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Towards standardizing taxonomic ranks using divergence times-a case study for reconstruction of the Agaricus taxonomic system

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Fungal diversity 2016年第3期78卷 239-292页

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin d Hyde Philippe Callac Luis A.parra Guo-Jie Li Jean-Marc Moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in Fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S 3B2Canada Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunming 650201China INRA-UR1264 Mycologie et Sécuritédes AlimentsCS 2003233882 Villenave d’Ornon cedexFrance Avda.Padre Claret n°7 5°G09400 Aranda de DueroBurgosSpain

The recognition of taxonomic ranks in the Linnean classification system is largely *** authors have proposed the use of divergence time as a universally standardized ***(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial *** studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional *** this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and *** monophyletic groups were recognized,but most basal relationships were *** hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence *** times within the multi-gene phylogeny were estimated using BEAST *** on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic *** propose to segregate Agaricus into five subgenera and 20 *** Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are *** Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are *** Laeticolores is placed in the subgenus Minores and sections Rarolen

关键词： Agaricaceae divergence times Multi-gene phylogenetics Systematics Taxonomy

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Proteomic Study Identifies Proteins Involved in Brassinosteroid Regulation of Rice Growth

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Journal of Integrative Plant Biology 2010年第12期52卷 1075-1085页

作者： Fengru Wang Ming-Yi Bai Zhiping deng Juan A. Oses-Prieto alma L. Burlingame Tiegang Lu Kang Chong Zhi-Yong Wang Key Laboatory of PhotoSynthesis and Environmental Molecular Physiology Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Agriculture University of Hebei Baoding 071001 China department of Plant Biology Carnegie Institution for Science Stanford CA 94305 USA Mass Spectrometry Facilityl department of Pharmaceutical Chemistry University of California San Francisco CA 94143 USA Biotechnology Research Institute the Chinese Academy of Agriculture Sciences Beijing 100081 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China

Brassinosteroids （BRs） are essential hormones for growth and development of plant. In rice, BRs regulate multiple developmental processes and affect many important traits such as height, leaf angle, fertility and seed filling. We identified brassinosteroid-regulated proteins in rice using proteomic approaches and performed functional analysis of some BR-regulated proteins by overexpression experiments. Using two-dimensional difference gel electrophoresis （2-d dIGE） followed by protein identification by mass spectrometry, we compared proteomic differences in the shoots and roots of the BR-insensitive mutant d61-4 and BR-deficient mutant brd1-3. We identified a large number of proteins differentially expressed in the mutants compared with wild type control. These include a glycine-rich RNA-binding protein （OsGRP1） and a dREPP2 protein, which showed reduced levels in the BR mutants. Overexpression of these two proteins partially suppressed the dwarf phenotype of the Arabidopsis BR-insensitive mutant bri1-5. In contrast to the reduced protein level, the RNA level of OsGRP1 was not significantly affected in the BR mutants or by BR treatment, suggesting BR regulation of OsGRP1 at the posttranslational level. This study identifies many BR-regulated proteins and demonstrates that OsGRP1 functions downstream in the BR signal transduction pathway to promote cell expansion.

关键词： Regulations Brassinosteroids Bromine Proteins Protein products Rice Lymphocytes Electrophoresis RNA Mutants

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Application of formal languages in polynomial transformations of instances between NP-complete problems

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Journal of Zhejiang University-Science C(Computers and Electronics) 2013年第8期14卷 623-633页

作者： Jorge A. RUIZ-VANOYE Joaquín PREZ-ORTEGA Rodolfo A. PAZOS RANGEL Ocotlán díAZ-parra Héctor J. FRAIRE-HUACUJA Juan FRAUSTO-SOLíS Gerardo REYES-SALGAdO Laura CRUZ-REYES dACI Universidad Autónoma del Carmen Computer Science Centro Nacional de Investigación y Desarrollo Tecnológico Systems and Computer Science Instituto Tecnológico de Ciudad Madero Informatics Universidad Politécnica del Estado de Morelos Computer Science Instituto Tecnológico de Cuautla

We propose the usage of formal languages for expressing instances of NP-complete problems for their application in polynomial transformations. The proposed approach, which consists of using formal language theory for polynomial transformations, is more robust, more practical, and faster to apply to real problems than the theory of polynomial transformations. In this paper we propose a methodology for transforming instances between NP-complete problems, which differs from Garey and Johnson's. Unlike most transformations which are used for proving that a problem is NP-complete based on the NP-completeness of another problem, the proposed approach is intended for extrapolating some known characteristics, phenomena, or behaviors from a problem A to another problem B. This extrapolation could be useful for predicting the performance of an algorithm for solving B based on its known performance for problem A, or for taking an algorithm that solves A and adapting it to solve B.

关键词： Formal languages Polynomial transformations NP-completeness

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<i>d’addio</i>to Blackness

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International Journal of Astronomy and Astrophysics 2021年第4期11卷 509-516页

作者： Jose L. parra department of Physics Florida International University Miami USA

It is assumed here that the energy of a strong gravitational field creates non-linear effects over enclosed masses. This idea and the rigorous rules of the General Theory of Relativity output a metric that covers strong and weak gravitational fields. The proposed metric could be correct because it included the Schwarzschild’s metric as a particular case and has no singularities. Additionally, it appears here that the massive condition of the gravitational fields has properties like the so-called dark Matter.

关键词： Black Holes Event Horizon Schwarzschild Metric Singularity General Theory of Relativity dark Matter Neutron Stars

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Effects of dielectric stoichiometry on the photoluminescence properties of encapsulated WSe2 monolayers

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Nano Research 2018年第3期11卷 1399-1414页

作者： Javier Martfn-Sanchez Antonio Mariscal Marta de Luca Aitana Tarazaga Martin-Luengo Georg Gramse alma Halilovic Rosalia Serna Alberta Bonanni Ilaria Zardo Rinaldo Trotta Armando Rastelli Institute of Semiconductor and Solid State Physics Johannes Kepler University Linz Altenbergerstrasse 69 A-4040 Linz Austria Laser Processing Group Instituto de Optica CSIC C/Serrano 121 28006 Madrid Spain department of Physics University of Basel Klingelbergstrasse 82 4056 Basel Switzerland Institute for Biophysics Johannes Kepler University Linz Gruberstrasse 40 A-4020 Linz Austria

Two-dimensional transition metal dichalcogenide semiconductors have emerged as promising candidates for optoelectronic devices with unprecedented properties and ultra-compact footprints. However, the high sensitivity of atomically thin materials to the surrounding dielectric media imposes severe limitations on their practical applicability. Hence, to enable the effective integration of these materials in devices, the development of reliable encapsulation procedures that preserve their physical properties is required. Here, the excitonic photoluminescence （at room temperature and 10 K） is assessed on mechanically exfoliated WSe2 monolayer flakes encapsulated with SiOx and AlxOy layers by means of chemical and physical deposition techniques. Conformal coating on untreated and non- functionalized flakes is successfully achieved by all the techniques examined, with the exception of atomic layer deposition, for which a cluster-like oxide coating is formed. No significant compositional or strain state changes in the flakes are detected upon encapsulation, independently of the technique adopted. Remarkably, our results show that the optical emission of the flakes is strongly influenced by the stoichiometry quality of the encapsulating oxide. When the encapsulation is carried out with slightly sub-stoichiometric oxides, two remarkable phenomena are observed. First, dominant trion （charged exciton） photoluminescence is detected at room temperature, revealing a clear electrical doping of the monolayers. Second, a strong decrease in the optical emission of the monolayers is observed, and attributed to non-radiative recombination processes and/or carrier transfer from the flake to the oxide. Power- and temperature-dependent photoluminescence measurements further confirm that stoichiometric oxides obtained by physical deposition lead to a successful encapsulation, opening a promising route for the development of integrated two-dimensional devices.

关键词： two dimensional (2d)materials dielectric encapsulation transition metaldichalcogenides semiconductors photoluminescence WSe2

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Evolution of sexual size dimorphism and its relationship with sex ratio in carabid beetles of Genus Ceroglossus Solier

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Current Zoology 2013年第6期59卷 769-777页

作者： Hugo A. BENITEZ Jorge AVARIA-LLAUTUREO Cristian B.CANALES-AGUIRRE Viviane JEREZ Luis E. parra Cristifin E.HERNANdEZ Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT UK Instituto de Alta Investigaci6n Universidad de Tarapaca Casilla 7-D Arica Chile departamento de Zoologia Facultad de Ciencias Naturales y Oceanograficas Universidad de Concepcion Casilla 160-C Concepcion Chile departamento de Oceanografia Facultad de Ciencias Naturales y Oceanograficas Universidad de Concepci6n Casilla 160-C Concepcion Chile

Although the degree of mate competition, given extreme differences in sex ratio, explains much of the pattern of male-biased size dimorphism among diverse taxa, it fails for some species which have potential for intense male competition for mates and yet exhibit little or no sexual size dimorphism (SSd). This fact suggest that species with low SSd should be express the effect of evolutionary pressure in non-obvious geometrical shape promoted by sex ratio in an evolutionary time scale. To evaluate this hypothesis we used phylogenetic comparative method in a Bayesian framework to investigate the evolution of SSd and the role of sex ratio at inter-specific level in the species ofCeroglossus(Coleoptera: Carabidae). In our results the proportion farthest from 1:1 is associated with more disparate body shape, even though the entire group has minimum variation in sex ratio, which is an intrinsic life history character of this group considering its phylogenetic conservatism or phylogenetic signal. We suggest that the sex ratio has determined the dimorphism degree during evolution of this group, since both traits have increased or decreased together during the species divergence (i.e. positive phylogenetic correlation: r2≈0.85). We suggest that morphological studies of SSd will benefit from using comparative method with Bayesian approaches to assess the effect of phylogenetic history and its uncertainty. Finally, this will be allow to researchers to quantify the uncertainty of specific evolutionary hypotheses accounting for observed sexual dimorphism patterns.

关键词：进化保守性性别比例两性异形步甲科贝叶斯方法物种分化系统发育不确定性

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diet switch and omega-3 hydroxy-fatty acids display differential hepatoprotective effects in an obesity/nonalcoholic fatty liver disease model in mice

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World Journal of Gastroenterology 2018年第4期24卷 461-474页

作者： Roberto Rodriguez-Echevarria Jose Macias-Barragan Marcela parra-Vargas Judith Rebeca davila-Rodriguez Eduardo Amezcua-Galvez Juan Armendariz-Borunda Institute for Molecular Biology and Gene Therapy-CUCS Department of Molecular Biology and GenomicsUniversity of GuadalajaraGuadalajara 44340Mexico department of Health Sciences-CUValles University of GuadalajaraGuadalajara 46600Mexico Hospital Civil de Guadalajara Guadalajara 46600Mexico

AIM To study the effect of 18-hydroxy-eicosapentaenoic acid(18-HEPE) and 17-hydroxy-docosahexaenoic acid(17-HdHA) in a murine model of obesity/nonalcoholic fatty liver *** C57 BL/6 mice were fed with standard chow diet(Cd) or high-fat, fructose-enriched diet(HFd) for 16 wk. Then, three groups were treated for 14 d with either, diet switch(HFd for Cd), 18-HEPE, or 17-HdHA. Weightand fasting glucose were recorded on a weekly basis. Insulin tolerance test was performed at the end of treatment. Histological analysis(HE and Masson's trichrome stain) and determination of serum insulin, glucagon, glucagon-like peptide 1(GLP-1), glucose-dependent insulinotropic polypeptide, adiponectin and resistin were carried out as well as liver proteins by western *** Mice treated with hydroxy-fatty acids 18-HEPE and 17-HdHA displayed no weight loss or improved insulin sensitivity. However, these mice groups showed a significant amelioration on serum GLP-1, adiponectin and resistin levels. Also, a significant reduction on inflammatory infiltrate was observed at both portal and lobular zones. Furthermore, up-regulation of PPARα/γ protein levels was observed in liver tissue and it was associated with decreased levels of NF-κB also determined by western blot analysis. On the other hand, diet switch regimen resulted in a marked improvement in most parameters including: weight loss, increased insulin sensitivity, decreased steatosis, restored levels of insulin, glucagon, leptin, adiponectin and resistin. However, no significant changes were observed regarding inflammatory infiltrate in this last *** 18-HEPE and 17-HdHA differentially exert hepatoprotective effects through up-regulation of nuclear receptors PPARα/γ and amelioration of serum adipokines profile.

关键词： Nonalcoholic fatty liver disease Polyunsaturated fatty acids 18-hydroxy-eicosapentaenoic acid 17-hydroxy-docosahexaenoic acid Obesity

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The Knowledge of Antibiotics in Veternary Students and Repercution in Human Health

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Health 2020年第12期12卷 1632-1639页

作者： Silvia d. Peña Betancourt Silvia denise Posadas Peña Lyda Y. parra-Forero departamento de Producción Agrícola y Animal Laboratorio de Toxicología Universidad Autonoma Metropolitana Ciudad de México Mexico Instituto de Estudios Superiores de Monterrey Ciudad de México México departamento de Producción Agrícola y Animal Ciudad de México Mexico

The concept of single health is currently undoubtedly one of the most relevant in pandemic times, where humans and animals are together in the same world. Penicillin was discovered in the last century by Alexander Fleming, used against infectious agents mainly of bacterial types, such as Staphylococcus aureus, Corynebacterium, Streptococcus, Brucella and Mycobacterium are examples of cattle pathogens. The bacteria have developed defense mechanisms allowing them to survive in the host cell (mutation) even in the presence of antimicrobials (bacterial selection). The aim of the study was to examine the degree of knowledge of antibiotics through a structured survey of ten questions, addressed to eighty-six students from the Bachelor of Veterinary Medicine and Zootechnics in 2019. Based on the information collected and after analyzing their answers, 63.14% of the students work in Clinics and Universities, 89.47% recognize the need for a quantified prescription, 47.36% mentioned that the Veterinary Medicine can prescribe antimicrobials, 52.63% support the use of antimicrobials for all microorganisms including viruses, 52.63% use the labeling to consult the withdrawal time and 100% identify that it is the withdrawal time and the practices that lead to the development of antimicrobial resistance. It is concluded that most of the students identify malpractice as the trigger for bacterial resistance, however their knowledge is not adequate to avoid antibiotic resistance to humans. It is recommended to reinforce the courses of microbiology, pharmacology and virology in the Veterinary Medicine and Zootechnics degree, as well as to be updated on alternatives such as the use of phytobiotics.

关键词： Antibiotics Resistance Bacteria Veterinary Students

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What Is the Relation between Aerobic Capacity and Physical Activity Level in Adults with Congenital Heart disease?

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Congenital Heart disease 2021年第6期16卷 585-595页

作者： Kelly Ferri Maite doñate Mireia parra Guillermo ROviedo Myriam Guerra-Balic Laia Rojano-doñate Nicole Blackburn Ricard Serra-Grima FPCEE-Blanquerna Ramon Llull UniversityBarcelonaSpain Cardiology department Santa Creu and Sant Pau HospitalIIB Sant PauBarcelonaSpain Cors Units Foundation BarcelonaSpain Zoophysiology Department of BiologyAarhus UniversityAarhusDenmark Institute of Nursing and Health Research Ulster UniversityJordanstownNorthern Ireland

Background:Aerobic capacity(AC)in adults with congenital heart disease(CHd)is often reduced,mainly due to low confidence levels towards physical activity(PA).The main objective of this study was to estimate the association between PA level and AC(measured as peak of oxygen consumption,VO_(2peak))in adults with ***:A total of 183 individuals(83 women and 100 men;mean(Sd)age 36.9(11.0)years old)from Vall d’Hebron Hospital,Barcelona-Spain in 2019,participated in this cross-sectional *** AC was assessed by cardiopulmonary exercise testing(CPET)using a treadmill ramp *** values of metabolic equivalent of task(MET,MET-min·week-1)obtained by the short International Physical Activity Questionnaire(IPAQ),participants were divided into three categories of PA:health-enhancing PA(HEPA),minimally active,and ***:Median(Sd)PA was 2737.2(2835.7)MET-min·week-1,with 60 participants(32.8%)reporting HEPA,91(49.7%)minimally active,and 32(17.5%)*** demonstrated a mean VO_(2peak) of 28.9(8.8)mL·Kg^(-1)·min^(-1),showing AC values on average 13%lower than expected in a healthy ***,PA and AC were positively *** for sex and age,an increase of 1000 MET-min·week^(-1) was associated with an increase in VO_(2peak) of 0.8 units(95%CI 0.4–1.2;pdifferences in the degree of increase between sexes(p=0.427).Conclusion:These findings suggest that an increase in PA in patients with CHd significantly improves their AC,and hence,could be recommended when the goal is to improve their physical condition.

关键词： Physical activity level aerobic capacity congenital heart disease

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Refractive errors among children, adolescents and adults attending eye clinics in Mexico

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International Journal of Ophthalmology(English edition) 2017年第5期10卷 796-802页

作者： Francisco Gomez-Salazar Abraham campos-Romero Humberto Gomez-Campana Cinthia Cruz-Zamudio Mariano Chaidez-Felix Nidia Leon-Sicairos Jorge Velazquez-Roman Hector Flores-Villasenor Secundino Muro-Amador alma Marlene Guadron-Llanos Javier J.Martinez-Garcia Joel Murillo-Llanes Jaime Sanchez-Cuen Alejando Llausas-Vargas Gerardo Alapizco-Castro Ana Irineo-Cabrales Enrique Graue-Hernandez Tito Ramirez-Luquin Adrian Canizalez-Roman Salud digna Para Todos I.A.P Culiacan Sinaloa 80000Mexico CIASaP School of Medicine Autonomous University of Sinaloa Culiacan Sinaloa 80246 Mexico Pediatric Hospital of Sinaloa Culiacan Sinaloa 80200Mexico The Women's Hospital Secretariat of Health Culiacan Sinaloa 80127 Mexico department of Gastroenterology Regional Hospital ISSSTECuliacan 80230 Sinaloa Mexico Education and Research department Regional general Hospital No. 1 IMSS Culiacan Sinaloa 80220 Mexico department of Cornea and Refractive Surgery Institute of Ophthalmology 'Conde de Valenciana' Mexico City 06800Mexico

AIM：To assess the proportion of refractive errors in the Mexican population that visited primary care optometry clinics in fourteen states of Mexico. METHOdS：Refractive data from 676 856 patients aged 6 to 90 y were collected from optometry clinics in fourteen states of Mexico between 2014 and 2015. The refractive errors were classified by the spherical equivalent（SE）, as follows：sphere＋？ cylinder. Myopia（SE〉-0.50 d）, hyperopia（SE〉＋0.50 d）, emmetropia（-0.50≤SE≤＋0.50）, and astigmatism alone（cylinder≥-0.25 d）. A negative cylinder was selected as a ***：The proportion（95% confidence interval） among all of the subjects was hyperopia 21.0%（20.9-21.0）, emmetropia 40.7%（40.5-40.8）, myopia 24.8%（24.7-24.9） and astigmatism alone 13.5%（13.4-13.5）. Myopia was the most common refractive error and frequency seemed to increase among the young population（10 to 29 years old）, however, hyperopia increased among the aging population（40 to 79 years old）, and astigmatism alone showed a decreasing trend with age（6 to 90y; from 19.7% to 10.8%）. There was a relationship between age and all refractive errors（approximately 60%, aged 50 and older）. The proportion of any clinically important refractive error was higher in males（61.2%） than in females（58.3%; P〈0.0001）. From fourteen states that collected information, the proportion of refractive error showed variability in different geographical areas of ***：Myopia is the most common refractive error in the population studied. This study provides the first data on refractive error in Mexico. Further programs and studies must be developed to address the refractive errors needs of the Mexican population.

关键词： refractive errors hyperopia myopia astigmatism

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