 orders,183 families,and 392 genera from the phyla Basidiomycota(including the newly recognized subphylum Wallemiomycotina)and Entorrhizomycota,and 13 species representing 13 classes of Ascomycota as outgroup *** also conducted a molecular dating analysis based on these six genes for 116 species representing 17 classes and 54 orders of Basidiomycota and *** we performed a phyloproteomics analysis from 109 Basidiomycota species and 6 outgroup taxa using amino-acid sequences retrieved from 396 orthologous *** of higher taxa follows the criteria in Zhao et al(Fungal Divers 78:239–292,2016):(i)taxa must be monophyletic and statistically well-supported in molecular dating analyses,(ii)their respective stem ages should be roughly equivalent,and(iii)stem ages of higher taxa must be older than those of lower level *** time-tree indicates that the mean of stem ages of Basidiomycota and Entorrhizomycota are ca.530 Ma;subphyla of Basidiomycota are 406–490 Ma;most classes are 358–393 Ma for those of Agaricomycotina and 245–356 Ma for those of Pucciniomycotina and Ustilaginomycotina;most orders of those subphyla split 120–290 *** of most higherlevel taxa of Basidiomycota are generally supported,especially those taxa introduced in the recent ten years:phylum Entorrhizomycota,classes Malasseziomycetes,Moniliellomycetes,Spiculogloeomycetes,Tritirachiomycetes and orders Amylocorticiales,Golubeviales,Holtermanniales,Jaapiales,Lepidostromatales,Robbauerales,Stereopsidales and Tricho

关键词： Fungi Systematics Taxonomy Wallemiomycotina

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Populism as a Crisis of Democratic Legitimacy:With Some References to France and the United States

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Fudan Journal of the Humanities and Social Sciences 2024年第2期17卷 193-209页

作者： jean-marc Coicaud Law and Global Affairs Rutgers UniversityRutgersUSA Fudan Institute for Advanced Study in Social Sciences ShanghaiChina

Populism combines the following characteristics:a rejection of economic policies linked to globalization;a condemnation of political and economic elites perceived as allied,directly or indirectly,to globalization policies;a nationalist conception of the national interest;a mistrust of immigration,seen as a threat to identity;as for populism’s supporters,a rather popular sociological profile,and an electoral profile that tends toward the“hard right”(“droite dure”),without ruling out bridges to the“hard left”(“gauche dure”).Having said this,I propose to defend three theses:populism is not the solution to the problems of the countries where it is developing,whether in France,the United States or elsewhere;it would be dangerous,however,to ignore the crises of which populism is the product;it is essential to take the measure of the problems that favor its emergence and to try to provide answers to them.

关键词： Populism Democratic legitimacy Hard right Hard left

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Divergence times and the reconstruction of a standardized taxonomic system based on multigene sequences:case from the genus Agaricus

Divergence times and the reconstruction of a standardized ta...

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中国菌物学会2015年学术年会

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li jean-marc moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry University Institute of Excellence in Fungal Research Mae Fah Luang University School of Science Mae Fah Luang University Department of Natural History Royal Ontario Museum Department of Ecology and Evolutionary Biology University of Toronto Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences INRA-UR1264 Mycologie et Sécurité des AlimentsCS 2003233882Villenave d'Ornon cedexFrance

the recognition of taxonomic ranks in current systematic and taxonomic research is lacking universally standardized criteria. Now molecular clock methods allow us to estimate divergence times based on multilocus sequences from extant and fossil agaric specimens. Agaricus（Agaricaceae, Agaricales） is a genus that contains many species of high commerial value. Recent research using ITS sequences discovered eleven new phylogenetic lineages. Proper taxonomic recognition and ranking of new lineages is essential to complete the natural systematics in this important group. In this study, we firstly conducted a preliminary ITS-only phylogenetic reconstruction using 745 ITS sequences（nearly 600 ITS sequences are new taxonomic contributions） including 59 from type specimens. Based on the preliminary ITS tree, 114 samples represented species from all twelve previously recognized Agaricus sections and seven of the eleven recently discovered clades were selected for producing LSU, tef-1α, and rpb2 sequences. Then the divergence time of the genus Agaricus and main clades within Agaricus were estamated using BEAST v1.8. Based on a phylogenetic consensus using a combination of multigene sequences genes（ITS, LSU, tef-1α and rpb2） and morphology, we propose a revised taxonomic system of Agaricus that considers the divergence time as a criterion for standardizing taxonomic rank, which can reflect evolutionary time while concomitantly redefining taxonomic groups based on phylogenetic relationships. The genus Agaricus was divided into five subgenera and 20 sections. Subgenera Minores and Spissicaules were created, subgenus Pseudochitonia was substantially emended, and circumscription of the subgenera Agaricus and Flavoagaricus was restricted to the members of sections Agaricus and Arvenses, respectively. Four new sections were created（Rubricosi, Crassispori, Flocculenti, and Amoeni）. Subsections Bohusia and Hondenses were raised to the sectional rank and placed into subgenus Pseudochiton

关键词： Agaricaceae divergence times multigene phylogenetics systematics taxonomy

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Pd_(20)Pt_(20)Cu_(20)Ni_(20)P_(20)高熵金属玻璃的热稳定性和热塑成形性

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稀有金属材料与工程 2024年第1期53卷 1-7页

作者： Cardinal Sandrine Pelletier jean-marc Kato Hidemi 里昂大学里昂国立应用科学学院法国里昂F-69621 东北大学金属材料研究所日本仙台980-8577

采用差示扫描量热法、X射线衍射和热力学分析研究了Pd_(20)Pt_(20)Cu_(20)Ni_(20)P_(20)高熵金属玻璃(HEMG)的热稳定性和热力学性能。结果表明,与其他经典贵金属基金属玻璃相比,Pd_(20)Pt_(20)Cu_(20)Ni_(20)P_(20)HEMG具有相当的性能... 详细信息

采用差示扫描量热法、X射线衍射和热力学分析研究了Pd_(20)Pt_(20)Cu_(20)Ni_(20)P_(20)高熵金属玻璃(HEMG)的热稳定性和热力学性能。结果表明,与其他经典贵金属基金属玻璃相比,Pd_(20)Pt_(20)Cu_(20)Ni_(20)P_(20)HEMG具有相当的性能和鲜明的特点。

关键词：高熵合金金属玻璃热塑性成形结晶

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Hf元素添加对CuZr基非晶合金动态弛豫的影响

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力学学报 2024年第8期56卷 2282-2293页

作者：朱凡邢光辉 jean-marc Pelletier 乔吉超西北工业大学力学与土木建筑学院西安710072 东莞市三航军民融合创新研究院广东东莞523808 INSA-Lyon MATEIS UMR5510F-69621 VilleurbanneFrance

考虑到非晶合金具有独特的无序微观结构,其表现出极为复杂的弛豫动力学特性.动态弛豫行为在非晶合金中普遍存在,深刻理解其机制对于解构非晶合金固有的非均匀微观结构至关重要.少量元素的添加是调控非晶合金微观结构有效手段之一.本研... 详细信息

考虑到非晶合金具有独特的无序微观结构,其表现出极为复杂的弛豫动力学特性.动态弛豫行为在非晶合金中普遍存在,深刻理解其机制对于解构非晶合金固有的非均匀微观结构至关重要.少量元素的添加是调控非晶合金微观结构有效手段之一.本研究以玻璃形成能力良好的Cu_(46)Zr_(47-x)Hf_(x)Al_(7)(x=0,8)非晶合金为模型合金,运用动态力学分析方法研究复模量随频率和温度的变化,进而探究Hf元素取代Zr元素对动态弛豫的影响.在动态力学频率谱中,借助准点缺陷理论阐明非晶合金在玻璃转变温度T_(g)以下处于等构型状态,准点缺陷浓度保持恒定;而在T_(g)以上,准点缺陷浓度随温度的上升呈线性增加.Hf元素的添加会降低玻璃体系等构型状态下的准点缺陷浓度,并抑制原子迁移能力.通过获取连续和离散的弛豫时间分布,直观展示了非晶合金的动力学非均匀性特征.在动态力学温度谱中,Hf元素的引入增加了玻璃体系的混合焓,抑制了β弛豫强度.进一步从内耗角度表明,Hf元素的引入不仅提高了与β弛豫相关的基本结构单元的激活难度,还增加了整个β弛豫过程的激活能.

关键词：非晶合金动态弛豫微合金化准点缺陷微观结构非均匀性

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Pulsed lavage in joint arthroplasty: A systematic review and metaanalysis

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World Journal of Orthopedics 2024年第3期15卷 293-301页

作者： Mohammad Daher Gaby Haykal Marven Aoun marc Moussallem Ali Ghoul jean Tarchichi Amer Sebaaly Department of Orthopedics Saint Joseph UniversityBeirut 1001Lebanon

BACKGROUND Knee and hip osteoarthritis affects millions of people around the world and is expected to rise even more in frequency as the population *** arthroplasty is the surgical management of choice in these *** ossi-fication and radiolucent lines formation are two frequent problems faced in hip and knee replacements *** studies show that the usage of pulsed lavage may prevent their *** To compare pulsed lavage to standard lavage in joint *** PubMed,Cochrane,and Google Scholar(page 1-20)were searched till December *** comparative studies were *** clinical outcomes evaluated were the heterotopic ossification formation in hip replacements,radiolucent lines formation,and functional knee scores in knee *** Four studies met the inclusion criteria and were included in this *** lavage was shown to reduce the formation of radiolucent lines(P=0.001).However,no difference was seen in the remaining outcomes CONCLUSION Pulsed lavage reduced the formation of radiolucent lines in knee *** difference was seen in the remaining ***,the clinical significance of these radiolucent lines is poorly *** conducted randomized controlled studies and cost-effectivity studies are needed to reinforce these findings.

关键词： Knee arthroplasty Hip arthroplasty Pulsed lavage Syringe lavage Heterotopic ossification Radiolucent lines

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Molecular phylogeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales)

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Fungal Diversity 2014年第1期64卷 1-99页

作者： D.jean Lodge Mahajabeen Padamsee P.Brandon Matheny M.Catherine Aime Sharon A.Cantrell David Boertmann Alexander Kovalenko Alfredo Vizzini Bryn T.M.Dentinger Paul M.Kirk A.Martyn Ainsworth jean-marc moncalvo Rytas Vilgalys Ellen Larsson Robert Lücking Gareth W.Griffith Matthew E.Smith Lorelei L.Norvell Dennis E.Desjardin Scott A.Redhead Clark L.Ovrebo Edgar B.Lickey Enrico Ercole Karen W.Hughes Régis Courtecuisse Anthony Young Manfred Binder Andrew M.Minnis Daniel L.Lindner Beatriz Ortiz-Santana John Haight Thomas Læssøe Timothy J.Baroni József Geml Tsutomu Hattori Center for Forest Mycology Research Northern Research StationUSDA-Forest ServiceLuquilloPR 00773-1377USA Systematics Team Landcare Research231 Morrin RoadAuckland 1072New Zealand Ecology&Evolutionary Biology University of TennesseeKnoxvilleTN 37996-1610USA Department of Botany&Plant Pathology Purdue UniversityWest LafayetteIN 47907USA Science and Technology Universidad del TuraboGuraboPR 00778-3030USA Department of Bioscience Aarhus UniversityFrederiksborgvej 399DK-4000 RoskildeDenmark Komarov Botanical Institute of the Russian Academy of Sciences 2 Prof.Popov Str.St.Petersburg 197376Russia Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale P.A.Mattioli 2510125 TorinoItaly Mycology Royal Botanic GardensKewRichmondSurrey TW93DSUK Royal Ontario Museum 100 Queen’s ParkTorontoONCanada Biology Department Duke UniversityDurhamNC 27708-0338USA Biological&Environmental Sciences University of GothenburgGöteborgSweden Science&Eduaction Integrative Research&Collections(Botany)The Field Museum of Natural History1400 Lake Shore Dr.ChicagoIL 60605-2496USA University of Wales AberystwythCeredigion SY233DDUK Department of Plant Pathology University of FloridaGainesvilleFL 32611-0680USA Pacific Northwest Mycology Service 6720 NW Skyline BvdPortlandOR 97229-1309USA Department of Biology San Francisco State University1600 Holloway Ave.San FranciscoCA 94132USA National Mycological Herbarium(DAOM) Science and Technology BranchAgriculture&Agri-FoodsCanada960 Carling AvenueOttawaOntarioCanada ONT K1A 0C6 Department of Biology University of Central OklahomaEdmondOK 73034USA Department of Biology Bridgewater College402 E.College St.BridgewaterVA 22812USA Department of Botany Faculty of Pharmaceutical&Biological SciencesLilleFrance 100 Langton Road BlackbuttQld 4306Australia CBS Fungal Biodiversity Centre Evolutionary PhytopathologyInst.of the Royal Netherlands Academy of Arts&Sciences(KNAW)Uppsalalaan 83584 CT UtrechtThe Netherlands

Molecular phylogenies using 1–4 gene regions and information on ecology,morphology and pigment chemistry were used in a partial revision of the agaric family *** phylogenetically supported genera we recognize here in the Hygrophoraceae based on these and previous analyses are:Acantholichen,Ampulloclitocybe,Arrhenia,Cantharellula,Cantharocybe,Chromosera,Chrysomphalina,Cora,Corella,Cuphophyllus,Cyphellostereum,Dictyonema,Eonema,Gliophorus,Haasiella,Humidicutis,Hygroaster,Hygrocybe,Hygrophorus,Lichenomphalia,Neohygrocybe,Porpolomopsis and Pseudoarmillariella.A new genus that is sister to Chromosera is described as *** were made at the ranks of subfamily,tribe,genus,subgenus,section and *** present three new subfamilies,eight tribes(five new),eight subgenera(one new,one new combination and one ***.),26 sections(five new and three new combinations and two ***.)and 14 subsections(two new,two ***.).Species of Chromosera,Gliophorus,Humidicutis,and Neohygrocybe are often treated within the genus Hygrocybe;we therefore provide valid names in both classification *** used a minimalist approach in transferring genera and creating new names and ***,we retain in the Hygrophoraceae the basal cuphophylloid grade comprising the genera Cuphophyllus,Ampulloclitocybe andCantharocybe,despite weak phylogenetic *** include Aeruginospora and Semiomphalina in Hygrophoraceae based on morphology though molecular data are *** lower hygrophoroid clade is basal to Hygrophoraceae s.s.,comprising the genera Aphroditeola,Macrotyphula,Phyllotopsis,Pleurocybella,Sarcomyxa,Tricholomopsis and Typhula.

关键词： Hygrophoraceae Fungi Revisionary systematics Nomenclatural revision Phylogenetics Pigment chemistry Lamellar trama construction Hymenial morphology Ecology

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Compartmentalization of the inflammatory response during bacterial sepsis and severe COVID-19

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Journal of Intensive Medicine 2024年第3期4卷 326-340页

作者： jean-marc Cavaillon Benjamin G.Chousterman Tomasz Skirecki Institut Pasteur ParisFrance Department of Anesthesia and Critical Care Lariboisière University HospitalDMU ParabolAPHP NordParisFrance Inserm U942 University of ParisParisFrance Department of Translational Immunology and Experimental Intensive Care Centre of Postgraduate Medical EducationWarsawPoland

Acute infections cause local and systemic disorders which can lead in the most severe forms to multi-organ failure and eventually to death. The host response to infection encompasses a large spectrum of reactions with a concomitant activation of the so-called inflammatory response aimed at fighting the infectious agent and removing damaged tissues or cells, and the anti-inflammatory response aimed at controlling inflammation and initiating the healing process. Fine-tuning at the local and systemic levels is key to preventing local and remote injury due to immune system activation. Thus, during bacterial sepsis and Coronavirus disease 2019 (COVID-19), concomitant systemic and compartmentalized pro-inflammatory and compensatory anti-inflammatory responses are occurring. Immune cells (e.g., macrophages, neutrophils, natural killer cells, and T-lymphocytes), as well as endothelial cells, differ from one compartment to another and contribute to specific organ responses to sterile and microbial insult. Furthermore, tissue-specific microbiota influences the local and systemic response. A better understanding of the tissue-specific immune status, the organ immunity crosstalk, and the role of specific mediators during sepsis and COVID-19 can foster the development of more accurate biomarkers for better diagnosis and prognosis and help to define appropriate host-targeted treatments and vaccines in the context of precision medicine.

关键词： Acute respiratory distress syndrome Bone marrow Cytokines Lungs Mucosa Vaccines

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