338 Works

Data from: An auditory illusion reveals the role of streaming in the temporal misallocation of perceptual objects

Anahita H. Mehta, Nori Jacoby, Ifat Yasin, Andrew J. Oxenham & Shihab A. Shamma
This study investigates the neural correlates and processes underlying the ambiguous percept produced by a stimulus similar to Deutsch's ‘octave illusion’, in which each ear is presented with a sequence of alternating pure tones of low and high frequencies. The same sequence is presented to each ear, but in opposite phase, such that the left and right ears receive a high–low–high … and a low–high–low … pattern, respectively. Listeners generally report hearing the illusion of...

Data from: Targeted next-generation sequencing panels in the diagnosis of Charcot Marie Tooth disease

Andrea Cortese, Janel Wilcox, James M. Polke, Roy Poh, Mariola Skorupinska, Alexader Rossor, Matilde Laura, Pedro J. Tomaselli, Henry Houlden, Michael E. Shy & Mary M. Reilly
Objective: To investigate the effectiveness of targeted NGS panels in achieving a molecular diagnosis in CMT and related disorders in a clinical setting Methods: We prospectively enrolled 220 patients from two tertiary referral centres, one in London, UK (n=120) and one in Iowa, US (n=100) in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon...

Data from: Reprogramming the antigen specificity of B cells using genome-editing technologies

James E. Voss, Alicia Gonzalez-Martin, Raiees Andrabi, Roberta P. Fuller, Ben Murrell, Laura E. McCoy, Katelyn Porter, Deli Huang, Wenjuan Li, Devin Sok, Khoa Le, Bryan Briney, Morgan Chateau, Geoffrey Rogers, Lars Hangartner, Ann J. Feeney, David Nemazee, Paula Cannon & Dennis R. Burton
We have developed a method to introduce novel paratopes into the human antibody repertoire by modifying the immunoglobulin (Ig) genes of mature B cells directly using genome editing technologies. We used CRISPR-Cas9 in a homology directed repair strategy, to replace the heavy chain (HC) variable region in B cell lines with that from an HIV broadly neutralizing antibody, PG9. Our strategy is designed to function in cells that have undergone VDJ recombination using any combination...

Data from: Long-term use benefits of personal frequency-modulated systems for speech in noise perception in patients with stroke with auditory processing deficits: a non-randomised controlled trial study

Nehzat Koohi, Deborah Vickers, Jason Warren, David Werring & Doris-Eva Bamiou
Objectives: Approximately one in five stroke survivors suffer from difficulties with speech reception in noise, despite normal audiometry. These deficits are treatable with personal Frequency Modulated systems (FMs). This study aimed to evaluate long term benefits in speech reception in noise, after daily 10 week use of personal FMs, in non-aphasic stroke patients with auditory processing deficits. Design: This was a prospective non randomised controlled trial study. Patients were allocated to an intervention care group...

Data from: The present and future effects of land use on ecological assemblages in tropical grasslands and savannas in Africa

Tim Newbold, Elizabeth H. Boakes, Samantha L.L. Hill, Michael B.J. Harfoot & Ben Collen
The world is currently experiencing a period of rapid, human-driven biodiversity loss. Over the past decade, numerous metrics for biodiversity have been used to create indicators to track change in biodiversity. However, our ability to predict future changes has been limited. In this study, we use two very different models to predict the status and possible futures for the composition and diversity of ecological assemblages in African tropical grasslands and savannas under land-use change. We...

Data from: Within- and between-group dynamics in an obligate cooperative breeder

Rosie Woodroffe, Helen O'Neill & Daniella Rabaiotti
1. Cooperative behaviour can have profound effects on demography. In many cooperative species, components of fitness (e.g. survival, reproductive success) are diminished in smaller social groups. These effects (termed group-level component Allee effects) may lead smaller groups to grow relatively slowly or fail to persist (termed group-level demographic Allee effects). 2. If these group-level effects were to propagate to the population level, small populations would grow slowly or decline to extinction (termed population-level demographic Allee...

Data from: Lepidosaurian diversity in the Mesozoic–Paleogene: the potential roles of sampling biases and environmental drivers

Terri J. Cleary, Roger B.J. Benson, Susan E. Evans, Paul M. Barrett & Roger B. J. Benson
Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon-richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic–Paleogene (252–23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the...

Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

Carola Gómez-Rodríguez, Alex Crampton-Platt, Martijn J. T. N. Timmermans, Andrés Baselga & Alfried P. Vogler
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes...

Data from: Reproductive trade-offs in extant hunter-gatherers suggest adaptive mechanism for the Neolithic expansion

Abigail E. Page, Sylvain Viguier, Mark Dyble, Daniel Smith, Nikhil Chaudhary, Gul Deniz Salali, James Thompson, Lucio Vinicius, Ruth Mace & Andrea Bamberg Migliano
The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality–quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose...

Data from: Alien species richness is currently unbounded in all but the most urbanized bird communities

Toby P. Tsang, Ellie E. Dyer & Tim C. Bonebrake
Urban areas suffer high pressure of introductions of alien species compared to other habitats due to intensive human activities. As trading globally continues to rise, more species will likely be introduced into urban areas. To determine whether this increase in introduction pressure will lead to increased alien species richness in urban areas, or whether other processes would act to impose an upper limit on species richness, we examined how the shape of the relationship between...

Data from: Not just passengers: Pigeons, Columba livia, can learn homing routes while flying with a more experienced conspecific

Benjamin Pettit, Andrea Flack, Robin Freemain, Tim Guilford, Dora Biro & R. Freeman
For animals that travel in groups, the directional choices of conspecifics are potentially a rich source of information for spatial learning. In this study, we investigate how the opportunity to follow a locally experienced demonstrator affects route learning by pigeons over repeated homing flights. This test of social influences on navigation takes advantage of the individually distinctive routes that pigeons establish when trained alone. We found that pigeons learn routes just as effectively while flying...

Data from: The evolution of locomotor rhythmicity in tetrapods

Callum F. Ross, Richard W. Blob, David R. Carrier, Monica A. Daley, Stephen M. Deban, Brigitte Demes, Janaya L. Gripper, Jose Iriarte-Diaz, Brandon Michael Kilbourne, Tobias Landberg, John D. Polk, Nadja Schilling & Bieke Vanhooydonck
Differences in rhythmicity (relative variance in cycle period) between mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intra-individual coefficients of variation in cycle period were compared while controlling for gait and substrate. Variance in...

Data accompanying ‘Microstructural controls on thermal crack damage and the presence of a temperature-memory effect during cyclic thermal stressing of rocks’ submitted for publication in Geophysical Research Letters

John Browning, Ali Daoud, Philip Meredith & Thomas Mitchell
Acoustic emissions (AE) and ultrasonic wave velocity data recorded during a series of high temperature thermal cracking experiments by Daoud et al., in the Rock and Ice Physics Laboratory of the University College London. The data gives the time and magnitude of AE output which were recorded contemporaneously whilst cyclically heating three rock types (A Slaufrudalur Granophyre, A Santorini Andesite and a Seljadalur Basalt). The ultrasonic wave velocity data was recorded pre- and post- heating....

Mg/Ca ratios from multiple species of planktonic foraminifera from the Middle Miocene to modern from multiple sites in the global ocean

E.M. Mawbey, F. Boscolo-Galazzo, B.S. Wade & P.N. Pearson
Mg/Ca in multiple species of planktonic foraminifera from five time slices since the Middle Miocene to present (target ages 15, 12.5, 10, 7.5, 4.5, 2.5 and 0 Ma). These samples are from a range of globally and latitudinally distributed DSDP (Deep Sea Drilling Program), ODP (Ocean Drilling Program), IODP (International Ocean Discovery Program) open ocean sites. From low to high latitudes these are: Site U1338, U1489 (Eastern and Western Equatorial Pacific), Sites 871, 872, and...

Nitrogen and Carbon isotope data from 210Pb dated lake sediment cores in the United Kingdom

S.D. Turner & N.L. Rose
A dataset of historical sediment Carbon and Nitrogen isotope measurements from lake cores (n=95) spanning the range of lake types and catchments found across the UK. These data have been obtained from the Environmental Change Research Centre (ECRC) lake sediment core archive with well-resolved time intervals (1850, 1900, 1980 and present) determined by radiometric dating (210Pb; 137Cs). This data has been collated to investigate historical sources and accumulation of C and N in lakes. This...

Plant biodiversity data and environmental and spatial data from Jebel Ichkeul, a limestone mountain in northern Tunisia (1983)

D.A. Kirk, K. Hébert & F. B. Goldsmith
Records for herbaceous and woody plants at 78 nested quadrats on a limestone mountain (Jebel Ichkeul) in Le Parc National de L’Ichkeul are presented. Data for plants represent percent cover (Braun-Blanquet scale), to identify environmental gradients and investigate phytosociology of plant communities. Environmental variables are also presented: altitude, slope, aspect, rock out cropping, index of grazing intensity (78 sites) and olive tree densities by size class (69 sites). Soil pH was collected for 50 sites....

Indoor Residual Spraying (IRS) Impact Evaluation Survey 2009

Arianna Legovini, Pedro Carneiro &

Correlative 3D SBFSEM data from: Intermittent bulk release of human cytomegalovirus

Felix Flomm, Timothy K Soh, Carola Schneider, Linda Wedemann, Hannah M Britt, Konstantinos Thalassinos, Soeren Pfitzner, Rudolph Reimer, Kay Grünewald & Jens Bernhard Bosse
Human Cytomegalovirus (HCMV) can infect a variety of cell types by using virions of varying glycoprotein compositions. It is still unclear how this diversity is generated, but spatio-temporally separated envelopment and egress pathways might play a role. So far, one egress pathway has been described in which HCMV particles are individually enveloped into small vesicles and are subsequently exocytosed continuously. However, some studies have also found enveloped virus particles inside multivesicular structures but could not...

Data from: Current ecology, not ancestral dispersal patterns, influences menopause symptom severity

Yuping Yang, Megan Arnot & Ruth Mace
All human females who reach midlife experience menopause, however, it is currently unclear why women experience this period of infertility, and why it is accompanied by many unpleasant symptoms. Using primary data from four ethnic groups in China, we test an existing theory that age of menopause and its symptoms are the result of intragenomic conflict between maternally and paternally inherited genes, with the outcome of such conflict predicted to be contingent on the ancestral...

Data from: Near-infrared dual bioluminescence imaging in mouse models of cancer using infraluciferin

James Anderson & Martin Pule
Bioluminescence imaging (BLI) is ubiquitous in scientific research for the sensitive tracking of biological processes in small animal models. However, due to the attenuation of visible light by tissue, and the limited set of near-infrared bioluminescent enzymes, BLI is largely restricted to monitoring single processes in vivo. Here we show, that by combining stabilised colour mutants of firefly luciferase (FLuc) with the luciferin (LH2) analogue infraluciferin (iLH2), near-infrared dual BLI can be achievedin vivo. The...

Immigrant males’ memory acts to reduce ranging overlap and mating competition in wild baboons

Julien Collet, Nathalie Pettorelli, Alice Baniel, Alecia Carter, Elise Huchard, Andrew King, Alexander Lee, Harry Marshall & Guy Cowlishaw
Mechanistic models suggest that information acquired by animals (“knowledge”) could shape home range patterns and dynamics, and how neighbours share space. In social species this would suggest that immigrants could bring new knowledge into social groups, potentially affecting the dynamics of home range overlap. We tested this “immigrant knowledge hypothesis” in a wild population of chacma baboons (Papio ursinus). We used data collected between 2005 and 2013 on two neighbouring troops in Namibia, comprising GPS...

Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of the erato-sara group of Heliconius butterflies

Yuttapong Thawornwattana, Fernando Seixas, Ziheng Yang & James Mallet
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer...

Bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting as predicted by the Madingley General Ecosystem Model

Tatsiana Barychka, Georgina Mace & Drew Purves
The datasets contain data generated using the Madingley General Ecosystem Model for experiments decribed in the paper: "T. Barychka, G.M.Mace and D.W.Purves (2021) The Madingley General Ecosystem Model predicts bushmeat yields, species extinction rates and ecosystem-level impacts of bushmeat harvesting. Oikos." The Madingley General Ecosystem Model was used to generate predictions of bushmeat yields, extinction rates and broader ecosystem impacts for a range of harvesting intensities of duiker-sized endothermic herbivores. Duiker antelope (such as Cephalophus...

Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

Jennifer Zou, Shyam Gopalakrishnan, Clarissa Parker, Jerome Nicod, Richard Mott, Na Cai, Arimantas Lionikas, Robert Davies, Abraham Palmer & Jonathan Flint
Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3,076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction...

Evolution and development at the origin of a phylum

Bradley Deline, Jeffery Thompson, Nicholas Smith, Samuel Zamora, Imran Rahman, Sarah Sheffield, William Ausich, Thomas Kammer & Colin Sumrall
Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define...

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