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Paleontology Knowledge Graph for Data-Driven discovery

Journal of Earth Science 2024年第3期35卷 1024-1034页

作者： Yiying Deng Sicun Song Junxuan Fan Mao Luo Le Yao Shaochun Dong Yukun Shi Linna Zhang Yue Wang Haipeng Xu Huiqing Xu Yingying Zhao Zhaohui Pan Zhangshuai Hou Xiaoming Li Boheng Shen Xinran Chen Shuhan Zhang Xuejin Wu Lida Xing Qingqing Liang Enze Wang School of Resources and Environmental Engineering Hefei University of TechnologyHefei 230009China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and PaleoenvironmentChinese Academy of SciencesNanjing 210008China School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling Nanjing UniversityNanjing 210023China State Key Laboratory for Mineral Deposits Research Nanjing UniversityNanjing 210023China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China centre for Research and Education on Biological Evolution and Environment Nanjing UniversityNanjing 210023China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China School of the Earth Sciences and Resources China University of GeosciencesBeijing 100083China

A knowledge graph(KG)is a knowledge base that integrates and represents data based on a graph-structured data model or *** have made efforts to construct geosciencerelated KGs to overcome semantic heterogeneity and facilitate knowledge representation,data integration,and text ***,there is currently no comprehensive paleontology KG or data-driven discovery based on *** this study,we constructed a two-layer model to represent the ordinal hierarchical structure of the paleontology KG following a top-down construction *** ontology containing 19365 concepts has been defined up to *** this basis,we derived the synonymy list based on the paleontology KG and designed corresponding online functions in the OneStratigraphy database to showcase the use of the KG in paleontological research.

关键词： paleontology knowledge graph ontology synonymy list OneStratigraphy big data ge-ology.

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Population normative models of human brain growth across development

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Science Bulletin 2020年第22期65卷 1872-1873,M0003页

作者： Bharath Holla Jakob Seidlitz Richard A.I.Bethlehem Gunter Schumann Departments of Psychiatry and Integrative Medicine National Institute of Mental Health and Neuro Sciences(NIMHANS)Bengaluru 5600029India Department of Child and Adolescent Psychiatry and Behavioral Science Children’s Hospital of PhiladelphiaPhiladelphiaPA 19104USA Department of Psychiatry University of PennsylvaniaPhiladelphiaPA 19104USA Autism Research centre Department of PsychiatryUniversity of CambridgeCambridge CB28AHUK Brain Mapping Unit Department of PsychiatryUniversity of CambridgeCambridge CB28AHUK centre for Population Neuroscience and Stratified Medicine(PONS) SGDP CentreIoPPNKCLLondon SE58AFUK PONS-centre Dept of Psychiatry and PsychotherapyCampus Charite MitteHumboldt UniversityBerlin D 10117Germany PONS centre Institute for Science and Technology of Brain-inspired Intelligence(ISTBI)Fudan UniversityShanghai 200433China

Growth charts for gross anthropometric traits,such as height,weight,and head circumference,are cornerstones of pediatric care around the *** modelling approach is centered around measuring the relative deviations from normative trajectories rather than the absolute values of these phenotypes[1].To this end,it is imperative that normative models are not only robust in terms of the statistical framework on which they are built。

关键词： corners absolute ant

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Epidemiology, Clinical Features and Antifungal Resistance Profile of Candida auris in Africa: Systematic Review

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Journal of Biosciences and Medicines 2024年第1期12卷 126-149页

作者： Isidore Wendkièta Yerbanga Seydou Nakanabo Diallo Toussaint Rouamba Delwendé Florence Ouedraogo Katrien Lagrou Rita Oladele Jean-Pierre Gangneux Olivier Denis Hector Rodriguez-Villalobos Isabel Montesinos Sanata Bamba centre Hospitalier Universitaire Régional de Ouahigouya Ouahigouya Burkina Faso Ecole Doctorale des Sciences De la Santé Université Nazi Boni Bobo-Dioulasso Burkina Faso centre Muraz/Institut National de Santé Publique Bobo-Dioulasso Burkina Faso Clinical Research Unit of Nanoro Institute for Research in Health Sciences National Center for Scientific and Technological Research Ouagadougou Burkina Faso Department of Microbiology Immunology and Transplantation KU Leuven Leuven Belgium and Department of Laboratory Medicine and National Reference Center for Mycosis Excellence Center for Medical Mycology (ECMM) University Hospitals Leuven Leuven Belgium College of Medicine University of Lagos Lagos Nigeria Univ Rennes CHU Rennes Inserm Irset (Institut de recherche en santé environnement et travail) European ECMM Excellence Center in Medical Mycology Université de Rennes Rennes France Department of Microbiology CHU Namur site-Godinne Université Catholique de Louvain Yvoir Belgium Ecole de Santé Publique Université Libre de Bruxelles Brussels Belgium Department of Microbiology Cliniques Universitaires Saint-Luc—Université Catholique de Louvain Bruxelles Belgium centre Hospitalier Universitaire Sour? Sanou Bobo-Dioulasso Burkina Faso

Candida auris since it discovery in 2009 is becoming a severe threat to human health due to its very quickly spread, its worldwide high resistance to systemic antifungal drugs. In resource-constrained settings where several conditions are met for its emergence and spread, this worrisome fungus could cause large hospital and/or community-based outbreaks. This review aimed to summarize the available data on C. auris in Africa focusing on its epidemiology and antifungal resistance profile. Major databases were searched for articles on the epidemiology and antifungal resistance profile of C. auris in Africa. Out of 2,521 articles identified 22 met the inclusion criteria. In Africa, nearly 89% of African countries have no published data on C. auris. The prevalence of C. auris in Africa was 8.74%. The case fatality rate of C. auris infection in Africa was 39.46%. The main C. auris risk factors reported in Africa were cardiovascular disease, renal failure, diabetes, HIV, recent intake of antimicrobial drugs, ICU admissions, surgery, hemodialysis, parenteral nutrition and indwelling devices. Four phylogenetic clades were reported in Africa, namely clades I, II, III and IV. Candida auris showed a pan-African very high resistance rate to fluconazole, moderate resistance to amphotericin B, and high susceptibility to echinocandins. Finally, C. auris clade-specific mutations were observed within the ERG2, ERG3, ERG9, ERG11, FKS1, TAC1b and MRR1 genes in Africa. This systematic review showed the presence of C. auris in the African continent and a worrying unavailability of data on this resilient fungus in most African countries.

关键词： Africa Antifungal Resistance Candida auris Clinical Features Phylogenetic Clades

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Ultrasensitive Indium Phosphide Nanomembrane Wearable Gas Sensors

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Energy & Environmental Materials 2024年第6期 213-221页

作者： Shiyu Wei Tuomas Haggren Zhe Li Hark Hoe Tan Chennupati Jagadish Antonio Tricoli Lan Fu Department of Electronic Materials Engineering Australian Research Council Centre of Excellence for Transformative Meta-Optical SystemsResearch School of PhysicsThe Australian National University Nanotechnology Research Laboratory Research School of ChemistryCollege of ScienceThe Australian National University Nanotechnology Research Laboratory Faculty of EngineeringThe University of Sydney

Air quality is deteriorating due to continuing urbanization and *** particular,nitrogen dioxide（NO2） is a biologically and environmentally hazardous byproduct from fuel combustion that is ubiquitous in urban *** address this issue,we report a high-performance flexible indium phosphide nanomembrane NO2sensor for real-time air quality *** ultralow limit of detection of ～200 ppt and a fast response have been achieved with this device by optimizing the film thickness and doping concentration during indium phosphide epitaxy.

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The amazing potential of fungi:50 ways we can exploit fungi industrially

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Fungal Diversity 2019年第4期97卷 1-136页

作者： Kevin D.Hyde Jianchu Xu Sylvie Rapior Rajesh Jeewon Saisamorn Lumyong Allen Grace T.Niego Pranami D.Abeywickrama Janith V.S.Aluthmuhandiram Rashika S.Brahamanage Siraprapa Brooks Amornrat Chaiyasen K.W.Thilini Chethana Putarak Chomnunti Clara Chepkirui Boontiya Chuankid Nimali I.de Silva Mingkwan Doilom Craig Faulds Eleni Gentekaki Venkat Gopalan Pattana Kakumyan Dulanjalee Harishchandra Hridya Hemachandran Sinang Hongsanan Anuruddha Karunarathna Samantha C.Karunarathna Sehroon Khan Jaturong Kumla Ruvishika S.Jayawardena Jian-Kui Liu Ningguo Liu Thatsanee Luangharn Allan Patrick G.Macabeo Diana S.Marasinghe Dan Meeks Peter E.Mortimer Peter Mueller Sadia Nadir Karaba N.Nataraja Sureeporn Nontachaiyapoom Meghan O’Brien Watsana Penkhrue Chayanard Phukhamsakda Uma Shaanker Ramanan Achala R.Rathnayaka Resurreccion B.Sadaba Birthe Sandargo Binu C.Samarakoon Danushka S.Tennakoon Ramamoorthy Siva Wasan Sriprom T.S.Suryanarayanan Kanaporn Sujarit Nakarin Suwannarach Thitipone Suwunwong Benjarong Thongbai Naritsada Thongklang Deping Wei S.Nuwanthika Wijesinghe Jake Winiski Jiye Yan Erandi Yasanthika Marc Stadler 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 School of Science 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.PaPaeA.Mae TaengChiang Mai 50150Thailand Aix Marseille Université INRAUMR1163 BBF13288 Marseille Cedex 09France Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China Center of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097People’s Republic of China Center of Chemical Innovation for Sustainability Mae Fah Luang UniversityTasudMuangChiang Rai 57100Thailand Center of excellence in Microbial Diversity and Sustainable Utilization Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Center for Mountain Ecosystem Studies Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China Institute of Fungal Research School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Department Microbial Drugs Helmholtz Centre for Infection Researchand German Centre for Infection Research(DZIF)partner site Hannover-BraunschweigInhoffenstrasse 738124 BrunswickGermany Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Department of Chemistry and Biochemistry The Ohio State UniversityColumbusOH 43210USA Department of Chemistry University of Science and TechnologyBannuKhyber PakhtunkhwaPakistan Department of Crop Physiology University of Agricultural SciencesGKVKBengaluruKarnataka 560065India Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai Univers

Fungi are an understudied,biotechnologically valuable group of *** to the immense range of habitats that fungi inhabit,and the consequent need to compete against a diverse array of other fungi,bacteria,and animals,fungi have developed numerous survival *** unique attributes of fungi thus herald great promise for their application in biotechnology and ***,fungi can be grown with relative ease,making production at scale *** search for fungal biodiversity,and the construction of a living fungi collection,both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel *** manuscript reviews fifty ways in which fungi can potentially be utilized as *** provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable *** also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential *** have provided the world with penicillin,lovastatin,and other globally significant medicines,and they remain an untapped resource with enormous industrial potential.

关键词： Biocontrol Biodiversity Biotechnology Food Fungi Mushrooms

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Integrative approaches for species delimitation in Ascomycota

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Fungal Diversity 2021年第4期109卷 155-179页

作者： Sajeewa S.N.Maharachchikumbura Yanpeng Chen Hiran A.Ariyawansa Kevin D.Hyde Danny Haelewaters Rekhani H.Perera Milan C.Samarakoon Dhanushka N.Wanasinghe Danilo E.Bustamante Jian-Kui Liu Daniel P.Lawrence Ratchadawan Cheewangkoon Marc Stadler School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Entomology and Plant Pathology Department Faculty of AgricultureChiang Mai UniversityChiang MaiThailand Department of Plant Pathology and Microbiology College of Bio-Resources and AgricultureNational Taiwan UniversityTaipei City 10617Taiwan Center of excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Research Group Mycology Department of BiologyGhent University9000 GhentBelgium Faculty of Science University of South Bohemia37005 Ceske BudejoviceCzech Republic Center for Mountain Futures Kunming Institute of BotanyHonghe County 654400YunnanPeople’s Republic of China Instituto de Investigación Para el Desarrollo Sustentable de Ceja de Selva(INDES-CES) Universidad Nacional Toribio Rodríguez de MendozaChachapoyasAmazonasPeru Department of Civil and Environmental Engineering(FICIAM) Universidad Nacional Toribio Rodríguez de MendozaChachapoyasAmazonasPeru Department of Plant Pathology University of CaliforniaDavisDavisCAUSA Helmholtz centre for Infection Research GmbH Department Microbial Drugs and German Centre for Infection Research(DZIF)Partner Site Hannover-Braunschweig38124 BraunschweigGermany Institute of Microbiology Technische Universität BraunschweigInhoffenstraße 738124 BraunschweigGermany

Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing *** high number of species that have yet to be described have generated extreme crisis to the ***,more than in any other era,effective ways to discover and delimitate species are *** paper reviews the historically fore-most approaches used to delimit species in Ascomycota,the most speciose phylum of *** include morphological,biological,and phylogenetic species *** argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and *** the rate of species discovery has increased because of the advancement of phylogenetic ***,traditional phylogenetic methods with few gene regions lack species-level resolution,and do not allow unambiguous *** detail the processes that affect gene tree heterogeneity,which acts as barriers to delimiting species boundaries in classical low-rank *** far,limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal *** addition to reviewing concepts and methodologies used to delimit species,we present a case *** applied differ-ent species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta(Dothideomycetes,Botryosphaeriales).Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single *** problems can be resolved by using multiple loci and coalescence-based ***,we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.

关键词： Ascomycetes Phylogenetics Species concept Systematics

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Multidimensional synthetic chiral-tube lattices via nonlinear frequency conversion

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Light(Science & Applications) 2020年第1期9卷 803-812页

作者： Kai Wang Bryn A.Bell Alexander S.Solntsev Dragomir N.Neshev Benjamin J.Eggleton Andrey A.Sukhorukov Nonlinear Physics centre Research School of PhysicsThe Australian National UniversityCanberraACT 2601Australia Institute of Photonics and Optical Science(IPOS) School of PhysicsUniversity of SydneySydneyNSW 2006Australia Department of Physics QOLSImperial College LondonLondon SW72AZUK School of Mathematical and Physical Sciences University of Technology SydneyUltimoNSW 2007Australia Ginzton Laboratory Stanford UniversityStanfordCA 94305USA

Geometrical dimensionality plays a fundamentally important role in the topological effects arising in discrete *** direct experiments are limited by three spatial dimensions,the research topic of synthetic dimensions implemented by the frequency degree of freedom in photonics is rapidly *** manipulation of light in these artificial lattices is typically realized through electro-optic modulation;yet,their operating bandwidth imposes practical constraints on the range of interactions between different frequency *** we propose and experimentally realize all-optical synthetic dimensions involving specially tailored simultaneous short-and long-range interactions between discrete spectral lines mediated by frequency conversion in a nonlinear *** realize triangular chiral-tube lattices in three-dimensional space and explore their four-dimensional *** implement a synthetic gauge field with nonzero magnetic flux and observe the associated multidimensional dynamics of frequency combs,all within one physical spatial *** anticipate that our method will provide a new means for the fundamental study of high-dimensional physics and act as an important step towards using topological effects in optical devices operating in the time and frequency domains.

关键词： dimensions chiral nonlinear

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Relativistic domain-wall dynamics in van der Waals antiferromagnet MnPS_(3)

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npj Computational Materials 2022年第1期8卷 27-35页

作者： Ignacio M.Alliati Richard F.L.Evans Kostya S.Novoselov Elton J.G.Santos School of Mathematics and Physics Queen’s University BelfastBelfastBT71NNUK Department of Physics The University of YorkYorkYO105DDUK Institute for Functional Intelligent Materials National University of SingaporeSingapore117544Singapore Institute for Condensed Matter Physics and Complex Systems School of Physics and AstronomyThe University of EdinburghEdinburghEH93FDUK Higgs centre for Theoretical Physics The University of EdinburghEdinburghEH93FDUK

The discovery of two-dimensional(2D)magnetic van der Waals(vdW)materials has flourished an endeavor for fundamental problems as well as potential applications in computing,sensing and storage *** particular interest are antiferromagnets,which due to their intrinsic exchange coupling show several advantages in relation to ferromagnets such as robustness against external magnetic *** we show that,despite of this cornerstone,the magnetic domains of recently discovered 2D vdW MnPS_(3)antiferromagnet can be controlled via magnetic fields and electric *** achieve ultrafast domain-wall dynamics with velocities up to~3000 m s^(−1)within a relativistic *** contraction and emission of spin-waves in the terahertz gap are observed with dependence on the edge termination of the *** results indicate that the implementation of 2D antiferromagnets in real applications can be further controlled through edge engineering which sets functional characteristics for ultrathin device platforms with relativistic features.

关键词： relativistic dynamics antiferromagnet

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Deep simulated annealing for the discovery of novel dental anesthetics with local anesthesia and anti-inflammatory properties

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Acta Pharmaceutica Sinica B 2024年第7期14卷 3086-3109页

作者： Yihang Hao Haofan Wang Xianggen Liu Wenrui Gai Shilong Hu Wencheng Liu Zhuang Miao Yu Gan Xianghua Yu Rongjia Shi Yongzhen Tan Ting Kang Ao Hai Yi Zhao Yihang Fu Yaling Tang Ling Ye Jin Liu Xinhua Liang Bowen Ke State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases West China Hospital of StomatologySichuan UniversityChengdu 610041China College of Computer Science Sichuan UniversityChengdu 610065China Department of Anesthesiology Laboratory of Anesthesia and Critical Care MedicineNational-Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyFrontiers Science Center for Disease-Related Molecular NetworkWest China HospitalSichuan UniversityChengdu 610041China

Multifunctional therapeutics have emerged as a solution to the constraints imposed by drugs with singular or insufficient therapeutic *** primary challenge is to integrate diverse pharmacophores within a single-molecule *** address this,we introduced DeepSA,a novel edit-based generative framework that utilizes deep simulated annealing for the modification of articaine,a wellknown local *** integrates deep neural networks into metaheuristics,effectively constraining molecular space during compound *** framework employs a sophisticated objective function that accounts for scaffold preservation,anti-inflammatory properties,and covalent *** a sequence of local editing to navigate the molecular space,DeepSA successfully identified AT-17,a derivative exhibiting potent analgesic properties and significant anti-inflammatory activity in various animal *** insights into AT-17 revealed its dual mode of action:selective inhibition of NaV1.7 and 1.8 channels,contributing to its prolonged local anesthetic effects,and suppression of inflammatory mediators via modulation of the NLRP3 inflammasome *** findings not only highlight the efficacy of AT-17 as a multifunctional drug candidate but also highlight the potential of DeepSA in facilitating AI-enhanced drug discovery,particularly within stringent chemical constraints.

关键词： Multifunctional drugs Deep simulated annealing Molecule generation Articaine derivatives AI-enhanced drug discovery

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Can we use environmental DNA as holotypes?

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Fungal Diversity 2018年第5期92卷 1-30页

作者： Sinang Hongsanan Rajesh Jeewon Witoon Purahong Ning Xie Jian-Kui Liu Ruvishika S.Jayawardena Anusha H.Ekanayaka Asha Dissanayake Olivier Raspe Kevin D.Hyde Marc Stadler Derek Persoh Shenzhen Key Laboratory of Microbial Genetic Engineering College of Life Sciences and OceanographyShenzhen UniversityShenzhen 518060People’s Republic of China Shenzhen Key Laboratory of Laser Engineering College of Optoelectronic EngineeringShenzhen UniversityShenzhen 518060People’s Republic of China Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduit 80837Mauritius UFZ-Helmholtz centre for Environmental Research Department of Soil EcologyTheodor-Lieser-Str.406120 Halle(Saale)Germany Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyangGuizhou 550006People’s Republic of China Center of excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Botanic Garden Meise Nieuwelaan 381860 MeiseBelgium Fédération Wallonie–Bruxelles Service général de l’Enseignement universitaire et de la Recherche scientifiqueRue Adolphe Lavallée 11080 BrusselsBelgium Department of Microbial Drugs Helmholtz-Zentrum für Infektionsforschung GmbHInhoffenstrasse 738124 BraunschweigGermany Ruhr-Universität Bochum GeobotanyUniversitätstrasse 15044801 BochumGermany

The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological *** idea of using intracellular DNA("mgDNA")from environmental samples as holotypes seems at face value,to be a good idea,considering the expansion of knowledge among these‘dark taxa’or‘dark matter fungi’that it could provide(*** based taxa without physical specimens and formal nomenclature).However,the limitations of using mgDNA as holotypes needs careful thought,*** we use a short mgDNA fragment,which may contain a small amount of genetic information,to allow discrimination between species?What is the point and are the potential problems of giving valid scientific names to mgDNA?Numerous mycologists and taxonomists,who have many years of experience working on the taxonomy and phylogeny of different groups of fungi,are concerned about the consequences of providing valid names to *** has been much debate,through several publications on the considerable problems of using mgDNA as *** proponents have tried to debate the virtues of using mgDNA as *** against have shown that identification to species using mgDNA does not work in many fungal groups,while those for have shown cases where species can be identified with *** disciplines have different reasons and opinions for using mgDNA as holotypes,however even groups of the same disciplines have dissimilar *** this paper we explore the use of mgDNA as *** provide evidences and opinions as to the use of mgDNA as holotypes from our own *** no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa,but relate the issues to fungal *** fact we show the value of using sequence data from these approaches,in dealing with the discovery of already named taxa,taxa numbers and ecological *** discuss the

关键词： DNA-based sequence Fungal identification ITS Next-generation sequencing Nomenclature Taxonomy

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