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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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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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How to manage inflammatory bowel disease during the COVID-19 pandemic:A guide for the practicing clinician

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World Journal of Gastroenterology 2021年第11期27卷 1022-1042页

作者： Júlio Maria Fonseca Chebli Natália Sousa Freitas Queiroz Adérson Omar Mourão Cintra Damião Liliana Andrade Chebli Márcia Henriques de Magalhães Costa Rogério Serafim parra Division of Gastroenterology Department of MedicineInflammatory Bowel Disease CenterFederal University of Juiz de ForaJuiz de Fora 36036-900MGBrazil Department of Gastroenterology University of São Paulo School of MedicineSão Paulo 05403-000SPBrazil Department of Clinical Medicine Fluminense Federal UniversityRio de Janeiro 24210-200RJBrazil Department of Surgery and Anatomy Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto 14048-900SPBrazil

Managing inflammatory bowel disease(IBD)during the coronavirus disease 2019(COVID-19)pandemic has been a challenge faced by clinicians and their patients,especially concerning whether to proceed with biologics and immunosuppressive agents in the background of a global outbreak of a highly contagious new coronavirus(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2).The knowledge about the impact of this virus on patients with IBD,although it is still scarce,is rapidly *** particular,concerns surrounding medications’impact for IBD on the risk of acquiring SARS-CoV-2 infection or developing COVID-19,and potentially exacerbate viral replication and the COVID-19 course,are a current thinking of both practicing clinicians and providers caring for patients with *** patients with IBD infected with SARS-CoV-2 depends on both the clinical activity of the IBD and the occasional development and severity of *** this review,we summarize the current data regarding gastrointestinal involvement by SARS-CoV-2 and pharmacologic and surgical management for IBD concerning this infection,and the COVID-19 impact on both the patient's psychological functioning and endoscopy services,and we concisely summarize the telemedicine roles during the COVID-19 pandemic.

关键词： Inflammatory bowel disease SARS-CoV-2 COVID-19 Crohn disease Colitis ulcerative Biological therapy

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Estimation of Timber Production of Five Species of the Tamaulipas Thorny Shrubs Growing in Native Stands and Plantations

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Open Journal of Forestry 2014年第3期4卷 239-248页

作者： Ngangyo Heya Maginot Foroughbakhch Pournavab Rahim Carrillo-parra Artemio Salas Cruz Lidia-Rosaura Department of Botany Faculty of Biological Sciences University Autonomous of Nuevo León University Town San Nicolás de los Garza Mexico Laboratory of Wood Tecnology Faculty of Forestry Sciences University Autonomous of Nuevo León Linares Mexico

Shrub species have a great capacity to develop in extreme climatic conditions;this ability has a direct influence on their development and productivity in timber and firewood. In this paper, the timber’s production of experimental plantation aged 28 years of Acacia berlandieri (Benth.), Havardia pallens (Benth.) Britton & Rose, Helietta parvifolia (Gray) Benth., Ebenopsis ebano (Berl.) Barneby and Acacia wrightii (Benth.) species is quantified and compared with the production of the same species developed naturally in the native bush. The variables recorded were the number of shoots per tree, total height, basal diameter and diameter at breast height of each tree to determine the volume of wood with the Smalian equation. The results indicate that the volume of usable wood was higher in experimental plantation than that on native vegetation for H. parvifolia, A. berlandieri and H. pallens. The species that produced the highest volume of timber were H. parvifolia (0.396 m3·ha-1·year-1) in plantations and E. ebano (0.118 m3·ha-1·year-1) in native shrubs, species with lower production were H. pallens (0.059 m3·ha-1·year-1) and A. berlandieri (0.052 m3·ha-1·year-1) in the native area. The highest number of shoots was registered for A. berlandieri and H. parvifolia, with eight shoots per tree in experimental plantations of both species compared with native vegetation, which was five and three shoots per tree respectively. These results high-light the importance of developing plantations in degraded areas of scrub, which can increase timber volume production.

关键词： Timber Shoots Tamaulipas Thorny Scrub Plantation Native Vegetation

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Laccases stabilization with phosphatidylcholine liposomes

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Journal of Biophysical Chemistry 2012年第1期3卷 81-87页

作者： Meritxell Martí Andrea Zille Artur Cavaco-Paulo José Luís parra Luisa Coderch Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain

In recent years, there has been an upsurge of interest in enzyme treatment of textile fibres. Enzymes are globular proteins whose catalytic function is due to their three dimensional structure. For this reason, stability strategies make use of compounds that avoid dismantling or distorting protein 3D structures. This study is concerned with the use of microencapsulation techniques to optimize enzyme stabilization. Laccases were embedded in phophatidylcholine liposomes and their encapsulation capacity was assessed. Their enzymatic activity and stability were analyzed, comparing free-enzymes, enzymes in liposomes, and the lipid fraction separated from the aqueous fraction. An increase in their encapsulation efficiency was found at higher lipid/laccase ratios. Relative activity of enzyme-containing vesicles has also been shown to be retained much more than that of free native enzymes. The loss of activity of laccases entrapped in the vesicles in the total stability process is lower than 10% compared with 40% to 60% of loss of free-laccases after heating the samples for 3 days. Laccase stabilization could be of interest to future textile or cosmetic applications because of their potential for environmentally friendly oxidation technologies.

关键词： MLV Liposome Enzymes Laccases Encapsulation Stability

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Role of chemokines and their receptors in viral persistence and liver damage during chronic hepatitis C virus infection

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World Journal of Gastroenterology 2008年第47期14卷 7149-7159页

作者： Juan R Larrubia Selma Benito-Martínez Miryam Calvino Eduardo Sanz-de-Villalobos Trinidad parra-Cid Department of Gastroenterology Guadalajara University HospitalUniversity of AlcaláDonante de Sangre st.19002 GuadalajaraSpain Guadalajara University Hospital University of AlcaláDonante de Sangre st.19002 GuadalajaraSpain

Chemokines produced in the liver during hepatitis C virus(HCV) infection induce migration of activated T cells from the periphery to infected *** milieu of chemokines secreted by infected hepatocytes is predominantly associated with the T-helper cell/Tc1 T cell(Th1/Tc1) *** chemokines consist of CCL3(macrophage inflammatory protein-1α;MIP-1α),CCL4(MIP-1β),CCL5(regulated on activation normal T cell expressed and secreted;RANTES),CXCL10(interferon-γ-inducible protein-10;IP-10),CXCL11(interferon-inducible T-cell α chemoattractant;I-TAC),and CXCL9(monokine induced by interferon γ;Mig) and they recruit T cells expressing either CCR5 or CXCR3 chemokine *** and peripheral blood levels of these chemokines are increased during chronic hepatitis *** interaction between chemokines and their receptors is essential in recruiting HCV-specific T cells to control the *** the adaptive immune response fails in this task,non-specific T cells without the capacity to control the infection are also recruited to the liver,and these are ultimately responsible for the persistent hepatic *** modulation of chemokine receptor expression and chemokine secretion could be a viral escape mechanism to avoid specific T cell migration to the liver during the early phase of infection,and to maintain liver viability during the chronic phase,by impairing non-specific T cell *** chemokines and their receptors correlate with liver damage,and CXCL10(IP-10) and CXCR3 levels have shown a clinical utility as predictors of treatment response *** regulation of chemokines and their receptors could be a future potential therapeutic target to decrease liver inflammation and to increase specific T cell migration to the infected liver.

关键词： Chemokines Chemokine receptors Hepatitis C virus Viral hepatitis pathogenesis Persistentinfection Viral escape mechanism

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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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Rice(Oryza sativa L.)plant protection using dual biological control and plant growth-promoting agents:Current scenarios and future prospects

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Pedosphere 2023年第2期33卷 268-286页

作者： Debasis MITRA Sergio DE LOS SANTOS-VILLALOBOS Fannie Isela parra-COTA Ana María Garcia MONTELONGO Erika Lorena BLANCO Vanessa L.LIRA Adeyemi N.OLATUNBOSUN Bahman KHOSHRU Rittick MONDAL Parameswaran CHIDAMBARANATHAN Periyasamy PANNEERSELVAM Pradeep K.DAS MOHAPATRA Department of Microbiology Raiganj UniversityRaiganjUttar DinajpurWest Bengal 733134(India) Instituto Tecnológico de Sonora 5 de febrero 818.Col.CentroCd.ObregónSonora 85000(Mexico) Campo Experimental Norman E.Borlaug-Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias(INIFAP)Norman E.Borlaug Km.12C.P.Ciudad ObregónSonora 85000(Mexico) Laboratorio de Investigación en Biotecnología y Química de Polímeros Decanato de InvestigaciónUniversidad Nacional Experimental del TáchiraSan Cristóbal 5001(Venezuela) Departamento de Micologia Federal University of PernambucoRecifePE 50670-901(Brazil) Department of Plant Physiology and Crop Production Federal University of AgricultureAbeokuta 111101(Nigeria) Department of Soil Science Faculty of AgricultureUniversity of TabrizTabriz 51664(Iran) Department of Sericulture Raiganj UniversityRaiganjUttar DinajpurWest Bengal 733134(India) Biotechnology Crop Improvement DivisionIndian Council of Agricultural Research(ICAR)-National Rice Research InstituteCuttackOdisha 753006(India) Microbiology Crop Production DivisionICAR-National Rice Research InstituteCuttackOdisha 753006(India) Professor A.K.Bothra Environment Conservation Centre Raiganj UniversityRaiganjUttar DinajpurWest Bengal 733134(India)

Various microorganisms live in association with different parts of plants and can be harmful,neutral,or beneficial to plant *** microbial inhabitants of plants can control plant diseases by contesting with,predating on,or antagonizing plant pathogens and by inducing systems for plant defense.A range of methods,including plant growth-promoting microorganisms(PGPMs)as biological control agents(BCAs)(BCA-PGPMs)are used for the biological management and control of plant *** BCAs interact with plants by inducing resistance or priming plants without direct interaction with the *** BCAs operate via nutrient competition or other mechanisms to modulate the growth conditions for the ***,PGPMs can be applied alone or together with other chemicals or carriers to control various crop *** review highlights the effective types of BCA-PGPMs and their applications,roles,carrier based-formulations,and responses to rice(Oryza sativa L.)*** plant disease management prospects are promising,and growers’increasing demand for BCA-PGPM products can be exploited as an effective approach to the management of plant diseases,as well as to improve yield,environmental protection,biological resources,and agricultural system sustainability.

关键词： biological control agent plant disease plant growth-promoting microorganism plant health plant pathogen

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Effect of Sn on synthesis of nanocrystalline Ti-based alloy with fcc structure

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Transactions of Nonferrous Metals Society of China 2020年第8期30卷 2119-2131页

作者： C.AGUILAR E.PIO A.MEDINA C.parra R.MANGALARAJA P.MARTIN I.ALFONSO K.TELLO Departamento de Ingeniería Metalúrgica y de Materiales Departamento de Física(+)Universidad Técnica Federico Santa MaríaValparaísoChile Instituto de Investigación en Metalurgia y Materiales Universidad Michoacana de San Nicolás de HidalgoMoreliaMéxico Laboratorio de Cerámicos Avanzados y Nanotecnologia Departamento de Ingeniería de MaterialesUniversidad de ConcepciónConcepciónChile Instituto de Investigaciones en Materiales Universidad Nacional Autónoma de MéxicoCampus Morelia UNAMMoreliaMéxico

The effect of the amount of Sn on the formation of fcc phase in Ti-13 Ta-x Sn(x=3,6,9 and 12,at.%)alloys was *** alloys were synthesized by mechanical alloying using a planetary mill,jar and balls of stabilized *** Rietveld refinement,it was found that the obtained fcc phase has crystallite size smaller than 10 nm and microstrain larger than *** conditions are required to form an fcc phase in Ti-based *** all samples,the microstructure of the fcc phase consists of equiaxial crystallites with sizes smaller than 10 *** largest presence of fcc phase in the studied Ti alloy was found with 6 at.%Sn,because this alloy exhibits the largest microstrain(1.5×10-2)and crystallite size of 6.5 *** data reveal that a solid solution and an amorphous phase were formed during *** necessary conditions to promote the formation of solid solution and amorphous phases were determined using thermodynamic *** the amount of Sn increases,the energy required to form an amorphous phase varies from approximately 10 to approximately-5 k J/mol for 3 and 12 at.%Sn,*** thermodynamic calculations are in agreement with XRD patterns analysis and HRTEM results.

关键词： Ti-based alloy phase transformation fcc phase Rietveld analysis mechanical alloying

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Costimulatory molecule programmed death-1 in the cytotoxic response during chronic hepatitis C

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World Journal of Gastroenterology 2009年第41期15卷 5129-5140页

作者： Juan Ramón Larrubia Selma Benito-Martínez Joaquín Miquel Miryam Calvino Eduardo Sanz-de-Villalobos Trinidad parra-Cid Translational Hepatology Unit Guadalajara University Hospital University of Alcalá

Hepatitis C virus（HCV）-specific CD8^＋ T cells play an important role in the resolution of HCV infection. Nevertheless, during chronic hepatitis C these cells lack their effector functions and fail to control the virus. HCV has developed several mechanisms to escape immune control. One of these strategies is the upregulation of negative co-stimulatory molecules such us programmed death-1 （PD-1）. This molecule is upregulated on intrahepatic and peripheral HCV-specific cytotoxic T cells during acute and chronic phases of the disease, whereas PD-1 expression is low in resolved infection. PD-1 expressing HCV-specific CD8^＋ T cells are exhausted with impairment of several effector mechanisms, such as： type-1 cytokine production, expansion ability after antigen encounter and cytotoxic ability. However, PD-1 associated exhaustion can be restored by blocking the interaction between PD-1 and its ligand （PD-L1）. After this blockade, HCV-specific CD8^＋ T cells reacquire their functionality. Nevertheless, functional restoration depends on PD-1 expression level. High PD-l-expressing intrahepatic HCV-specific CD8^＋ T cells do not restore their effector abilities after PD-1/ PD-L1 blockade. The mechanisms by which HCV is able to induce PD-1 up-regulation to escape immune control are unknown. Persistent TCR stimulation by a high level of HCV antigens could favour early PD-1 induction, but the interaction between HCV core protein and gClq receptor could also participate in this process. The PD-1/PD-L1 pathway modulation could be a therapeutic strategy, in conjunction with the regulation of others co-stimulatory pathways, in order to restore immune response aclainst HCV to succeed in clearing the infection.

关键词： Chronic hepatitis Exhaustion Hepatitis C virus core Hepatitis C virus Programmed death-1 Programmed death-1 ligand

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