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Deep convolutional neural network for damaged vegetation segmentation from RGB images based on virtual NIR-channel estimation

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Artificial Intelligence in Agriculture 2022年第1期6卷 199-210页

作者： Artzai Picon Arantza Bereciartua-Perez Itziar Eguskiza Javier Romero-Rodriguez Carlos Javier Jimenez-ruiz Till Eggers christian Klukas Ramon Navarra-Mestre TECNALIA Basque Research and Technology Alliance(BRTA)Parque Tecnológico de BizkaiaC/Geldo.Edificio 700E-48160 Derio-BizkaiaSpain University of the Basque Country Plaza Torres Quevedo48013 BilbaoSpain BASF Espanola S.L.Carretera A376 41710 Utrera SevillaSpain BASF SE Speyererstrasse 267117 LimburgerhofGermany

Performing accurate and automated semantic segmentation of vegetation is a first algorithmic step towards more complex models that can extract accurate biological information on crop health,weed presence and phenological state,among ***,models based on normalized difference vegetation index(NDVI),near infrared channel(NIR)or RGB have been a good indicator of vegetation ***,these methods are not suitable for accurately segmenting vegetation showing damage,which precludes their use for downstream phenotyping *** this paper,we propose a comprehensive method for robust vegetation segmentation in RGB images that can cope with damaged *** method consists of a first regression convolutional neural network to estimate a virtual NIR channel from an RGB ***,we compute two newly proposed vegetation indices from this estimated virtual NIR:the infrared-dark channel subtraction(IDCS)and infrared-dark channel ratio(IDCR)***,both the RGB image and the estimated indices are fed into a semantic segmentation deep convolutional neural network to train a model to segment vegetation regardless of damage or *** model was tested on 84 plots containing thirteen vegetation species showing different degrees of damage and acquired over 28 *** results show that the best segmentation is obtained when the input image is augmented with the proposed virtual NIR channel(F1=0:94)and with the proposed IDCR and IDCS vegetation indices(F1=0:95)derived from the estimated NIR channel,while the use of only the image or RGB indices lead to inferior performance(RGB(F1=0:90)NIR(F1=0:82)or NDVI(F1=0:89)channel).The proposed method provides an end-to-end land cover map segmentation method directly from simple RGB images and has been successfully validated in real field conditions.

关键词： Vegetation indices estimation Vegetation coverage map Near infrared estimation Convolutional neural network Deep learning

Modelling Thermo-Electro-Mechanical Effects in Orthotropic Cardiac Tissue

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Communications in Computational Physics 2020年第1期27卷 87-115页

作者： Ricardo ruiz-Baier Alessio Gizzi Alessandro Loppini christian Cherubini Simonetta Filippi Mathematical Institute University of OxfordWoodstock RoadOxford OX26GGUnited Kingdom Laboratory of Mathematical Modelling Institute of Personalised MedicineSechenov UniversityMoscowRussian Federation Nonlinear Physics and Mathematical Modeling Department of EngineeringUniversity Campus Bio-Medico of RomeVia A.del Portillo 2100128RomeItaly International Center for Relativistic Astrophysics(ICRA) and ICRANetPiazza delle Repubblica 10I-65122 PescaraItaly

In this paper we introduce a new mathematical model for the active contraction of cardiac muscle,featuring different thermo-electric and nonlinear conductivity *** passive hyperelastic response of the tissue is described by an orthotropic exponential model,whereas the ionic activity dictates active contraction in-corporated through the concept of orthotropic active *** use a fully incompressible formulation,and the generated strain modifies directly the conductivity mechanisms in the medium through the pull-back *** also investigate the influence of thermo-electric effects in the onset of multiphysics emergent spatiotem-poral dynamics,using nonlinear *** turns out that these ingredients have a key role in reproducing pathological chaotic dynamics such as ventricular fibrillation during inflammatory events,for *** specific structure of the governing equations suggests to cast the problem in mixed-primal form and we write it in terms of Kirchhoff stress,displacements,solid pressure,dimensionless electric potential,activation generation,and ionic *** also advance a new mixed-primal finite element method for its numerical approximation,and we use it to explore the properties of the model and to assess the importance of coupling terms,by means of a few computational experiments in 3D.

关键词： Cardiac electromechanics orthotropic active strain thermo-electric coupling scroll wave propagation numerical simulations

Comparative mitogenome phylogeography of two anteater genera (Tamandua and Myrmecophaga;Myrmecophagidae, Xenarthra): Evidence of discrepant evolutionary traits

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Zoological Research 2021年第5期42卷 525-547页

作者： Manuel ruiz-García Daniel Pinilla-Beltrán Oscar E.Murillo-García christian Miguel Pinto Jorge Brito Joseph Mark Shostell Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva Departamento de BiologíaFacultad de CienciasPontificia Universidad JaverianaBogotáDC 110231Colombia Grupo de Investigación en Ecología Animal Departamento de BiologíaFacultad de Ciencias Naturales y ExactasUniversidad del ValleApartado AéreoCali 25360Colombia Instituto de Ciencias Biológicas Escuela Politécnica NacionalQuito 17012759Ecuador Instituto Nacional de Biodiversidad(INABIO) Quito 170135Ecuador Math Science and Technology DepartmentUniversity of Minnesota CrookstonCrookstonMN 56716USA

The species within Xenarthra(sloths,anteaters,and armadillos)are quintessential South American *** the three groups,Vermilingua(anteaters)contains the fewest extant and paleontological ***,we sampled and sequenced the entire mitochondrial genomes(mitogenomes)of two Tamandua species(Tamandua tetradactyla and ***)(n=74)from Central and South America,as well as Myrmecophaga tridactyla(n=41)from South *** Tamandua,we detected three different *** oldest(THI)contained many specimens with the *** morphotype(but also several with the *** morphotype)and originated in southeastern South America(currently Uruguay)before moving towards northern South America,where the THII haplogroup *** primarily contained specimens with the *** morphotype(but also several with the *** morphotype)and was distributed in Central America,Colombia,and *** and THII yielded a genetic distance of 4%.THII originated in either northern South America or“in situ”in Central America with haplogroup THIII,which consisted of~50%*** and 50%*** *** was mostly located in the same areas as THII,i.e.,Central America,Ecuador,and Colombia,though mainly in the *** three haplogroups overlapped in Colombia and ***,*** and *** were not reciprocally *** this reason,we considered that a unique species of Tamandua likely exists,i.e.,*** contrast to Tamandua,*** did not show different morphotypes throughout its geographical range in the ***,two very divergent genetic haplogroups(MHI and MHII),with a genetic distance of~10%,were *** basal haplogroup,MHI,originated in northwestern South America,whereas the more geographically derived haplogroup,MHII,overlapped with MHI,but also expanded into central and southern South ***,Tamandua migrated from south to north whereas Myrmecophaga migrated from

关键词： Anteaters Genetic diversity Mitogenomes Myrmecophaga Neotropics Phylogeography Spatial structure Tamandua

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Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea(Spix,1823)resolves a taxonomic conundrum

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Zoological Research 2021年第6期42卷 761-771页

作者： Jean P.Boubli Mareike C.Janiak Leila M.Porter Stella de la Torre Liliana Cortes-Ortiz Maria N.Fda Silva Anthony B.Rylands Stephen Nash Fabricio Bertuol Hazel Byrne Felipe E.Silva Fabio Rohe Dorien de Vries Robin M.D.Beck Irune ruiz-Gartzia Lukas F.K.Kuderna Tomas Marques-Bonet Tomas Hrbek Izeni P.Farias Anneke Hvan Heteren christian Roos School of Science Engineering&EnvironmentUniversity of SalfordSalford M54WTUK Instituto Nacional de Pesquisas da Amazonia ManausAmazonas 69060-001Brazil Department of Anthropology Northern Illinois UniversityDeKalbIL 60115-2828USA College of Biological and Environmental Sciences Universidad San Francisco de QuitoQuito 170901Ecuador Department of Ecology and Evolutionary Biology University of MichiganAnn ArborMI 48109USA Re:wild AustinTX 78767USA Laboratorio de Evolução e Genética Animal Universidade Federal do AmazonasManausAmazonas 69080-900Brazil Department of Anthropology University of UtahSalt Lake CityUT 84112USA Research Group on Primate Biology and Conservation MamirauaInstitute for Sustainable DevelopmentTeféAmazonas 69553-225Brazil Experimental and Health Sciences Department(DCEXS) Institut de Biologia EvolutivaUniversitat Pompeu Fabra-CSICBarcelona 08002Spain Department of Biology Trinity UniversitySan AntonioTX 78212USA Bavarian State Collection of Zoology Zoologische Staatssammlung MünchenStaatliche Naturkundliche Sammlungen Bayerns81247 MunichGermany GeoBio-Center Ludwig-Maximilians-Universitat München80333 MunichGermany Department Biologie II Ludwig-Maximilians-Universitat München82152 MunichGermany Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate Research37077 GottingenGermany

The pygmy marmoset,the smallest of the anthropoid primates,has a broad distribution in Western *** studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimoes-Amazonas ***,reconciling this new biological evidence with current taxonomy,i.e.,two subspecies,Cebuella pygmaea pygmaea(Spix,1823)and Cebuella pygmaea niveiventris(Lönnberg,1940),was problematic given the uncertainty as to whether Spix’s pygmy marmoset(Cebuella pygmaea pygmaea)was collected north or south of the Napo and Solimoes-Amazonas rivers,making it unclear to which of the two newly revealed species the name pygmaea would ***,we present the first molecular data from Spix’s type specimen of Cebuella pygmaea,as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality(Tabatinga)on both sides of the *** these data,we can confirm the correct names of the two species identified,i.e.,*** for animals north of the Napo and Solimoes-Amazonas rivers and *** for animals south of these two *** analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to reevaluate the geographical distribution for the two Cebuella *** dated the split of these two species to 2.54 million years *** discuss additional,more recent,subdivisions within each lineage,as well as potential contact zones between the two species in the headwaters of these rivers.

关键词： Historic DNA DNA taxonomy Pygmy marmoset Cebuella pygmaea C.niveiventris Amazon Type specimen

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基于APS的微型星跟踪器

控制工程（北京） 2004年第2期 28-38,27页

作者： Carl christian Liebe Leon Alkalai George Domingo Burce Hancock Don Hunter Jeff Mellstrom Ian ruiz Cesar Sepulveda Bedabrata Pain 郑克隆

JPL实验室已经就如何设计未来小型化星跟踪器的问题安排了一个研究课题。该研究项目推荐发展以APS为核心的超低功耗(70mW)、超轻质量(42g)的高速(50Hz)微型星跟踪器(MAST)。当数据更新率为50Hz时,这种MAST的精度约为7.5"。对于所有轻质... 详细信息

JPL实验室已经就如何设计未来小型化星跟踪器的问题安排了一个研究课题。该研究项目推荐发展以APS为核心的超低功耗(70mW)、超轻质量(42g)的高速(50Hz)微型星跟踪器(MAST)。当数据更新率为50Hz时,这种MAST的精度约为7.5"。对于所有轻质量与低功耗的微型卫星来说,MAST都是不可缺少的,因为在这些卫星上,质量与功耗参数是人们特别关心的。MAST仅由两个芯片组成一一个是为星跟踪器应用而优化的CMOS有源像元敏感器(APS)图像探测器,这是一项技术突破;另一个是包含内部集成电路(I^2C)接口、存储器和一个8051微控制器的专用集成电路(ASIC)芯片。MAST的强大功能使它可从几个小窗口同时输出像元数据,而由星上计算机执行处理任务。

关键词：微型星跟踪器 APS CMOS成像器微型卫星

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Sex-specific pathways in early cardiac response to pressure overload in mice

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世界最新医学信息文摘 2015年第99期 1-1页

作者： Henning Witt Carola Schubert Juliane Jaekel Daniela Fliegner Adam Penkalla Klaus Tiemann Joerg Stypmann Stefan Roepcke Sebastian Brokat Shokoufeh Mahmoodzadeh Eva Brozova Mercy M.Davidson Patricia ruiz Noppinger christian Grohé Vera Regitz-Zagrosek

Pressure overload(PO) first causes cardiac hypertrophy and then heart failure(HF), which are associated with sex differences in cardiac morphology and function. We aimed to identify genes that may cause HF-related sex differences. We used a transverse aortic constriction(TAC) mouse model leading to hypertrophy without sex differences in cardiac function after 2 weeks, but with sex differences in hypertrophy 6 and 9 weeks after TAC. Cardiac gene expression was analyzed 2 weeks after surgery. Deregulated genes were classified into functional gene ontology(GO) categories and used for pathway analysis. Classical marker genes of hypertrophy were similarly upregulated in both sexes(α-actin, ANP, BNP, CTGF). Thirty-five genes controlling mitochondrial function(PGC-1, cytochrome oxidase, carnitine palmitoyl transferase, acyl-CoA dehydrogenase, pyruvate dehydrogenase kinase) had lower expression in males compared to females after TAC. Genes encoding ribosomal proteins and genes associated with extracellular matrix remodeling exhibited relative higher expression in males(collagen 3, matrix metalloproteinase 2, TIMP2, and TGFβ2, all about twofold) after TAC. We confirmed 87% of the gene expression by real-time polymerase chain reaction. By GO classification, female-specific genes were related to mitochondria and metabolism and males to matrix and biosynthesis. Promoter studies confirmed the upregulation of PGC-1 by E2. Less downregulation of metabolic genes in female hearts and increased protein synthesis capacity and deregulation of matrix remodeling in male hearts characterize the sex-specific early response to PO. These differences could contribute to subsequent sex differences in cardiac function and HF.

关键词： Pressure overload Hypertrophy Gene expression Sex Heart

Sex-specific pathways in early cardiac response to pressure overload in mice

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世界最新医学信息文摘 2015年第A期 8-8页

Pressure overload(PO) first causes cardiac hypertrophy and then heart failure(HF), which are associated with sex differences in cardiac morphology and function. We aimed to identify genes that may cause HF-related sex differences. We used a transverse aortic constriction(TAC) mouse model leading to hypertrophy without sex differences in cardiac function after 2 weeks, but with sex differences in hypertrophy 6 and 9 weeks after TAC. Cardiac gene expression was analyzed 2 weeks after surgery. Deregulated genes were classified into functional gene ontology(GO) categories and used for pathway analysis. Classical marker genes of hypertrophy were similarly upregulated in both sexes(α-actin, ANP, BNP, CTGF). Thirty-five genes controlling mitochondrial function(PGC-1, cytochrome oxidase, carnitine palmitoyl transferase, acyl-Co A dehydrogenase, pyruvate dehydrogenase kinase) had lower expression in males compared to females after TAC. Genes encoding ribosomal proteins and genes associated with extracellular matrix remodeling exhibited relative higher expression in males(collagen 3, matrix metalloproteinase 2, TIMP2, and TGFβ2, all about twofold) after TAC. We confirmed 87% of the gene expression by real-time polymerase chain reaction. By GO classification, female-specific genes were related to mitochondria and metabolism and males to matrix and biosynthesis. Promoter studies confirmed the upregulation of PGC-1 by E2. Less downregulation of metabolic genes in female hearts and increased protein synthesis capacity and deregulation of matrix remodeling in male hearts characterize the sex-specific early response to PO. These differences could contribute to subsequent sex differences in cardiac function and Hf.

关键词： Pressure overload Hypertrophy Gene expression Sex Heart

Sex-specific pathways in early cardiac response to pressure overload in mice

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世界最新医学信息文摘 2016年第2期 8-8页

Pressure overload(PO) first causes cardiac hypertrophy and then heart failure(HF),which are associated with sex differences in cardiac morphology and *** aimed to identify genes that may cause HF-related sex *** used a transverse aortic constriction(TAC) mouse model leading to hypertrophy without sex differences in cardiac function after 2 weeks,but with sex differences in hypertrophy 6 and 9 weeks after *** gene expression was analyzed 2 weeks after *** genes were classified into functional gene ontology(GO) categories and used for pathway *** marker genes of hypertrophy were similarly upregulated in both sexes(α-actin,ANP,BNP,CTGF).Thirty-five genes controlling mitochondrial function(PGC-1,cytochrome oxidase,carnitine palmitoyl transferase,acyl-CoA dehydrogenase,pyruvate dehydrogenase kinase) had lower expression in males compared to females after *** encoding ribosomal proteins and genes associated with extracellular matrix remodeling exhibited relative higher expression in males(collagen 3,matrix metalloproteinase 2,TIMP2,and TGFβ2,all about twofold) after *** confirmed 87% of the gene expression by real-time polymerase chain *** GO classification,female-specific genes were related to mitochondria and metabolism and males to matrix and *** studies confirmed the upregulation of PGC-1 by *** downregulation of metabolic genes in female hearts and increased protein synthesis capacity and deregulation of matrix remodeling in male hearts characterize the sex-specific early response to *** differences could contribute to subsequent sex differences in cardiac function and HF.

关键词： Pressure overload Hypertrophy Gene expression Sex Heart

Notes for genera:Ascomycota

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Fungal Diversity 2017年第5期86卷 1-594页

作者： Nalin N.Wijayawardene Kevin D.Hyde Kunhiraman C.Rajeshkumar David L.Hawksworth Hugo Madrid Paul M.Kirk Uwe Braun Rajshree V.Singh Pedro W.Crous Martin Kukwa Robert Lücking Cletus P.Kurtzman Andrey Yurkov Danny Haelewaters Andre´Aptroot H.Thorsten Lumbsch Einar Timdal Damien Ertz Javier Etayo Alan J.L.Phillips Johannes Z.Groenewald Moslem Papizadeh Laura Selbmann Monika C.Dayarathne Gothamie Weerakoon E.B.Gareth Jones Satinee Suetrong Qing Tian Rafael F.Castanda-ruiz Ali H.Bahkali Ka-Lai Pang Kazuaki Tanaka Dong Qin Dai Jariya Sakayaroj Martina Hujslová Lorenzo Lombard Belle D.Shenoy Ave Suija Sajeewa S.N.Maharachchikumbura Kasun M.Thambugala Dhanushka N.Wanasinghe Bharati O.Sharma Subhash Gaikwad Gargee Pandit Laura Zucconi Silvano Onofri Eleonora Egidi Huzefa A.Raja Rampai Kodsueb Marcela E.S.Caceres Sergio Perez-Ortega Patrícia O.Fiuza Josiane Santana Monteiro Larissa N.Vasilyeva Roger G.Shivas Maria Prieto Mats Wedin Ibai Olariaga Adebola Azeez Lateef Yamini Agrawal Seyed Abolhassan Shahzadeh Fazeli Mohammad Ali Amoozegar Guo Zhu Zhao Walter P.Pfliegler Gunjan Sharma Magdalena Oset Mohamed A.Abdel-Wahab Susumu Takamatsu Konstanze Bensch Nimali Indeewari de Silva AndréDe Kesel Anuruddha Karunarathna Saranyaphat Boonmee Donald H.Pfister Yong-Zhong Lu Zong-Long Luo Nattawut Boonyuen Dinushani A.Daranagama Indunil C.Senanayake Subashini C.Jayasiri Milan C.Samarakoon Xiang-Yu Zeng Mingkwan Doilom Luis Quijada Sillma Rampadarath Gabriela Heredia Asha J.Dissanayake Ruvishika S.Jayawardana Rekhani H.Perera Li Zhou Tang Chayanard Phukhamsakda Margarita Hernańdez-Restrepo Xiaoya Ma Saowaluck Tibpromma Luis F.P.Gusmao Darshani Weerahewa Samantha C.Karunarathna Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom Research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand National Fungal Culture Collection of India(NFCCI) Biodiversity and Palaeobiology(Fungi)GroupAgharkar Research InstitutePuneMaharashtra 411004India Royal Botanic Gardens KewRichmondSurrey TW93DSUK Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Jilin Agricultural University Changchun 130118JilinPeople’s Republic of China Centro de Geno´mica y Bioinforma´tica Facultad de CienciasUniversidad Mayor de ChileCamino La Pira´mide 5750HuechurabaSantiagoChile Martin-Luther-Universita¨t Institut fu¨r BiologieBereich Geobotanik und Botanischer GartenHerbariumNeuwerk 2106099 Halle(Saale)Germany Westerdijk Fungal Biodiversity Institute Uppsalalaan 83584 CT UtrechtThe Netherlands Department of Plant Taxonomy and Nature Conservation Faculty of BiologyUniversity of Gdan´skWita Stwosza 5980-308 Gdan´skPoland Botanic Garden and Botanical Museum Königin-Luise-Str.6-814195 BerlinGermany Mycotoxin Prevention and Applied Microbiology Research Unit National Center for Agricultural Utilization ResearchAgricultural Research ServiceU.S.Department of AgriculturePeoriaIL 61604USA Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B38124 BrunswickGermany Farlow Reference Library and Herbarium of Cryptogamic Botany Harvard University22 Divinity AvenueCambridgeMA 02138USA Department of Organismic and Evolutionary Biology Harvard University22 Divinity AvenueCambridgeMA 02138USA ABL Herbarium G.v.d.Veenstraat 1073762 XK SoestThe Netherlands Science&Education The Field Museum1400

Knowledge of the relationships and thus the classification of fungi,has developed rapidly with increasingly widespread use of molecular techniques,over the past 10–15 years,and continues to *** genera have been found to be polyphyletic,and their generic concepts have subsequently been *** names have thus been introduced for species which are phylogenetically distinct from the type species of particular *** ending of the separate naming of morphs of the same species in 2011,has also caused changes in fungal generic *** order to facilitate access to all important changes,it was desirable to compile these in a single *** present article provides a list of generic names of Ascomycota(approximately 6500 accepted names published to the end of 2016),including those which are *** and summaries of the changes since the last edition of‘Ainsworth&Bisby’s Dictionary of the Fungi’in 2008 are *** notes include the number of accepted species,classification,type species(with location of the type material),culture availability,life-styles,distribution,and selected publications that have appeared since *** work is intended to provide the foundation for updating the ascomycete component of the"Without prejudice list of generic names of Fungi"published in 2013,which will be developed into a list of protected generic *** will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists,and scrutiny by procedures determined by the Nomenclature Committee for Fungi(NCF).The previously invalidly published generic names Barriopsis,Collophora(as Collophorina),Cryomyces,Dematiopleospora,Heterospora(as Heterosporicola),Lithophila,Palmomyces(as Palmaria)and Saxomyces are validated,as are two previously invalid family names,Bartaliniaceae and *** species of Lalaria,which were invalidly published are trans

关键词： Article 59 Classification One name Pleomorphic fungi Taxonomy