83 Works

Convex hull estimation of mammalian body segment parameters

Sam Coatham, William Sellers & Thomas Püschel
Obtaining accurate values for body segment parameters (BSPs) is fundamental in many biomechanical studies, particularly for gait analysis. Convex hulling, where the smallest-possible convex object that surrounds a set of points is calculated, has been suggested as an effective and time-efficient method to estimate these parameters in extinct animals, where soft tissues are rarely preserved. We investigated the effectiveness of convex hull BSP estimation in a range of extant mammals, to inform the potential future...

Simulated distribution of the fluid salinity, Cu and temperature in a sub-volcanic region

Jon Blundy, Andrey Afanasyev, Oleg Melnik, Brian Tattitch, Steve Sparks, Alison Rust & Ivan Utkin
The files brinelens.00.vtu, brinelens.01.vtu,... contain the simulated distributions of the fluid bulk salinity (a), the Cu concentration in fluid for the 'no sulfur' case (b), the Cu concenration in fluid for the 'sulfur unlimited' case (c), the Cu deposition for the 'sulfur unlimited' case (d), and the temperature (e) at t=0 yr, 10000 yr, 20000 yr,..., respectively. The distributions shown in Fig. 6a-e are in brinelens.10.vtu. The file brinelens.csv contains the simulated time evolution of...

Data and code for Heterogeneous selection on exploration behavior within and among West European populations of a passerine bird

Alexia Mouchet, Ella Cole, Erik Matthysen, Marion Nicolaus, John Quinn, Allison Roth, Joost Tinbergen, Kees Van Oers, Thijs Van Overveld & Niels Dingemanse
Heterogeneous selection is often proposed as a key mechanism maintaining repeatable behavioral variation (“animal personality”) in wild populations. Previous studies largely focused on temporal variation in selection within single populations. The relative importance of spatial versus temporal variation remains unexplored, despite these processes having distinct effects on local adaptation. Using data from >3500 great tits (Parus major) and 35 nest box plots situated within five West-European populations monitored over 4-18 years, we show that selection...

The first Silurian trilobite with three-dimensionally preserved soft parts reveals novel appendage morphology

Mark Sutton, Derek Siveter, Richard Fortey, Derek Briggs & David Siveter
The first Silurian trilobite known with soft parts preserved, a Dalmanites species, is described from the Herefordshire Lagerstätte. Biramous appendages and much of the alimentary system are evident. High-fidelity three-dimensional preservation reveals a novel, double arrangement of the exopod filaments, interconnected by a presumed membranous sheet. This morphology explains a misinterpretation of the exopod as supporting spiral structures, originally reported nearly 150 years ago. The new exopod morphology is considered primarily respiratory in function and...

Early‐life seasonal, weather and social effects on telomere length in a wild mammal

Sil H.J. Van Lieshout, Elisa P. Badás, Julius G. Bright Ross, Amanda Bretman, Chris Newman, Christina D. Buesching, Terry Burke, David W. Macdonald & Hannah L. Dugdale
Early-life environmental conditions can provide a source of individual variation in life-history strategies and senescence patterns. Conditions experienced in early life can be quantified by measuring telomere length, which can act as a biomarker of survival probability in some species. Here, we investigate whether seasonal changes, weather conditions, and group size are associated with early-life and/or early-adulthood telomere length in a wild population of European badgers (Meles meles). We found substantial intra-annual changes in telomere...

Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores - Phylogenetic dataset

Luke Parry, Rudy Lerosey Aubril, James Weaver & Javier Ortega-Hernández
Ctenophores are a group of predatory macroinvertebrates whose controversial phylogenetic position has prompted several competing hypotheses regarding the evolution of animal organ systems. Although ctenophores date back at least to the Cambrian, they have a poor fossil record due to their gelatinous bodies. Here, we describe two ctenophore species from the Cambrian of Utah, which illuminate the early evolution of nervous and sensory features in the phylum. Thalassostaphylos elegans has 16 comb rows, an oral...

The Spinout Journey: Barriers and Enablers to Gender Inclusive Innovation. Summary Report

Heather Griffiths, Louise Grisoni, Simonetta Manfredi, Alexis Still & Charikleia Tzanakou

AI3SD Video: Skills4Scientists - Poster & Careers Symposium - Poster Compilation

András Vekassy, Aspen Fenzl, Erhan Gulsen, Hewan Zewdu, Jamie Longio, Maximilian Hoffman, Rhyan Barrett, Rubaiyat Khondaker, Anna Catton, Hongyang Dong, Kevin Calvache, Kaylee Patel, King Wong, Louis Greenhalgh, Rebecca Jane Clements, Thomas Allam, Sarah Scripps, Gavin Man, Samuel Munday, Michael Blakey, Graeme M. Day, Chris-Kriton Skylaris, Simon J. Coles, Stephen Gow & William Brocklesby
This video forms part of the Skills4Scientists Series which has been organised as a joint venture between the Artificial Intelligence for Scientific Discovery Network+ (AI3SD) and the Physical Sciences Data-Science Service (PSDS). This series ran over summer 2021 and aims to educate and improve scientists skills in a range of areas including research data management, python, version control, ethics, and career development. This series is primarily aimed at final year undergraduates / early stage PhD...

Data from: Fossils improve phylogenetic analyses of morphological characters

Nicolás Mongiardino Koch, Russell Garwood & Luke Parry
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here we use simulations to evaluate the performance of inference methods across different levels of fossil...

Stabian Baths in Pompeii. New Research on the Archaic Defenses of the City

Mark Robinson, Monika Trümper, Clemens Brünenberg, Jens-Arne Dickmann, Domenico Esposito, Antonio F. Ferrandes, Giacomo Pardini, Alessandra Pegurri & Christoph Rummel
The plan of the Archaic city of Pompeii and the existence of a distinct walled Altstadt have been much debated in scholarship. The area of the Stabian Baths plays a key role in this debate. Based on a series of excavations in the palaestra of the baths, Heinrich Sulze (1940) and particularly Hans Eschebach (1970s) reconstructed a defensive wall and parallel ditch in this area. Eschebach also identified an Archaic street and city gate in...

A shift in ontogenetic timing produced the unique sauropod skull

Matteo Fabbri, Guillermo Navalón, Nicolás Mongiardino Koch, Michael Hanson, Holger Petermann & Bhart-Anjan Bhullar
Sauropod dinosaurs include the largest terrestrial vertebrates that have ever lived. Virtually every part of the sauropod body is heavily modified in association with gigantic size and associated physiological alterations. Sauropod skulls are no exception: they feature elongated, telescoped facial regions connected to tilted neurocrania and reoriented jaw adductor muscles. Several of these cranial features have been suggested to be adaptations for feeding on the one hand and the result of paedomorphic transformation near the...

Clinician-researcher’s perspectives on clinical research during the COVID-19 pandemic

Sarah Silverberg, Lisa Puchalski-Ritchie, Nina Gobat, Alistair Nichol & Srinavas Murthy
Objectives: The outcome of well-performed clinical research is essential for evidence-based patient management during pandemics. However, conducting clinical research amidst a pandemic requires researchers to balance clinical and research demands. We seek to understand the values, experiences, and beliefs of physicians working at the onset of the COVID-19 pandemic in order to inform clinical research planning. We aim to understand whether pandemic settings affect physician comfort with research practices, and how physician experiences shape their...

An island-hopping bird reveals how founder events shape genome-wide divergence

Ashley Sendell-Price, Kristen Ruegg, Bruce Robertson & Sonya Clegg
When populations colonise new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the...

Middle Ages in Renaissance

Maria Clotilde Camboni & Chiara Lastraioli

Atmospheric and surface gravity wave data for role of surface gravity waves in aquaplanet ocean climates

Joshua Studholme, Margarita Markina & Sergey Gulev
This data corresponds to the runs analysed in the manscript: Role of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In this work, we present a set of idealised numerical experiments that demonstrate the thermodynamic and dynamic implications of surface gravity waves for the oceanic climate of an aquaplanet. We study the impact of accounting for modulations by such waves upon air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis force. This dataset is made...

Comparison of size-structured and species-level trophic networks reveals antagonistic effects of temperature on vertical trophic diversity at the population and species level

Willem Bonnaffé, Alain Danet, Stephane Legendre & Eric Edeline
It is predicted that warmer conditions should lead to a loss of trophic levels, as larger bodied consumers, which occupy higher trophic levels, experience higher metabolic costs at high temperature. Yet, it is unclear whether this prediction is consistent with the effect of warming on the trophic structure of natural systems. Furthermore, effects of temperature at the species level, which arise through a change in species composition, may differ from those at the population level,...

Data from: Substantial intraspecific variation in energy budgets: biology or artefact?

Tomos Potter, David Reznick & Tim Coulson
Data on the growth and reproduction of Trinidadian guppies (Poecilia reticulata) from sixteen different populations, reared under experimental conditions of either high or low food availability. These data were used to fit dynamic energy budgets models for each of the populations. For twelve populations, there are three sets of observations per individual, recorded at each successive parturition event. For four of the populations, data were recorded at each parturition event over the full lifespan of...

Data associated with 'Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region'

Dheeraj Prakaash, Graham Cook, oreste acuto & Antreas Kalli
The T cell receptor (TCR-CD3) initiates T cell activation by binding to peptides of Major Histocompatibility Complexes (pMHC). The TCR-CD3 topology is well understood but the arrangement and dynamics of its cytoplasmic tails remains unknown, limiting our grasp of the signalling mechanism. Here, we use molecular dynamics simulations and modelling to investigate the entire TCR-CD3 embedded in a model membrane. Our study demonstrates conformational changes in the extracellular and transmembrane domains, and the arrangement of...

Neisseria cinerea 346T whole genome sequence

Rafael Custodio, Christoph Tang & Rachel Exley
Type VI Secretion Systems (T6SS) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can...

A habenula-insular circuit encodes the willingness to act

Nima Khalighinejad, Neil Garrett, Luke Priestley, Patricia Lockwood & Matthew FS Rushworth
The decision that it is worth doing something rather than nothing is a core yet understudied feature of voluntary behaviour. Here we study “willingness to act”, the probability of making a response given the context. Human volunteers encountered opportunities to make effortful actions in order to receive rewards, while watching a movie inside a 7T MRI scanner. Reward and other context features determined willingness- to-act. Activity in the habenula tracked trial-by-trial variation in participants’ willingness-to-act....

Intraspecific variation in symbiont density in an insect-microbe symbiosis

Benjamin Parker, Jan Hrcek, Ailsa McLean, Charles Godfray & Jennifer Brisson
Many insects host vertically-transmitted microbes, which can confer benefits to their hosts but are costly to maintain and regulate. A key feature of these symbioses is variation: for example, symbiont density can vary among host and symbiont genotypes. However, the evolutionary forces maintaining this variation remain unclear. We studied variation in symbiont density using the pea aphid (Acyrthosiphon pisum) and the bacterium Regiella insecticola, a symbiont that can protect its host against fungal pathogens. We...

Auditory cortical representation of music favours the perceived beat

Vani G. Rajendran, Nicol S. Harper & Jan W. H. Schnupp
Previous research has shown that musical beat perception is a surprisingly complex phenomenon involving widespread neural coordination across higher-order sensory, motor, and cognitive areas. However, the question of how low-level auditory processing must necessarily shape these dynamics, and therefore perception, is not well understood. Here, we present evidence that the auditory cortical representation of music, even in the absence of motor or top-down activations, already favors the beat that will be perceived. Extracellular firing rates...

The implications of interrelated assumptions on estimates of divergence times and rates of diversification

Tom Carruthers & Robert Scotland
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field – including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling....

Causes of delayed outbreak responses and their impacts on epidemic spread

Yun Tao, Matthew Ferrari, Katriona Shea, William Probeert, Michael Runge, Kevin Lafferty & Michael Tildesley
Livestock diseases have devastating consequences economically, socially, and politically across the globe. In certain systems, pathogens remain viable after host death, which enables residual transmissions from infected carcasses. Rapid culling and carcass disposal are well-established strategies for stamping out an outbreak and limiting its impact, however, wait-times for these procedures, i.e., response delays, are typically farm-specific and time-varying due to logistical constraints. Failing to incorporate variable response delays in epidemiological models may understate outbreak projections...

Comparative analysis of angiogenesis models: MATLAB data files

William Martinson
This data set contains the MATLAB files that were used to generate figures located in the article "Comparative analysis of angiogenesis models" (J. Math. Biol, in press). The article's abstract may be found below. Although discrete approaches are increasingly employed to model biological phenomena, it remains unclear how complex, population-level behaviours in such frameworks arise from the rules used to represent interactions between individuals. Discrete-to-continuum approaches, which are used to derive systems of coarse-grained equations...

Registration Year

  • 2021
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Affiliations

  • University of Oxford
    83
  • Yale University
    8
  • University of Leeds
    5
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
    4
  • University of Cambridge
    3
  • University of Manchester
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  • University College London
    3
  • University of Leicester
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  • University of Groningen
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  • University of Warwick
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