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Amplitude-mode spectroscopy of chemically injected and photogenerated charge carriers in semiconducting single-walled carbon nanotubes

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Nano Research 2023年第4期16卷 5619-5625页

作者： Shai R。Vardeny alan phillips Kira A。Thurman ZValy Vardeny Jeffrey L.Blackburn Division of Electrical Electronicand Infocommunications EngineeringOsaka University2-1 Yamada-okaSuitaOsaka 565-0871Japan Materials Chemistryand Computation Science DirectorateNational Renewable Energy LaboratoryGoldenCO 80401USA Department of Physics Colorado School of MinesGoldenCO 80401USA Department of Physics&Astronomy University of UtahSalt Lake CityUT 84112USA

In one-dimensional semiconductors such as conjugated polymers and semiconducting single-walled carbon nanotubes(s-SWCNTs),injected charge carriers(electrons or holes)can have profound impacts on both electronic conductivity and optical spectra,even at low carrier *** charge-related spectral features is a key fundamental challenge with important technological ***,we employ a systematic suite of experimental and theoretical tools to understand the mid-infrared charge signatures of heavily p-type doped polymer-wrapped *** a broad range of nanotube diameters,we find that hole charge carriers induce strong Fano anti-resonances in mid-infrared transmission spectra that correspond to defect-related(D-band)and in-plane tangential(G-band)Raman-active vibrational modes,along with antiresonances arising from infrared(IR)-active polymer and SWCNT *** employ^(13)C isotope-labeled s-SWCNTs and a removable wrapping polymer to clarify the relative intensities,energies,and sources of all observed *** performed with the“amplitude mode model”are used to quantitatively reproduce Raman spectra and also help to explain the outsized intensity of the D-band anti-resonance,relative to the G-band,observed for both moderately and degenerately doped *** results provide a framework for future studies of ground-and excited-state charge carriers in s-SWCNTs and a variety of low-dimensional materials.

关键词： carbon nanotubes doping charge carriers phonons electron-phonon coupling

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Feasibility of a finger prick-based self-testing kit in first- and second-degree relatives of children with coeliac disease

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World Journal of Gastroenterology 2011年第14期17卷 1840-1843页

作者： Judith Pichler Matthias Zilbauer Franco Torrente Robert Heuschkel alan phillips Camilla Salvestrini Department of Paediatrics and Adolescent Medicine Medical University of Vienna1090 ViennaAustria Department of Paediatric Gastroenterology Addenbrooke's HospitalCambridge CB2 0QQUnited Kingdom Centre for Paediatric Gastroenterology Royal Free HospitalLondon NW3 2QGUnited Kingdom

AIM:To assess feasibility of a finger prick-based kit as method for self-testing of first and second-degree relatives of coeliac disease (CD) patients. METHODS:A total number of 379 subjects were invited to participate in this study,consisting of 197 first- degree and 182 second-degree relatives of CD patients. The self-testing kit (BiocardTM) was sent out with included instructions for use. Completed tests were sent back to the study coordinator for assessment. RESULTS:One hundred and ninety-six invited relatives carried out the BiocardTM test at home. Amongst these,70% were children. In 97% of the cases the test was performed correctly. Three tests revealed a positive result,all of which were later confirmed by serology and histology as coeliac ***:Our study indicates that BiocardTM test is a reliable,easy to use and well-accepted tool for home testing of first- and second-degree relatives of CD patients.

关键词： Coeliac disease Self-testing kit Second-degree relatives

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Using divergence times in fungal classification

Using divergence times in fungal classification

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多彩菌物美丽中国——中国菌物学会2019年学术年会

作者： Jian-Kui Liu Sheng-Nan Zhang alan phillips Milan C.Samarakoon Kevin D.Hyde School of Life Science and Technology University of Electronic Science and Technology of China Chiang Mai University Center of Excellence in Fungal Research Mae Fah Luang University Biosystems and Integrative Sciences Institute Universidade de Lisboa

The current classification system for the recognition of taxonomic ranks among fungi, especially at highranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split;and Pleosporales, the largest order of Dothideomycetes contains 55 families, to establish family divergence times. We have assembled a multi-gene data set（LSU, SSU, TEF1 and RPB2） from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times（crown age） for most orders（20 out of 32, or 63%） are between 100 and 220 Mya, while divergence times for most families（39 out of 55, or 71%）) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi（Liu et al 2017）. A new family Striatiguttulaceae was introduced based on morphology and phylogeny, and the divergence times was used to justify its family level in Pleosporales（Zhang et al 2019）. Fami

关键词： Ascomycota1 Classification2 Divergence times3 Dothideomycetes4 Phylogeny5 Taxonomy6

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Diversity of Endophytic Diaporthe associated with Citrus grandis cv“Tomentosa”in China

Diversity of Endophytic Diaporthe associated with Citrus gra...

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中国植物病理学会2021年学术年会

作者：董章勇 MANAWASINGHE Ishara Sandeepani HUANG Yinghua SHU Yongxin phillips alan John Lander DISSANAYAKE Asha Janadaree HYDE Kevin David XIANG Meimei 罗梅 Innovative Institute for Plant Health Zhongkai University of Agriculture and Engineering Center of Excellence in Fungal Research Mae Fah Luang University Faculdade de Ciencias Biosystems and Integrative Sciences Institute(BioISI)Universidade de Lisboa School of Life Sciences and Technology University of Electronic Science and Technology of China

Diaporthe species are associated with Citrus as endophytes,pathogens,and saprobes ***,little is known about Diaporthe as endophytes in Citrus grandis in *** this study,24 endophytic Diaporthe isolates were obtained from cultivated *** cv."Tomentosa" in Huazhou,Guangdong Province in *** nuclear ribosomal internal transcribed spacer（ITS）,partial sequences of translation elongation factor 1-a（tef1）,b-tubulin（tub2）,and partial calmodulin（cal） gene regions were sequenced and employed to construct phylogenetic *** on morphology and combined multigene phylogeny,eleven Diaporthe species were identified including two new species,Diaporthe endocitricola and *** are the first report of ***,***,***,***,***,***,***,***,and *** on *** study provides the first intensive study of endophytic Diaporthe species on *** *** in *** results will improve the current knowledge of Diaporthe species associated with *** results obtained in this study will also help to understand the potential pathogens and biocontrol agents and to develop a platform in disease management.

关键词： new host records new species Diaporthales phylogeny taxonomy

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Ranking higher taxa using divergence times-a case study in Dothideomycetes

Ranking higher taxa using divergence times-a case study in D...

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中国菌物学会第七届全国会员代表大会暨2017年学术年会

作者： Jian-Kui Liu Kevin D Hyde Rajesh Jeewon alan JL phillips Sajeewa S.N.Maharachchikumbura Martin Ryberg Zuo-Yi Liu Qi Zhao Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Guizhou Institute of Biotechnology Guizhou Academy of Agricultural Sciences Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural Sciences Center of Excellence in Fungal Research Mae Fah Luang University Departmental of Health Sciences Faculty of Science University of Mauritius University of Lisbon Faculty of Sciences Biosystems and Integrative Sciences Institute Department of Crop Sciences College of Agricultural and Marine Sciences Sultan Qaboos University Department of Organismal Biology Uppsala University

The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split;and Pleosporales, the largest order of Dothideomycetes contains 55 families,to establish family divergence times. We have assembled a multi-gene data set（LSU, SSU, TEF1 and RPB2）from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times（crown age） for most orders（20 out of 32, or 63%） are between 100 and 220 Mya, while divergence times for most families（39 out of 55, or 71%）) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesnerio

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Families in Botryosphaeriales:aphylogenetic,morphological and evolutionary perspective

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Fungal Diversity 2019年第1期94卷 1-22页

作者： alan J.L.phillips Kevin D.Hyde Artur Alves Jian-Kui(Jack)Liu Faculdade de Ciencias Biosystems and Integrative Sciences Institute(BioISI)Universidade de LisboaCampo Grande1749-016 LisbonPortugal Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Departamento de Biologia CESAMUniversidade de Aveiro3810-193 AveiroPortugal Guizhou Institute of Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China

Botryosphaeriales was introduced in 2006 for a single family *** then the number of families has increased as a result of the transfer of one family(Planistromellaceae)into the order,re-instatement of another(Phyllostictaceae),while others resulted from raising genera to family status(Aplosporellaceae,Endomelanconiopsisaceae,Melanopsaceae,Pseudofusicoccumaceae,Saccharataceae and Septorioideaceae).All these decisions were based solely on phylogenetic analyses of several different *** has been no consensus on which loci are suitable markers at this taxonomic level and in some cases the datasets used to construct the phylogenies were *** this paper,the families of Botryosphaeriales were re-assessed in terms of morphology of the sexual morphs,phylogenetic relationships based on ITS and LSU sequence data,and evolutionary divergence times of lineages in relation to major events in the evolution of their hosts on a geological *** main lineages were resolved in the phylogenetic analyses and these correspond to six groups as defined on morphology of the sexual *** lineages evolved during the Late epoch of the Cretaceous period and survived the catastrophic event that led to the mass extinction of non-avian dinosaurs and a great loss of plant diversity at the end of the Cretaceous *** then diversified during the Paleocene and Eocene epochs of the Paleogene *** six lineages are considered to represent families in ***,six families(Aplosporellaceae,Botryosphaeriaceae,Melanopsaceae,Phyllostictaceae,Planistromellaceae and Saccharataceae)are accepted in Botryosphaeriales,while three(Endomelanconiopsisaceae,Pseudofusicoccumaceae and Septorioideaceae)are reduced to synonymy under existing families.

关键词： Classification Dothideomycetes Evolutionary divergence times Morphology

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Ranking higher taxa using divergence times:a case study in Dothideomycetes

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Fungal Diversity 2017年第3期84卷 75-99页

作者： Jian-Kui Liu Kevin D.Hyde Rajesh Jeewon alan J.L.phillips Sajeewa S.N.Maharachchikumbura Martin Ryberg Zuo-Yi Liu Qi Zhao Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Guizhou Institute of Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Departmental of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius University of Lisbon Faculty of SciencesBiosystems and Integrative Sciences InstituteCampo Grande1749-016 LisbonPortugal Department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityPO Box 8123 Al KhoudOman Department of Organismal Biology Uppsala UniversityNorbyvägen 18D75236 UppsalaSweden

The current classification system for the recognition of taxonomic ranks among fungi,especially at highranking level,is *** the development of molecular approaches and the availability of fossil calibration data,the use of divergence times as a universally standardized criterion for ranking taxa has now become *** can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of *** chose Dothideomycetes,the largest class of the phylum Ascomycota,which contains 32 orders,to establish ages at which points orders have split;and Pleosporales,the largest order of Dothideomycetes with 55 families,to establish family divergence *** have assembled a multi-gene data set(LSU,SSU,TEF1 and RPB2)from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes *** separated datasets were analysed:(i)272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis,and(ii)191 taxa representing 55 families of Pleosporales were included for the family level *** results indicate that divergence times(crown age)for most orders(20 out of 32,or 63%)are between 100 and 220 Mya,while divergence times for most families(39 out of 55,or 71%)are between 20 and 100 *** believe that divergence times can provide additional evidence to support establishment of higher level taxa,such as families,orders and *** advantage of this added approach,we can strive towards establishing a standardized taxonomic system both within and outside *** this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders,namely Bezerromycetales and Wiesneriomycetales and these are treated as sy

关键词： BEAST Clade age Classification Calibration Family Order Phylogeny Pleosporales

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Botryosphaeria, Neofusicoccum, Neoscytalidium and Pseudofusicoccum species associated with mango in Brazil

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Fungal Diversity 2013年第4期61卷 195-208页

作者： Marília W.Marques Nelson B.Lima Marcos A.de Morais Jr Sami J.Michereff alan J.L.phillips Marcos P.S.Câmara Departamento de Agronomia Universidade Federal Rural de Pernambuco52171-900 RecifeBrazil Departamento de Genética Universidade Federal de Pernambuco50732-970 RecifeBrazil Centro de Recursos Microbiológicos Departamento de Ciências da VidaFaculdade de Ciências e TecnologiaUniversidade Nova de Lisboa2829-516 CaparicaPortugal

Members of the Botryosphaeriaceae are well known fungi associated with dieback,canker and fruit rot on various hosts worldwide,including *** aim of this study was identify a large collection of Botryosphaeriaceae species associated with dieback and stem-end rot of mango in the semi-arid region of Northeastern Brazil,and compare the species in relation to mycelial growth,pathogenicity and virulence.A total of 115 isolates were sampled and based on morphology and DNA sequence data(ITS and EF1-α)seven taxa were identified,namely,Botryosphaeria dothidea,***,Fusicoccum fabicercianum,Neofusicoccum parvum,*** ***,Neoscytalidium dimidiatum and Pseudofusicoccum *** and *** were the most commonly isolated species,which represented 37%and 33%of all isolates *** is reported for the first time in association with mango diseases *** were significant differences among the species obtained in this study in relation to optimum temperature for mycelial growth and mycelial growth *** species were pathogenic on mango *** were significant differences in virulence among the species,with *** and *** being the most virulent species,while *** was the least virulent.

关键词： Botryosphaeriaceae Dieback Stem-end rot Mangifera indica Pathogenicity Virulence Phylogeny

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Microfungi on Tamarix

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Fungal Diversity 2017年第1期82卷 239-306页

作者： Kasun M.Thambugala Dinushani A.Daranagama alan J.L.phillips Timur S.Bulgakov Darbhe J.Bhat Erio Camporesi Ali H.Bahkali Prapassorn D.Eungwanichayapant Zuo-Yi Liu Kevin D.Hyde Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouPeople’s Republic of China Centre of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing 100101People’s Republic of China Faculty of Sciences Biosystems and Integrative Sciences Institute(BioISI)University of LisbonCampo Grande1749-016 LisbonPortugal Academy of Biology and Biotechnology Southern Federal UniversityRostov-on-Don344090 Rostov RegionRussia Formerly Department of Botany Goa UniversityGoaIndia Curca No.128/1–JAzad Housing SocietyGoa VelhaIndia A.M.B.Gruppo Micologico ForliveseBAntonio Cicognani^ Via Roma 18ForlìItaly A.M.B.Circolo Micologico BGiovanni Carini^ C.P.314BresciaItaly Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia

Tamarix species are small trees that grow in various natural habitats and have a wide geographic *** species previously found on Tamarix and recently collected in Italy and Russia were identified based on morphological characters and analyses of gene sequence *** sexual morph of the coelomycetous genus Homortomyces was collected for the first time and is described and illustrated.A new family,Homortomycetaceae(Dothideomycetes,families incertae sedis)is introduced to accommodate *** new genera Neomicrosphaeropsis(Didymellaceae)and Tamaricicola(Pleosporaceae)are introduced in this *** tamaricicola was recollected and is placed in Neomicrosphaeropsis based on morphology and molecular *** new species,Cytospora italica,***,Diaporthe ravennica,Eutypella tamaricis,Neomicrosphaeropsis italica,***,***,Keissleriella tamaricicola,Paracamarosporium tamaricis and Tamaricicola muriformis are introduced,while Alternaria tenuissima,Dothiorella sarmentorum,Neofusicoccum luteum,Paraepicoccum amazonense,Pleospora herbarum and Pseudocamarosporium propinquum are reported for the first time on Tamarix *** descriptions and ***-gene analyses show that Paraepicoccum amazonense should be placed in Pleosporineae,Pleosporales,where it is closely related to Camarosporium sensu *** herbarium specimens were studied to illustrate other fungal species recorded on Tamarix species.A comprehensive account of microfungi on Tamarix is provided,which includes a list with data from the literature,as well as those identified in the present *** taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data.

关键词： Dothideomycetes Homortomycetaceae Incertae sedis New species Phylogeny Pleosporales Sordariomycetes Tamaricaceae Taxonomy

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Defining a species in fungal plant pathology:beyond the species level

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Fungal Diversity 2021年第4期109卷 267-282页

作者： Ishara S.Manawasinghe alan J.L.phillips Jianping Xu Abhaya Balasuriya Kevin D.Hyde Łukasz Stępień Dulanjalee L.Harischandra Anuruddha Karunarathna Jiye Yan Janith Weerasinghe Mei Luo Zhangyong Dong Ratchadawan Cheewangkoon Innovative Institute for Plant Health Zhongkai University of Agriculture and EngineeringGuangzhou 510225People’s Republic of China Faculdade de Ciências Biosystems and Integrative Sciences Institute(BioISI)Universidade de LisboaCampo Grande1749-016 LisbonPortugal Department of Biology McMaster University1280 Main St.WestHamiltonON L8S 4K1Canada Department of Plant Science Faculty of AgricultureRajarata University of Sri LankaAnuradhapuraSri Lanka Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang RaiThailand Institute of Plant Genetics Polish Academy of SciencesPoznańPoland Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai University50200Chiang MaiThailand School of Chemistry and Physics Queensland University of Technology2George StreetBrisbaneQLD 4000Australia

In plant pathology,the correct naming of a species is essential for determining the causal agents of *** names not only serve the general purpose of concise communication,but also are critical for effective plant quarantine,prevent-ing the introduction of new pathogens into a *** phytopathogenic genera have multiple species and,in several genera,disagreements between the multiple prevailing species concept definitions result in numerous cryptic *** of these species were previously called by various names;forma speciales(specialised forms),subspecies,or ***,based on new molecular evidence they are being assigned into new *** frequent name changes and lack of consistent criteria to delineate cryptic species,species,subspecies,forms,and races create increasing confusion,often making communication among biologists ***,such ambiguous information can convey misleading evo-lutionary concepts and species *** aim of this paper is to review these concepts,clarify their use,and evaluate them by referring to existing *** specifically address the question,“Do plant pathogens require a different ranking system?”We conclude that it is necessary to identify phytopathogens to species level based on data from multiple ***,this identification must go beyond species level to clearly classify hitherto known subspecies,forms and *** addition,when naming phytopathogenic genera,plant pathologists should provide more information about geographic locations and host ranges as well as host specificities for individual species,cryptic species,forms or *** describing a new phytopathogen,we suggest that authors provide at least three representative strains together with pathogenicity test *** Koch’s postulates cannot be fulfilled,it is necessary to provide complementary data such as associated disease severity on the host ***,more sequenced collections of spec

关键词： Cryptic species Forms Fungal nomenclature New pathogen Species concepts Subspecies Races

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