100 Works

Coronavirus prevalence in Brazilian Amazon and Sao Paulo city

Tassila Salomon, Oliver Pybus, Rafael França, Marcia Castro, Ester Cerdeira Sabino, Christopher Dye, Michael Busch, Moritz U. G. Kraemer, Charles Whittaker, Andreza Santos, Nuno Faria, Rafael Pereira, Lewis Buss, , Claudia Abrahim, Maria Carvalho, Allyson Costa, Manoel Barral-Netto, Crispim Myuki, Brian Custer, Cesar De Almeida-Neto, Suzete Ferreira, Nelson Fraiji, Susie Gurzenda, Leonardo Kamaura … & Maria Belotti
SARS-CoV-2 spread rapidly in the Brazilian Amazon. Mortality was elevated, despite the young population, with the health services and cemeteries overwhelmed. The attack rate in this region is an estimate of the final epidemic size in an unmitigated epidemic. Here we show that by June, one month after the epidemic peak in Manaus, capital of the Amazonas state, 44% of the population had detectable IgG antibodies. This equates to a cumulative incidence of 52% after...

Fatal outcome of chikungunya virus infection in Brazil

William Marciel Souza, Shirlene Telmos Silva De Lima, John Washington Cavalcante, Darlan Da Silva Candido, Marcilio Jorge Fumagalli, Jean-Paul Carrera, Leda Maria Simões Mello, Fernanda Montenegro De Carvalho Araújo, Izabel Letícia Cavalcante Ramalho, Francisca Kalline De Almeida Barreto, Deborah Nunes De Melo Braga, Adriana Rocha Simião, Mayara Jane Miranda Da Silva, Rhaquel De Morais Alves Barbosa Oliveira, Clayton Pereira Silva Lima, Camila De Sousa Lins, Rafael Ribeiro Barata, Marcelo Nunes Pereira Melo, Michel Platini Caldas De Souza, Luciano Monteiro Franco, Fábio Rocha Fernandes Távora, Daniele Rocha Queiroz Lemos, Carlos Henrique Morais De Alencar, Ronaldo De Jesus, Vagner De Souza Fonseca … & Fabio Miyajima
Abstract Background Chikungunya virus (CHIKV) emerged in the Americas in 2013 and has caused ~2.1 million cases and over 600 deaths. A retrospective investigation was undertaken to describe clinical, epidemiological and virus genomic features associated with deaths caused by CHIKV in Ceará state, northeast Brazil. Methods Sera, cerebrospinal fluid (CSF) and tissue samples from 100 fatal cases with suspected arbovirus infection were tested for CHIKV, dengue (DENV) and Zika virus (ZIKV). Clinical, epidemiological and death...

SARS-CoV-2 non-pharmaceutical interventions in Brazilian municipalities

Andreza Aruska De Souza Santos, Darlan Da Silva Cândido, William Marciel De Souza, Lewis Buss, Sabrina Li, Rafael H. M. Pereira, Chieh-Hsi Wu, Ester Sabino & Nuno R. Faria
Brazil has one of the fastest-growing COVID-19 epidemics worldwide. Non-pharmaceutical interventions (NPIs) have been adopted on a municipal level, with asynchronous actions taken across 5,568 municipalities and the Federal District. This paper addresses this complexity reporting on a novel dataset with survey responses from 4,027 mayors, 72.3% of the total municipalities in the country. This dataset responds to the urgency to track and share findings on fragmented policies to tackle health crises like the COVID-19...

Consistent concentrations of critically endangered Balearic shearwaters in UK waters revealed by at-sea surveys

Jessica Ann Phillips, Alex N. Banks, Mark Bolton, Tom Brereton, Pierre Cazenave, Natasha Gillies, Oliver Padget, Jeroen Van Der Kooij, James Waggit & Tim Guilford
Aim: Europe’s only globally critically endangered seabird, the Balearic shearwater (Puffinus mauretanicus), is thought to have expanded its post-breeding range northwards into UK waters, though its distribution there is not yet well understood. This study aims to identify environmental factors associated with the species’ presence, and map the probability of presence of the species across the western English Channel and southern Celtic Sea, and estimate the number of individuals in this area. Location: The western...

Association of gray matter atrophy patterns with clinical phenotype and progression in multiple sclerosis

Maria A Rocca, Paola Valsasina, Alessandro Meani, Claudio Gobbi, Chiara Zecca, Alex Rovira, Jaume Sastre-Garriga, Hugh Kearney, Olga Ciccarelli, Lucy Matthews, Jacqueline Palace, Antonio Gallo, Alvino Bisecco, Carsten Lukas, Barbara Bellenberg, Frederik Barkhof, Hugo Vrenken, Paolo Preziosa & Massimo Filippi
Objectives. Grey matter (GM) involvement is clinically relevant in multiple sclerosis (MS). Using source-based morphometry (SBM), we characterized GM atrophy and its 1-year evolution across different MS phenotypes. Methods. Clinical and MRI data were obtained at 8 European sites from 170 healthy controls (HCs) and 398 MS patients (34 clinically isolated syndromes [CIS], 226 relapsing-remitting [RR], 95 secondary progressive [SP] and 43 primary progressive [PP] MS). Fifty-seven HC and 144 MS underwent 1-year follow-up. Baseline...

In vivo microbial coevolution favours host protection and plastic downregulation of immunity

Suzanne Ford & Kayla King
Microbiota can protect their hosts from infection. The short timescales in which microbes can evolve presents the possibility that ‘protective microbes’ can take-over from the immune system of longer-lived hosts in the coevolutionary race against pathogens. Here, we found that coevolution between a protective bacterium (Enterococcus faecalis) and a virulent pathogen (Staphylococcus aureus) within an animal population (Caenorhabditis elegans) resulted in more disease suppression than when the protective bacterium adapted to uninfected hosts. At the...

Association of specific biotypes in patients with Parkinson's disease and disease progression

Linbo Wang, Wei Cheng, Edmund T. Rolls, Fuli Dai, Weikang Gong, Jingnan Du, Wei Zhang, Shouyan Wang, Fengtao Liu, Jian Wang, Peter Brown & Jianfeng Feng
Objective To identify biotypes in newly diagnosed Parkinson’s disease patients and test whether these biotypes could explain inter-individual differences in longitudinal progression. Methods In this longitudinal analysis, we use a data-driven approach clustering PD patients from the Parkinson’s Progression Markers Initiative (PPMI) (n = 314, age = 61.0 ± 9.5, 34.1% female, 5 years follow-up). Voxel-level neuroanatomical features were estimated using deformation-based morphometry (DBM) of T1-weighted MRI. Voxels whose deformation values were significantly correlated (P...

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Tomos Potter, Ronald D. Bassar, Paul Bentzen, Emily W. Ruell, Julián Torres-Dowdall, Corey A. Handelsman, Cameron K. Ghalambor, Joseph Travis, David N. Reznick & Tim Coulson
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in...

Multiple phenotypes conferred by a single insect symbiont are independent

Ailsa McLean, Jan Hrček, Benjamin Parker, Hugo Mathé-Hubert, Heidi Kaech, Chantal Paine & Charles Godfray
Many microbial symbionts have multiple phenotypic consequences for their animal hosts. However, the ways in which different symbiont-mediated phenotypes combine to affect fitness are not well understood. We investigated whether there are correlations between different symbiont-mediated phenotypes. We used the symbiont Spiroplasma, a striking example of a bacterial symbiont conferring diverse phenotypes on insect hosts. We took 11 strains of Spiroplasma infecting pea aphids (Acyrthosiphon pisum) and assessed their ability to provide protection against the...

Data from: Detecting the population dynamics of an autosomal sex-ratio distorter transgene in malaria vector mosquitoes

Paola Pollegioni, Ace North, Tania Persampieri, Alessandro Bucci, Roxana Minuz, David Alexander Groneberg, Tony Nolan, Philippos-Aris Papathanos, Andrea Crisanti & Ruth Muller
1. The development of genetically modified mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a lab strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization Guidance Framework for the...

Across-species differences in pitch perception are consistent with differences in cochlear filtering

Kerry M M Walker, Ray Gonzalez, Joe Z Kang, Josh H McDermott & Andrew J King
Pitch perception is critical for recognizing speech, music and animal vocalizations, but its neurobiological basis remains unsettled, in part because of divergent results across species. We investigated whether species-specific differences exist in the cues used to perceive pitch and whether these can be accounted for by differences in the auditory periphery. Ferrets accurately generalized pitch discriminations to untrained stimuli whenever temporal envelope cues were robust in the probe sounds, but not when resolved harmonics were...

Optimal control approaches for combining medicines and mosquito control in tackling dengue

Thomas Rawson, Kym Wilkins & Michael Bonsall
Dengue is a debilitating and devastating viral infection spread by mosquito vectors, and over half the world's population currently live at risk of dengue (and other flavivirus) infections. Here we use an integrated epidemiological and vector ecology framework to predict optimal approaches for tackling dengue. Our aim is to investigate how vector control and/or vaccination strategies can be best combined and implemented for dengue disease control on small networks, and whether these optimal strategies differ...

Identifying drivers of forest resilience in long-term records from the Neotropics

Carole Adolf, Carolina Tovar, Nicola Kühn, Hermann Behling, Juan Carlos Berrío, Gabriela Dominguez-Vázquez, Blanca Figueroa-Rangel, Zaire Gonzalez-Carranza, Gerald Alexander Islebe, Henry Hooghiemstra, Hector Neff, Miguel Olvera-Vargas, Bronwen Whitney, Matthew J. Wooller & Kathy J. Willis
Here we use 30 long-term, high-resolution palaeoecological records from Mexico, Central and South America to address two hypotheses regarding possible drivers of resilience in tropical forests as measured in terms of recovery rates from previous disturbances. First, we hypothesise that faster recovery rates are associated with regions of higher biodiversity, as suggested by the insurance hypothesis. And second, that resilience is due to intrinsic abiotic factors that are location specific, thus regions presently displaying resilience...

EVALUATION OF DAMAGE INDUCED IN GRAPHITE DUE TO SAMPLE PREPARATION BY STANDARD NON-DESTRUCTIVE TECHNIQUES

Michael Lasithiotakis, James T. Marrow & Barry J. Marsden
Damage introduced to graphite by mechanical polishing, argon ion beam polishing, fracture, and neutron bombardment has been studied in polycrystalline graphites and Highly Oriented Pyrolytic Graphite (HOPG). Scanning Electron Microscopy and Atomic Force Microscopy, as well as X-Ray Diffraction and Raman spectroscopy, were employed. The least disturbed surfaces are observed in pristine HOPG or by fracturing techniques that exposed pre-existing defects. A decrease of the mean particle size of the abrading medium and the use...

Data from: Are skyline plot-based demographic estimates overly dependent on smoothing prior assumptions?

Kris Varun Parag, Oliver Pybus & Chieh-Hsi Wu
In Bayesian phylogenetics, the coalescent process provides an informative framework for inferring changes in the effective size of a population from a phylogeny (or tree) of sequences sampled from that population. Popular coalescent inference approaches such as the Bayesian Skyline Plot, Skyride and Skygrid all model these population size changes with a discontinuous, piecewise-constant function but then apply a smoothing prior to ensure that their posterior population size estimates transition gradually with time. These prior...

Genetically determined blood pressure, antihypertensive drug classes and risk of stroke subtypes

Marios Georgakis, Dipender Gill, Alastair Webb, Evangelos Evangelou, Paul Elliott, Cathie Sudlow, Abbas Dehghan, Rainer Malik, Ioanna Tzoulaki & Martin Dichgans
Objective: We employed Mendelian Randomization to explore whether the effects of blood pressure (BP) and BP lowering through different antihypertensive drug classes on stroke risk vary by stroke etiology. Methods: We selected genetic variants associated with systolic and diastolic BP and BP-lowering variants in genes encoding antihypertensive drug targets from a GWAS on 757,601 individuals. Applying two-sample Mendelian randomization, we examined associations with any stroke (67,162 cases; 454,450 controls), ischemic stroke and its subtypes (large...

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean Wu, Penny Hancock, Arnaud Le Menach, Tanya Russell, Thomas Burkot, , Derek Cummings, Kelly Compton, Daniel Citron, John Marshall, Biyonka Liang, Catherine Moyes, Qian Zhang, David Smith, Samson Kiware, Anne Wilson, Thomas Scott, John Henry, Steven Lindsay, Amit Verma & Hector Sanchez C.
Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed...

Review of Energy Policy 2020

Robert Gross, Keith Bell, Mike Bradshaw, Christian Brand, Jason Chilvers, Paul Dodds, Antony Froggatt, Richard Hanna, Tom Hargreaves, Phil Heptonstall, Caroline Kuzemko, Richard Lowes, Faye Wade & Jan Webb

Data and R-code from 'Mode of death and mortality risk factors in Amazon trees'. Nature communications. 2020

Adriane Esquivel Muelbert, Oliver L. Phillips, Roel J. W. Brienen, Sophie Fauset, Martin J. P. Sullivan, Timothy R. Baker, Kuo-Jung Chao, Ted R. Feldpausch, Emanuel Gloor, Niro Higuchi, Jeanne Houwing-Duistermaat, Jon Lloyd, Haiyan Liu, Yadvinder Malhi, Beatriz Marimon, Ben Hur Marimon Junior, Abel Monteagudo-Mendoza, Lourens Poorter, Marcos Silveira, Emilio Vilanova Torre, Esteban Alvarez Dávila, Jhon del Aguila Pasquel, Everton Almeida, Patricia Alvarez Loayza & Ana Andrade

Proactive conservation to prevent habitat losses to agricultural expansion

David Williams, Michael Clark, Graeme M. Buchanan, G. Francesco Ficetola, Carlo Rondinini & David Tilman
The projected loss of millions of square kilometres of natural ecosystems to meet future demand for food, animal feed, fibre, and bioenergy crops is likely to massively escalate threats to biodiversity. Reducing these threats requires a detailed knowledge of how and where they are likely to be most severe. We developed a geographically explicit model of future agricultural land clearance based on observed historic changes and combine the outputs with species-specific habitat preferences for 19,859...

Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland

Adrian Allen, Jimena Guerrero, Andrew Byrne, John Lavery, Eleanor Presho, Emily Courcier, James O'Keeffe, Ursula Fogarty, Richard Delahay, Gavin Wilson, Chris Newman, Christina Buesching, Matthew Silk, Denise O'Meara, Robin Skuce, Roman Biek & Robbie A. McDonald
The colonization of Ireland by mammals, has been the subject of extensive study using genetic methods, and forms a central problem in understanding the phylo-geography of European mammals after the Last Glacial Maximum. Ireland exhibits a de-pauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger (Meles meles) have found conflicting microsatellite and...

Predicting tropical tree mortality with leaf spectroscopy

Chris Doughty, Alexander Cheesman, Terhi Ruitta & Andrew Nottingham
Do tropical trees close to death have a distinct change to their leaf spectral signature? Tree mortality rates have been increasing in tropical forests globally, reducing the global carbon sink. Upcoming hyperspectral satellites could be used to predict regions close to experiencing extensive tree mortality during periods of stress, such as drought. Here we show, for a tropical rainforest in Borneo, how imminent tropical tree mortality impacts leaf physiological traits and reflectance. We measured leaf...

Data from: An assay to investigate factors influencing initial orientation in nocturnally fledging seabirds.

Martyna Syposz, Oliver Padget, Joe Wynn, Natasha Gillies, Annette Fayet & Tim Guilford
The first solitary migration of juvenile birds is difficult to study because of a low juvenile survival rates and sometimes long delays in return to the breeding grounds. Consequently, little is known about this crucial life event for many bird species, in particular the sensory guidance mechanisms facilitating the first migratory journey. Initial orientation during the first migration is a key measure to investigate these mechanisms. Here, we developed an assay to measure initial orientation...

Ant-hill heterogeneity and grassland management

Timothy King
1. In many grasslands, some ants act as ecological engineers to produce long-lasting soil structures which have a considerable influence on the patterns and dynamics of plant, vertebrate and invertebrate species. They promote species richness and diversity. 2. The yellow meadow ant, Lasius flavus, is the most abundant allogenic ecological engineer in grazed European grasslands, producing vegetated long-lasting mounds. Its ratio of influence to biomass is remarkably high. Grassland restoration projects frequently attempt to re-introduce...

Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection

Ashley Sendell-Price & Kriste Clegg
Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential...

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