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| 1 | High-level classification of the Fungi and a tool for evolutionary ecological analyses显示文摘High-throughput sequencing studies generate vast amounts of taxonomic data.Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone.We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative.Based on phylogenies and divergence time estimates,we adopt phylum rank to Aphelidiomycota,Basidiobolomycota,Calcarisporiellomycota,Glomeromycota,Entomophthoromycota,Entorrhizomycota,Kickxellomycota,Monoblepharomycota,Mortierellomycota and Olpidiomycota.We accept nine subkingdoms to accommodate these 18 phyla.We consider the kingdom Nucleariae(phyla Nuclearida and Fonticulida)as a sister group to the Fungi.We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework,using this or any other classification system.We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set. | Leho Tedersoo Santiago Sanchez-Ramırez Urmas Koljalg Mohammad Bahram Markus Doring Dmitry Schigel Tom May Martin Ryberg Kessy Abarenkov | 2018 | Fungal Diversity2018，，3： | 7 |
| 2 | Towards a unified paradigm for sequence‐based identification of fungi显示文摘 | Urmas K?ljalg R. Henrik Nilsson Kessy Abarenkov Leho Tedersoo Andy F. S. Taylor Mohammad Bahram Scott T. Bates Thomas D. Bruns Johan Bengtsson‐Palme Tony M. Callaghan Brian Douglas Tiia Drenkhan Ursula Eberhardt Margarita Due?as Tine Grebenc Gareth W. Gri | 2013 | Mol Ecol2013，，21： | 2 |
| 3 | Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach显示文摘Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases. | Leho Tedersoo Sten Anslan Mohammad Bahram Urmas Kõljalg Kessy Abarenkov | 2020 | Fungal Diversity2020，，4： | 2 |
| 4 | Fine scale distribution of eetomycorrhizal fungi and roots across substrate layers in- cluding coarse woody debris in a mixed forest显示文摘 | LEHO T URMAS K NILS H | 2003 | New Phy- tologist2003，159，1： | 1 |
| 5 | Complications of chronic pancreatitis prior to and following surgical treatment:A proposal for classification显示文摘BACKGROUND Chronic pancreatitis(CP)is a long-lasting disease frequently associated with complications for which there is no comprehensive pathophysiological classification.AIM The aims of this study were to:Propose a pathophysiological classification of the complications of CP;evaluate their prevalence in a surgical cohort prior to,and following surgical management;and assess the impact of the surgical treatment on the occurrence of new complications of CP during follow-up.We hypothesized that optimal surgical treatment can resolve existing complications and reduce the risk of new complications,with the exclusion of pancreatic insufficiency.The primary outcomes were prevalence of complications of CP at baseline(prior to surgical treatment)and occurrence of new complications during follow-up.METHODS After institutional review board approval,a prospective observational cohort study with long-term follow-up(up to 20.4 years)was conducted.All consecutive single-center adult patients(≥18 years of age)with CP according to the criteria of the American Pancreas Association subjected to surgical management between 1997 and 2021,were included.The prevalence of CP complications evaluated,according to the proposed classification,in a surgical cohort of 166 patients.Development of the pathophysiological classification was based on a literature review on the clinical presentation,course,and complications of CP,as well a review of previous classification systems of CP.RESULTS We distinguished four groups of complications:Pancreatic duct complications peripancreatic complications,pancreatic hemorrhages,and pancreatic insufficiency(exocrine and endocrine).Their baseline prevalence was 20.5%,23.5%,10.2%,31.3%,and 27.1%,respectively.Surgical treatment was highly effective in avoiding new complications in the first and third groups.In the group of peripancreatic complications,the 15-year Kaplan-Meier prevalence of new complications was 12.1%.The prevalence of pancreatic exocrine and endocrine insufficiency increased during follow-up,being 66.4%and 47.1%,respectively,at 15 years following surgery.Pancreatoduodenal resection resulted optimal results in avoiding new peripancreatic complications,but was associated with the highest rate of pancreatic exocrine insufficiency.CONCLUSION The proposed complication classification improves the understanding of CP.It could be beneficial for clinical decision making,as it provides an opportunity for more comprehensive judgement on patient’s needs on the one hand,and on the pros and cons of the treatment under consideration,on the other.The presence of complications of CP and the risk of development of new ones should be among the main determinants of surgical choice. | Marko Murruste Ülle Kirsimägi Karri Kase Tatjana Veršinina Peep Talving Urmas Lepner | 2022 | World Journal of Clinical Cases2022，10，22： | 1 |
| 6 | Operational Monito- ring of Suspended Matter Distribution Using MO- DIS Images and Nerical Modeling显示文摘 | Liis S Urmas R Tarmo K | 2006 | Advances in Space Research2006，38，： | 1 |
| 7 | The Value of Diversity: Foreign Direct Investment and Employment in Central Europe During Economic Recovery 显示文摘 | Tomasz Mickiewicz Slavo Radosevic Urmas Varblane | 2000 | University of Tartu Faculty of Economics and Business Administration discussion paper2000，，： | 1 |
| 8 | Operational Monitoring of Suspended Matter Distribution Using MODIS Images and Nerical Modeling显示文摘 | Liis S Urmas R Tarmo K | 2006 | Advances in Space Research2006，38，： | 1 |
| 9 | Operational monitoring of suspended matter distribution using MODIS images and numerical modelling显示文摘 | Liis Sipelgas Urmas Raudsepp Tarmo K?uts | 2006 | Advances in Space Research2006，，10： | 1 |
| 10 | FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles显示文摘The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging.In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels.Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences.On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold. | Sergei Põlme Kessy Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson Kevin David Hyde Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli Jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis Yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John Y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad Bahram Niloufar Hagh-Doust Olesya Dulya Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.Jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay Bose Tanel Vahter Tarquin Netherway Teng Yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov Yongzhong Lu Yosuke Matsuda Yumiko Miyamoto Urmas Kõljalg Leho Tedersoo | 2020 | Fungal Diversity2020，，6： | 1 |
| 11 | Echinococcus granulosus genotype G1 dominated in cattle and sheep during 2003–2006 in Buenos Aires province, an endemic area for cystic echinococcosis in Argentina显示文摘 | María Vanesa Andresiuk Francisco Ponce Gordo Merilin Saarma Maria Celina Elissondo Ana Taraborelli Claudia Casalongue Guillermo Denegri Urmas Saarma | 2013 | Acta Tropica2013，，2： | 1 |
| 12 | Improving ITS sequence data for identification of plant pathogenic fungi显示文摘Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://gffzz7cc2bea597fa4d6chc0bbubb9o9no6cxc.ffgz.tsg.suse.edu.cn),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort. | R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias Artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad Bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna Friberg Tobias Guldberg Froslev Bettina Halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov | 2014 | Fungal Diversity2014，，4： | 1 |
| 13 | Governmental Support Measures for University–Industry Cooperation—Comparative View in Europe显示文摘 | Marge Seppo K?rt R?igas Urmas Varblane | 2014 | Journal of the Knowledge Economy2014，，2： | 1 |
| 14 | Can the national innovation systems of the new eu mem her states be improved显示文摘 | URMAS VARBLANE DAVID DYKER DOREL TAMM | 2007 | Post-Communist Economies2007，，4： | 1 |
| 15 | Water quality assessment using integrated modeling and monitoring in Narva Bay,Gulf of Finland,Environmental Modeling & Assessment显示文摘 | Gennadi Lessin Urmas Raudsepp | 2006 | 11(4):258-2632006，11，4： | 1 |
| 16 | 中欧和东欧国家生物多样性保护和人类活动之间的冲突显示文摘生物多样性和人类活动之间的冲突通常具有重要的政治、经济和环境响应,欧盟(EU)已经并将持续加强对这种冲突的关注。欧盟利用一整套自上而下和自下而上的方式来处理这些冲突,取得了不同程度的成功。欧洲目前面临的新挑战是10个新国家整合到欧盟的一体化,以及欧盟立法涵盖了一系列附加的生物多样性富集生境。中欧和东欧国家(CEEC)丰富的生物多样性很可能面临着这一一体化过程中某些方面的威胁,预计会出现一些生物多样性保护和人类活动之间的冲突。本文评述了中欧和东欧国家生物多样性保护和人类活动之间存在的一些冲突,预测了特别是新政策新立法执行后与欧盟一体化有关的冲突,最后,探讨了可能的冲突管理措施。 | Juliette Young Caspian Richards Anke Fischer Lubos Halada Tiiu Kull Antoni Kuzniar Urmas Tartes Yordan Uzunov Allan Watt 王仕琴(译) | 2007 | AMBIO-人类环境杂志2007，36，B11： | 1 |
| 17 | The influence of weather conditions (temperature and wind) on cyanobacterial bloom development in the Gulf of Finland (Baltic Sea)显示文摘 | Inga Kanoshina Urmas Lips Juha-Markku Lepp?nen | 2003 | Harmful Algae2003，，1： | 1 |
| 18 | Single and multiple stressor effect of road deicers and Cu on Atlantic salmon (Salmo salar) alevins from hatching till swim-up显示文摘Road salts are frequently used for deicing of roads in the Nordic countries. During snow-melt, the road run-off containing high concentrations of road salt and various metals such as Cu remobilized from sand, silt and dust may negatively influence organisms in downstream receiving water bodies. The present work focuses on the impact of road salt(NaCl) and Cu, separately and in mixtures on Atlantic salmon alevins from hatching till swim-up. The results showed that high road salt concentrations could induce a series of negative effects in alevins such as reduced growth, deformities, delayed swim-up and mortality. For alevins exposed to all tested road salt concentrations(100–1000 mg/L),mortality was significantly higher compared to control. In exposure to Cu solutions(5–20 μg Cu/L), no effects on growth, morphology, swim-up or mortality of alevins compared to control were observed. In mixture solutions(road salt and Cu), ultrafiltration of the exposure water demonstrated that only 20%–40% of Cu was present as positively charged low molecular mass(LMM) Cu species assumed to be bioavailable. When exposed to road salt and Cu mixtures, negative effects in alevins such as reduced growth, deformities,delayed swim-up and mortality were observed. The overall results indicated that the road salt application could seriously affect sensitive life stages of Atlantic salmon, and application of road salt should be avoided during the late winter–early spring period. | Urma Mahrosh BjФrn Olav Rosseland Brit Salbu Hans-Christian Teien | 2018 | Journal of Environmental Sciences2018，30，4： | 0 |
| 19 | 正常及患病心脏中的一氧化氮和一氧化氮合酶亚型(英文)显示文摘We have reviewed the role of nitric oxide synthase(NOS)isoforms and nitric oxide(NO)in the normal heart and in heart failure.NO is a highly reactive siganaling molecule produced normally in the heart and is an important modulator of myocardial function.NOS catalyzes the conversion of L-arginine to L-citrulline and NO.In the heart,three NOS isoforms are present:neuronal NOS(nNOS),and endothelial NOS(eNOS),are constitutively present enzymes in distinct subcellular locations within cardiomyocytes,whereas inducible NOS(iNOS)is absent in the healthy heart,but its expression is induced by inflammation and immune responses.In the tissue,NO has two main effects:(i)it stimulates the activity of guanylate cyclase,and(ii)nitrosylates tyrosine residues in proteins and thiol-groups of cysteine in proteins.Changes in subcellular compartmentalization of NOS isoforms lead to the increased NO synthesis,reduction of the specificity of its effects,disruption of calcium homeostasis,electromechanical uncoupling and myocardial contractile failure. | 李中言 Soban Urma | 2009 | 吉林医药学院学报2009，30，4： | 0 |
| 20 | ‘Short’pancreaticojejunostomy might be a valid option for treatment of chronic pancreatitis in many cases显示文摘BACKGROUND The Partington-Rochelle pancreaticojejunostomy(PJ)is an essential management option for patients with chronic pancreatitis(CP)associated with intractable pain and a dilated pancreatic duct(PD).Wide ductotomy and long PJ(L-PJ)have been advocated as the standard of care to ensure full PD decompression.However,the role of short PJ(S-PJ)in a uniformly dilated PD has not yet been evaluated.AIM To evaluate the possible advantages and disadvantages of S-PJ and L-PJ and to interpret the perspective of S-PJ in the treatment of CP.METHODS A retrospective review of prospectively collected cohort data was conducted on surgically treated CP patients subjected to side-to-side PJ.The length of the PJ was adapted to anatomical alterations in PD.A comparison was made of S-PJ(<50 mm)for uniformly dilated PD and L-PJ(50-100 mm)in the setting of multiple PD strictures,calcifications and dilatations.We hypothesized that S-PJ and L-PJ ensure comparable clinical outcomes.The primary outcomes were pain relief and quality of life(QOL);the secondary outcomes were perioperative characteristics,body weight,patients’satisfaction with treatment,and readmission rate due to CP.RESULTS Overall,91 patients underwent side-to-side PJ for CP,including S-PJ in 46 patients and L-PJ in 45 patients.S-PJ resulted in better perioperative outcomes:Significantly shorter operative time(107.5 min vs 134 min),lower need for intraoperative(0%vs 15.6%)and total(2.2%vs 31.1%)blood transfusions,and lower rate of perioperative complications(6.5%vs 17.8%).We noted no significant difference in pain relief,improvement in QOL,body weight gain,patients’satisfaction with surgical treatment,or readmission rate due to CP.CONCLUSION Based on our data,in the setting of a uniformly dilated PD,S-PJ provides adequate decompression of the PD.As the clinical outcomes following S-PJ are not inferior to those of L-PJ,S-PJ should be preferred as a surgical option in the case of a uniformly dilated PD. | Marko Murruste Ülle Kirsimägi Karri Kase Tatjana Veršinina Peep Talving Urmas Lepner | 2021 | World Journal of Gastrointestinal Surgery2021，13，12： | 0 |
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