97 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...

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...

Data from: Large-scale assessment of intra- and inter-annual breeding success using a remote camera network

Casey Youngflesh, Fiona M. Jones, Heather J. Lynch, Joan Arthur, Zuzana Ročkaiová, Holly R. Torsey & Tom Hart
Changes in the physical environment along the Antarctic Peninsula have been among the most rapid anywhere on the planet. In concert with environmental change, the potential for direct human disturbance resulting from tourism, scientific programs, and commercial fisheries continues to rise in the region. While seabirds, such as the gentoo penguin Pygoscelis papua, are commonly used to assess the impact of these disturbances on natural systems, research efforts are often hampered by limited spatial coverage...

Weekly volume of water pumped for handpumps monitored with Smart Handpump technology, Kwale County, Kenya

Patrick Thomson
This dataset contains a summary of the weekly volumetric output of pumps monitored using Smart Handpump sensors for 2014 and 2015. Grants that permitted the data collection include: Groundwater Risk Management for Growth and Development project (NE/M008894/1) funded by NERC/ESRC/DFID’s UPGro programme; New mobile citizens and waterpoint sustainability in rural Africa (ES/J018120/1) ESRC-DFID; Groundwater Risks and Institutional Responses for Poverty Reduction in Rural Africa (NE/L001950/1) funded by NERC/ESRC/DFID’s UPGro programme Notes: 1. The accuracy of...

Surface and Meteorological Data at Sand Creek, Great Sand Dunes National Park, Colorado, USA in March and April 2019

Joanna Nield, Pauline Delorme, Giles Wiggs & Matthew Baddock
Wind, sediment transport and surface morphological data collected at Sand Creek during a month long field campaign in March and April 2019 to investigate protodune development under bimodal winds. Data is used in the accepted paper ‘Dune initiation in a bimodal wind regime’, Journal of Geophysical Research: Earth Surface, by Delorme, P., Wiggs, G.F.S., Baddock, M.C., Claudin, P., Nield, J.M. and Valdez, A. (accepted 18th September 2020, article reference number 2020JF005757R; https://repository.lboro.ac.uk/articles/Dune_initiation_in_a_bimodal_wind_regime/12973817) Surface morphological data:...

Associational resistance to both insect and pathogen damage in mixed forests is modulated by tree neighbour identity and drought

Elsa Field, Bastien Castagneyrol, Melanie Gibbs, Hervé Jactel, Nadia Barsoum, Karsten Schonrogge & Andrew Hector
Tree health declines can be caused by interactions between pests and pathogens and many studies have shown a reduction in their damage in mixed species forests compared to monocultures. Yet few authors have considered tree diversity effects on both groups simultaneously. Moreover, it is unclear whether diversity effects on tree pests and pathogens are robust to changes in abiotic conditions, such as drought. We addressed tree diversity effects on foliar insect herbivory, oak powdery mildew...

Data from: Mate availability determines use of alternative reproductive phenotypes in hermaphrodites

Anja Felmy, Nora Weissert & Jukka Jokela
In many species individuals can employ alternative reproductive phenotypes, with profound consequences for individual fitness and population dynamics. This is particularly relevant for self-compatible hermaphrodites, which have exceptionally many reproductive options. Here we investigated the occurrence of reproductive phenotypes in the simultaneously hermaphroditic freshwater snail Radix balthica under experimentally simulated conditions of low vs. moderate population density. We captured all mating behavior on camera and measured individual female lifetime reproductive success. We found every possible...

Data from: Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

Christian Foth, Serjoscha W. Evers, Walter G. Joyce, Virginie S. Volpato & Roger B. J. Benson
The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties...

Data and code for: Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells

Helen K. Alexander & R. Craig MacLean
This dataset contains experimental data and custom R code for likelihood-based model-fitting associated with the manuscript "Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells". In particular, we estimate the per-cell establishment probability (i.e. probability that a single cell gives rise to a large population) of a resistant strain, in the presence of antibiotics at concentrations below its standard minimum inhibitory concentration. The experiments are conducted here with Pseudomonas aeruginosa, while...

Serial disparity in the carnivoran backbone unveil a complex adaptive role in metameric evolution

Francisco Borja Figueirido Castillo, Alberto Martín-Serra, Alejandro Pérez-Ramos, David Velasco, Francisco Pastor & Roger Benson
Multi-element systems such as the vertebral column of vertebrates represent a major challenge to phenotypic quantification and macroevolutionary analyses. The vertebral column is a metameric structure, composed of serially repeated subunits, and much of what is known so far has been inferred from sparse anatomical samples, providing little insight into local-scale (i.e. vertebra-to-vertebra) variation and its macroevolutionary importance. This limits understanding of how evolutionary constraints and functional adaptation interact during the evolution of multi-element phenotypes....

Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense

Yabin Guan, Yupeng Geng, Na Chang, Yuewan Zhao, Xiaoying Qin, Shugang Lu, James Crabbe & Ticao Zhang
Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation...

The role of boundary length and adjacent patch contrast in guppy mate choice: Dataset, Matlab and R codes

Adelaide Sibeaux, Thomas Camduras & John A. Endler
The presence of various combinations of adjacent colours within polymorphic species’ colour pattern could have a major impact on mate choice. We studied the role of pattern geometry in predicting mate choice in guppies using boundary strength analysis (BSA). BSA estimates the visual contrast intensity between two adjacent colour patches (ΔS) weighted by the lengths of the boundaries between these adjacent colour patches. We measured both the chromatic (hue and saturation) and achromatic (luminance) ΔS...

Registration Year

  • 2020
    97

Resource Types

  • Dataset
    97

Affiliations

  • University of Oxford
    97
  • Imperial College London
    11
  • University of Cambridge
    6
  • University of Leeds
    6
  • University of Birmingham
    6
  • University of Exeter
    5
  • University of Copenhagen
    4
  • University of Sheffield
    4
  • University of Southampton
    3
  • Anglia Ruskin University
    2