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The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

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Current Zoology 2015年第5期61卷 874-885页

作者： Konstantinos ANGELIS mario DOS rEIS Department of Genetics Evolution and Environment University College London Gower Street London WC 1E 6BT UK

Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].

关键词： Ancestral polymorphism Incomplete lineage sorting Divergence time estimation Gene tree Species tree

Estimating the Lost Economic Production Caused by Internal Displacement Because of Disasters

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International Journal of Disaster risk Science 2018年第4期9卷 496-506页

作者： mario A.Salgado-Gálvez Centre Internacional de Metodes Numerics en Enginyeria(CIMNE) 08034 BarcelonaSpain

Disasters are a large cause of internal displacement at the global level, in 2017 alone affecting more than19 million people. This dimension of disaster risk is usually overlooked in many disaster risk management strategies and assessments. It is only very recently that efforts to quantify displacement risk and integrate that dimension into existing physical risk models have been made. A key component of internal displacement assessment is the quantification of its economic impacts, both direct and indirect, not only to make a figure available but to raise awareness and increase accountability among governments, stakeholders, policymakers, and decision *** article presents a novel and peril-agnostic methodology with which to estimate, using a scenario-based approach, the economic production lost because of internal population displacement. The methodology is applied by using as a triggering event the April 2015 Gorkha, Nepal M7.8 earthquake. The method quantifies the indirect cost caused by internal population displacement because of that event in terms of lost economic production and estimates the loss to be between USD 400 and 850 million.

关键词： Disability adjusted life years Disaster risk Internally displaced people Lost economic production Disaster risk assessment

Avian preference for close proximity to human habitation and its ecological consequences

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Current Zoology 2018年第5期64卷 623-630页

作者： Anders Pape MOLLEr mario DiAZ Ecologie Systematique Evolution CNRS Universite Paris-Sud AgroParisTech Universite Pari-Saclay 0rsay Cedex F-91400 France Department of Biogeography and Global Change (BGC-MNCN-CSIC) National Museum of Natural Sciences CSIC c/Serrano 155bis Madrid E-28006 Spain

Human proximity often have negative consequences for wildlife. However, animals may also benefit from human proximity in terms of availability of resources and protection against predators and parasites. We recorded the distance between all birds detected during the breeding season along 18 5-kin transects and the nearest inhabited house in three areas of 50 km2 in Spain, France, and Denmark. More than three quarters of birds were located closer than 100 m to the nearest house, while the null expectation was less than a third. Mean distance for species was correlated with degree of bird urbanization and with flight initiation distance. Habitat specialist species with small breeding territories tended to live closer to houses. Birds from species having more broods per year, larger annual fecundity and lower nest predation rate lived closer to human habitation. Breeding range size, population density, and continental breeding population sizes were larger for species living closer to human habitation. Most relationships between distance to houses and bird traits had a strong phylogenetic signal, but most additive trait effects remained after phylogenetic correction. Proximity to human habitation was a main driver of the distribution of birds, with most individuals and species tightly linked to inhabited houses. Living close to human habitation was associated with success in the colonization of urban habitats and with consistent changes in distribution, abundance, behavior, and life history. replicated measurements of the spatial and tempo- ral variation in these distributions may be useful for monitoring and analyzing the ongoing process of organisms＇ urbanization.

关键词： birds distance to nearest house flight initiation distance humans refuge urbanization.

Applying rock mass classifications to carbonate rocks for engineering purposes with a new approach using the rock engineering system

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Journal of rock Mechanics and Geotechnical Engineering 2017年第2期9卷 364-369页

作者： Gioacchino Francesco Andriani mario Parise Dipartimento di Scienze della Terra e Geoambientali Università degli Studi di Bari Aldo MoroVia E. Orabona n. 4Bari 70125Italy

Classical rock mass classification systems are not applicable to carbonate rocks,especially when these are affected by karst *** applications to such settings could therefore result in outcomes not representative of the real stress-strain *** this study,we propose a new classification of carbonate rock masses for engineering purposes,by adapting the rock engineering system(rES) method by Hudson for fractured and karstified rock masses,in order to highlight the problems of implementation of geomechanical models to carbonate *** new approach allows a less rigid classification for carbonate rock masses,taking into account the local properties of the outcrops,the site conditions and the type of engineering work as well.

关键词： rock mass classification Carbonates Karst rock engineering system(rES)

Exosomes： multitask cargo carriers modulating innate mmunity to viruses

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Cellular & Molecular Immunology 2017年第5期14卷 476-477页

作者： mario U Mondelli research Laboratories Department of InfectioutDiseases Fondazione IRCCS Policlinico SanMatteo and Department of Internal Medicin~and Therapeutics University of Pavia Pavi~27100 Italy /

Chronic infection with hepatitis B virus （HBV） is a major cause, ofcirrhosis and liver cancer worldwide. HBV is a smart DNA virus that replicates through an rNA intermediate. The viral genome translocates to the nucleus where it is converted into covalently closed circttlar DNA （cccDNA） serving as a template for viral transcription.

关键词： multitask cargo carriers innate immunity viruses

Both comorbidity burden and low testosterone can explain symptoms and signs of testosterone deficiency in men consulting for sexual dysfunction

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Asian Journal of Andrology 2020年第3期22卷 265-273页

作者： Giulia rastrelli Giovanni Corona mario Maggi Sexual Medicine and Andrology Unit Department of Experimental and Clinical Biomedical SciencesUniversity of FlorenceViale Pieraccini 6Florence 50139Italy Endocrinology Unit Medical DepartmentMaggiore-Bellaria HospitalLargo Nigrisoli 2Bologna 40133Italy I.N.B.B. Biostructures and Biosystems National InstituteViale delle Medaglie d'Oro 305Rome(X)136Italy Endocrinology Unit Department of Experimental Clinical and Biomedical Sciences**Mario Serio"University of FlorenceViale Pieraccini 6Florence 50139Italy.

Low testosterone(T)is frequent in men with chronic *** clinical features of T deficiency(TD)overlap with those of chronic *** aim of this study is to evaluate the relative contribution of chronic disease score(CDS)and low T to the presenee of TD symptoms.A consecutive series of 3862 men(aged 52.1±13.1 years)consulting for sexual dysfunction were *** clinical and biochemical parameters were collected,in eluding the structured interview,ANDrOTEST,for the assessme nt of TD *** color Doppler ultrasound(PCDU)was also *** on the medications taken,the CDS was *** a subset of 1687 men,information on mortality was collected(follow-up of 4.3±2.6 years).Higher CDS was associated with lower free and total T(TT)as well as with higher ANDrOTEST *** introducing CDS and TT in multivariable models adjusted for age,severe erectile dysfunctio n and impaired morning erectio ns were associated with both CDS(odds ratio and 95%confide nee interaval,Or[95%Cl]=1.25[1.13;1.37]and 1.38[1.29;1.48],respectively)and low TT(Or[95%Cl]=1.11[1.00;1.23]and 1.13[1.06;1.21],respectively).Similar results were obtained for PCDU *** sexual desire was associated with low TT(Or[95%Cl]=1.21[1.13;1.30]),whereas it was inversely related with CDS(Or[95%Cl]=0.91[0.84;0.97]).When considering mortality for major cardiovascular events,TTredictor(hazard ratio[95%Cl]=5.57[1.51;20.63]).Chronic illnesses are associated with an overt *** chronic diseases and low T can be invoIved in determining symptoms present in subjects complaining for sexual *** should be considered in the diagnostic workup for TD.

关键词： chronic diseases erectile dysfunction sexual symptoms testosterone deficiency

Heterogeneous catalysis under flow for the 21st century fine chemical industry

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Green Energy & Environment 2021年第2期6卷 161-166页

作者： rosaria Ciriminna mario Pagliaro rafael Luque Istituto per Io Studio dei Mate riali Nanostnuturati CNRwia U.La Malfa 15390146PulemoItaly Deparamento de Quimica Orginica Univeridad de CordobaCampus de RabonalesEdificio Marie Curie(C-3)Cra Nnal IV-Akm 396Cordoba14014Spain Peoples Friendship University of russia(rUDN Universiy) 6 Miklukho Maklaya St117198MoscowRussia

Due to metal leaching and poor catalyst stability, the chemical industry's fine chemical and pharmaceutical sectors have been historically reluctant to use supported transition metal catalysts to manufacture fine chemicals and active pharmaceutical ingredients. With the advent of new generation supported metal catalysts and flow chemistry, we argue in this study, this situation is poised to quickly change. Alongside heterogenized metal nanoparticles, both single-site molecular and single-atom catalyst will become ubiquitous. This study offers a critical outlook taking into account both technical and economic aspects.

关键词： Fine chemical Heterogeneous catalysis Single atom catalysis Green chemistry Chemical industry

Fast Solvers of Fredholm Optimal Control Problems

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Numerical Mathematics(Theory,Methods and Applications) 2010年第4期3卷 431-448页

作者： mario Annunziato Alfio Borzi Universita degli Studi di Salerno Dipartimento di Matematica e InformaticaVia Ponte Don Melillo84084 Fisciano(SA)Italia Universita degli Studi del Sannio Dipartimento e Facolta di IngegneriaPalazzo Dell'Aquila Bosco LucarelliCorso Garibaldi 10782100 BeneventoItalia Institutfr Mathematik und Wissenschaftliches rechnen Karl-Franzens-Universitt GrazHeinrichstr.368010 GrazAustria.

The formulation of optimal control problems governed by Fredholm integral equations of second kind and an efficient computational framework for solving these control problems is presented. Existence and uniqueness of optimal solutions is proved.A collective Gauss-Seidel scheme and a multigrid scheme are discussed. Optimal computational performance of these iterative schemes is proved by local Fourier analysis and demonstrated by results of numerical experiments.

关键词： Optimal control theory Fredholm integral equations of second kind iterative methods

A brief review of genome editing technology for generating animal models

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Frontiers of Agricultural Science and Engineering 2020年第2期7卷 123-128页

作者： Haoyi WANG Sen WU mario r.CAPECCHI rudolf JAENISCH State Key Laboratory of Stem Cell and reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China Institute for Stem Cell and regeneration Chinese Academy of SciencesBeijing 100101China Beijing Advanced Innovation C enter for Food Nutrition and Human Health China Agricultural UniversityBeijing 100193China State Key L aboratory of Agrobiotechnology College of Biological SciencesChina Agricultural UniversityBeijing 100193China Departm ent of Human Genetics University of Utah School of MedicineSalt Lake CityUT 84112USA Whitehead Institute for Biomedical research CambridgeMA 02142USA Departm ent of Biology Massachusetts Institute of TechnologyCambridgeMA 02142USA

The recent development of genome editing technologies has given researchers unprecedented power to alter DNA sequences at chosen genomic loci,thereby generating various genetically edited animal *** mini-review briefly summarizes the development of major genome editing tools,focusing on the application of these tools to generate animal models in multiple species.

关键词： animal model CrISPr genome editing TALEN ZFN