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Scale dependence in the phylogenetic relatedness of alien and native taxa

journal of Plant Ecology 2020年第5期13卷 601-610页

作者： chris M.McGrannachan Gillis j.Horner Melodie A.McGeoch School of Biological Sciences Faculty of ScienceMonash UniversityMelbourne 3800Australia Manaaki Whenua-Landcare Research 231 Morrin RdSt.JohnsAuckland 1072New Zealand Greening Australia Ltd PO Box 470Flinders LaneMelbourne 8009Australia

Aims Darwin’s naturalization hypothesis proposes that successfully established alien species are less closely related to native species due to differences in their ecological *** have provided support both for and against this *** reason for this is the tendency for phylogenetic clustering between aliens and natives at broad spatial scales with overdispersion at fine ***,little is known about how the phylogenetic relatedness of alien species alters the phylogenetic structure of the communities they invade,and at which spatial scales effects may ***,we examine if invaded understorey plant communities,*** both native and alien taxa,are phylogenetically clustered or overdispersed,how relatedness changes with spatial scale and how aliens affect phylogenetic patterns in understorey *** Field surveys were conducted in dry forest understorey communities in south-east Australia at five spatial scales(1,20,500,1500 and 4500 m2).Standardized effect sizes of two metrics were used to quantify phylogenetic relatedness between communities and their alien and native subcommunities,and to examine how phylogenetic patterns change with spatial scale:(i)mean pairwise distance and(ii)mean nearest taxon distance(MNTD).Important Findings Aliens were closely related to each other,and this relatedness tended to increase with *** species and the full community exhibited either no clear pattern of relatedness with increasing spatial scale or were no different from *** intermediate spatial scales(20-500 m2),the whole community tended towards random whereas the natives were strongly overdispersed and the alien subcommunity strongly *** suggests that invasion by closely related aliens shifts community phylogenetic structure from overdispersed towards *** and natives were distantly related across spatial scales,supporting Darwin’s naturalization hypothesis,but only when phylogenetic distance

关键词： alien species community phylogenetics Darwin’s naturalization hypothesis spatial scale phylogenetic beta diversity

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Local predation risk shapes spatial and foraging neophobia patterns in Trinidadian guppies

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Current Zoology 2016年第5期62卷 457-462页

作者： chris K. ELVIDGE Pierre j.C. CHUARD Grant E. BROWN Department of Biology Concordia University 7141 Sherbrooke St. West Montreal QC H4B 1R6 Canada

The ＂dangerous niche＂ hypothesis posits that neophobia functions to reduce the cost of habitat use among animals exposed to unknown risks. For example, more dangerous foraging or higher competi- tion may lead to increased spatial neophobia. Likewise, elevated ambient predation threats have been shown to induce phenotypically plastic neophobic predator avoidance. In both cases, neophobia is argued to reduce the cost of living associated with ecological uncertainty. Here, we test the hypothesis that ambient predation shapes both neophobic predator avoidance and spatial and foraging neophobia in Trinidadian guppies. Guppies were exposed to a novel foraging arena paired with a known cue （conspecific alarm cue）, a novel cue （lemon odor）, or a stream water control in three streams differing in ambient predation risk. We demonstrate that guppies from a high-predation-risk stream exhibited risk-averse foraging patterns regardless of the chemical stimulus presented （high spatial neophobia） and that those from a low-predation-risk stream were only risk-averse when the foraging arenas were paired with conspecific alarm cue （lower spatial neophobia）. Those tested in the intermediate- predation-risk stream were consistently intermediate to the high-risk vs. low-risk populations. Our study suggests that ambient predation risk shapes both neophobic predator avoidance and space-use pat- terns and that neophobia may function as a ＂generalized＂ response to ecological uncertainty.

关键词： phenotypic plasticity predator recognition foraging predator recognition predator-prey interactions Trinidadian guppies.

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Nonalcoholic fatty liver disease: An overview of current insights in pathogenesis, diagnosis and treatment

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World journal of Gastroenterology 2008年第16期14卷 2474-2486页

作者： Tim CMA Schreuder Bart j Verwer Carin Mj van Nieuwkerk chris jj Mulder Department of Gastroenterology and Hepatology VU University Medical Center

Estimates of people suffering from overweight (one billion) and obesity (300 million) are increasing. The accumulation of triglycerides in the liver, in the absence of excess alcohol intake, has been described in the early sixties. It was not until 1980, however, that Ludwig et al named this condition nonalcoholic steatohepatitis (NASH). Subsequently, nonalcoholic fatty liver disease (NAFLD) has been used as a general name for conditions ranging from simple steatosis through steatohepatitis to end-stage liver disease (cirrhosis). Many studies have demonstrated the significant correlation with obesity and insulin resistance. Other studies have revealed a signifi- cant correlation between hepatic steatosis, cardiovascu- lar disease and increased intima-media thickness. WHO estimated that at least two million patients will develop cirrhosis due to hepatic steatosis in the years to come. Longitudinal cohort studies have demonstrated that those patients with cirrhosis have a similar risk to devel- op hepatocellular carcinoma as those with other causes of cirrhosis. Taken all together, NAFLD has become the third most important indication for liver transplantation. There- fore, training programmes in internal medicine, gastroen- terology and hepatology should stress the importance of diagnosing this entity and treat properly those at risk for developing complications of portal hypertension and con- comittant cardiovascular disease. This review will focus on the clinical characteristics, pathophysiology, imaging tech- niques and the readily available therapeutic options.

关键词： Non-alcoholic fatty liver disease Non-alcoholicsteatohepatitis Insulin resistance Liver Obesity Steatosis

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Coexistence of plastic and partially diffusive phases in a helium-methane compound

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National Science Review 2020年第10期7卷 1540-1547页

作者： Hao Gao Cong Liu Andreas Hermann Richard j.Needs chris j.Pickard Hui-Tian Wang Dingyu Xing jian Sun National Laboratory of Solid State Microstructures School of Physics and Collaborative Innovation Center of Advanced MicrostructuresNanjing University Centre for Science at Extreme Conditions and The School of Physics and Astronomy The University of Edinburgh Theory of Condensed Matter Group Cavendish Laboratory Department of Materials Science & Metallurgy University of Cambridge Advanced Institute for Materials Research Tohoku University

Helium and methane are major components of giant icy planets and are abundant in the universe. However,helium is the most inert element in the periodic table and methane is one of the most hydrophobic molecules, thus whether they can react with each other is of fundamental importance. Here, our crystal structure searches and first-principles calculations predict that a He;CH;compound is stable over a wide range of pressures from 55 to 155 GPa and a HeCH;compound becomes stable around 105 GPa. As nice examples of pure van der Waals crystals, the insertion of helium atoms changes the original packing of pure methane molecules and also largely hinders the polymerization of methane at higher pressures. After analyzing the diffusive properties during the melting of He;CH;at high pressure and high temperature, in addition to a plastic methane phase, we have discovered an unusual phase which exhibits coexistence of diffusive helium and plastic methane. In addition, the range of the diffusive behavior within the helium-methane phase diagram is found to be much narrower compared to that of previously predicted helium-water compounds. This may be due to the weaker van der Waals interactions between methane molecules compared to those in helium-water compounds, and that the helium-methane compound melts more easily.

关键词： crystal structure prediction ab initio molecular dynamics ab initio calculations high pressure and high temperature melting and phase transition collective motion

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Finite-size correction for slab supercell calculations of materials with spontaneous polarization

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npj Computational Materials 2021年第1期7卷 520-528页

作者： Su-Hyun Yoo Mira Todorova Darshana Wickramaratne Leigh Weston chris GVan de Walle jörg Neugebauer Department of Computational Materials Design Max-Planck-Institut für Eisenforschung GmbHDüsseldorfGermany Materials Department University of California Santa BarbaraSanta BarbaraCAUSA Center for Computational Materials Science US Naval Research LaboratoryWashingtonDCUSA

The repeated slab approach has become a de facto standard to accurately describe surface properties of materials by density functional theory calculations with periodic boundary *** materials exhibiting spontaneous polarization,we show that the conventional scheme of passivation with pseudo hydrogen is unable to realize a charge-neutral *** presence of a net surface charge induces via Gauss’s law a macroscopic electric field through the slab and results in poor size convergence with respect to the thickness of the *** propose a modified passivation method that accounts for the effect of spontaneous polarization,describes the correct bulk limits and boosts convergence with respect to slab *** robustness,reliability,and superior convergence of energetics and electronic structure achieved by the proposed method are demonstrated using the example of polar ZnO surfaces.

关键词： surface convergence size

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Building Expertise on FAIR Through Evolving Bring Your Own Data(BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé Lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis Luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel Lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort chris T.Evelo Alasdair j.G.Gray Marc Hanauer Kristina Hettne joep de Ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.Wilkinson Egon L.Willighagen Mascha jansen Barend Mons Marco Roos Annika jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly Department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands Department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands Department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands Department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands Department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The Leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring Your Own Data"workshops(BYODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The BYOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these BYODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring Your Own Data Workshop BYOD

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Reply:Is the evolution of tumors Darwinian or non-Darwinian?

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National Science Review 2018年第1期5卷 17-19页

作者： Marc j Williams Benjamin Werner chris P Barnes Trevor A Graham Andrea Sottoriva Evolution and Cancer Laboratory Barts CancerInstitute Queen Marry University of London Department of Cell and Developmental Biology University College London Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX) University College London Centre for Evolution and Cancer The Institute of Cancer Research Department of Genetics Evolution and EnvironmentUniversity College London

Wu and colleagues’letter discusses the limitations of the use of a single sample per tumor to investigate neutral evolution in human *** evolution describes the situation in which there is no differential clonal selection amongst the population of cells within a cancer:all mutations thataccrue during growth are passengers and all drivers were already present in the

关键词： Reply:Is the evolution of tumors Darwinian or non-Darwinian VAF

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The endoplasmic reticulum: A dynamic and well-connected organelle

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journal of Integrative Plant Biology 2015年第1期57卷 50-62页

作者： chris Hawes Petra Kiviniemi Verena Kriechbaumer Department of Biological and Medical Sciences Oxford Brookes University

The endoplasmic reticulum forms the first compart- ment in a series of organelles which comprise the secretory pathway, it takes the form of an extremely dynamic and pleomorphic membrane-bounded network of tubules and cisternae which have numerous different cellular functions. In this review, we discuss the nature of endoplasmic reticulum structure and dynamics, its relationship with closely associated organelles, and its possible function as a highway for the distribution and delivery of a diverse range of structures from metabolic complexes to viral particles.

关键词： Actin endomembranes Golgi microtubules myosin

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Evaluation of Cladribine treatment in refractory celiac disease type Ⅱ

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World journal of Gastroenterology 2011年第4期17卷 506-513页

作者： Greetje j Tack Wieke HM Verbeek Abdul Al-Toma Dirk j Kuik Marco Wj Schreurs Otto Visser chris jj Mulder Department of Gastroenterology and Hepatology VU University Medical Center Department of Gastroenterology and Hepatology St. Antonius Hospital Department of Epidemiology and Biostatistics VU University Medical Center Department of Pathology VU University Medical Center Department of Haematology VU University Medical Center

AIM: To evaluate cladribine [2-chlorodeoxyadenosine (2-CdA)] therapy in refractory celiac disease (RCD) Ⅱ. METHODS: An open-label cohort-study of RCD Ⅱ patients treated with 2-CdA was performed between 2000 and 2010. Survival rate, enteropathy associated T-cell lymphoma (EATL) occurrence, clinical course, and histological and immunological response rates were evaluated. RESULTS: Overall, 32 patients were included with a median follow-up of 31 mo. Eighteen patients responded well to 2-CdA. Patients responsive to 2-CdA had a statistically significant increased survival compared to those who were unresponsive. The overall 3- and 5-year survival was 83% in the responder and 63% and 22% in the non-responder group, respectively. The overall 2-year clinical, histological and immunological response rates were 81%, 47% and 41%, respectively. Progression into EATL was reported in 16%, all of these patients died. CONCLUSION: Treatment of RCD Ⅱ with 2-CdA holds promise, showing excellent clinical and histological response rates, and probably less frequent transition into EATL.

关键词： Cladribine Refractory celiac disease Clinical course Enteropathy associated T-cell lymphoma Survival

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Immunostimulation in the era of the metagenome

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Cellular & Molecular Immunology 2011年第3期8卷 213-225页

作者： Amy D Proal Paul j Albert Greg P Blaney Inge A Lindseth chris Benediktsson Trevor G Marshall Murdoch University PerthWAAustralia Weill Cornell Medical College New YorkNYUSA Stillpoint Centre VancouverBCCanada 4M-Klinikken OsloNorway Autoimmunity Research Foundation Thousand OaksCAUSA

Microbes are increasingly being implicated in autoimmune *** calls for a re-evaluation of how these chronic inflammatory illnesses are routinely *** standard of care for autoimmune disease remains the use of medications that slow the immune response,while treatments aimed at eradicating microbes seek the exact opposite-stimulation of the innate immune *** is complicated by a cascade of sequelae,including exacerbated inflammation,which occurs in response to microbial *** the past 8 years,we have collaborated with American and international clinical professionals to research a model-based treatment for inflammatory *** intervention,designed to stimulate the innate immune response,has required a reevaluation of disease progression and *** is the inherent conflict between palliation and microbicidal *** microbicidal activity was experienced as immunopathology-a temporary worsening of *** studies are needed,but they will require careful planning to manage this immunopathology.

关键词： antimicrobial peptides autoimmune disease immune reconstitution inflammatory syndrome immunopathology innate immunity metagenomics

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