98 Works

Flow cytometry analysis of water samples for bacterial and Pico-plankton enumeration, samples collected in the Barents Sea during 2017-2018

Elaine Mitchell, Sharon McNeil, Callum Whyte, Finlo Cottier, Joanne Hopkins & Keith Davidson
Collection and preservation of open ocean water samples from stations along a transect in the Barents Sea over the course of a year from July 2017 - July 2018. Four cruises in total to cover seasonal changes, two on board the James Clark Ross (RRS) and two aboard the Helmer Hansen (RV). A standard CTD cast was deployed to collect the samples, the depths were selected to support Primary Production experiments on board the ship,...

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...

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...

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,...

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...

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...

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...

Data from: Larval density, sex and allocation hierarchy affect life-history trait covariances in a bean beetle

Flavia Barbosa, Samuel Gascoigne & Desire Uwera Nalukwago
Life-history theory aims to understand how different environments result in differential investment in fitness-related traits. While trade-offs between traits are expected, many studies show positive or no correlation between pairs of costly traits. One hypothesis that may explain the inconsistency of trade-offs in the literature is that trait investment may occur in a dichotomous hierarchy (the tree model), that allows for differential trait investment weighted by the traits’ respective positions within the hierarchy. Previous mathematical...

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...

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...

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....

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...

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...

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...

Ecological consequences of large herbivore exclusion in an African savanna: 12 years of data from the UHURU experiment

Jesse Alston, Courtney Reed, Leo Khasoha, Bianca Brown, Gilbert Busienei, Nathaniel Carlson, Tyler Coverdale, Megan Dudenhoeffer, Marissa Dyck, John Ekeno, Abdikadir Hassan, Rhianna Hohbein, Rhiannon Jakopak, Buas Kimiti, Samson Kurukura, Peter Lokeny, Allison Louthan, Simon Musila, Paul Musili, Tosca Tindall, Sarah Weiner, Tyler Kartzinel, Todd Palmer, Robert Pringle & Jacob Goheen
Diverse communities of large mammalian herbivores (LMH), once widespread, are now rare. LMH exert strong direct and indirect effects on community structure and ecosystem functions, and measuring these effects is important for testing ecological theory and for understanding past, current, and future environmental change. This in turn requires long-term experimental manipulations, owing to the slow and often nonlinear responses of populations and assemblages to LMH removal. Moreover, the effects of particular species or body-size classes...

Imprinting on time-structured acoustic stimuli in ducklings

Tiago Monteiro, Tom Hart & Alex Kacelnik
Filial imprinting is a dedicated learning process that lacks explicit reinforcement. The phenomenon itself is narrowly heritably canalized, but its content, the representation of the parental object, reflects the circumstances of the newborn. Imprinting has recently been shown to be even more subtle and complex than previously envisaged, since ducklings and chicks are now known to select and represent for later generalization abstract conceptual properties of the objects they perceive as neonates, including movement pattern,...

A pilot study of thiamin and folic acid in hemodialysis patients with cognitive impairment

Renhua Lu, Yan Fang, Yijun Zhou, Miaolin Che, Jianxiao Shen, Qian Liu, Haifen Zhang, Shuting Pan, Yan Lin, Qin Wang, Shan Mou, Zhaohui Ni & Leyi Gu
This study aimed to explore the effectiveness of thiamin and folic acid supplementation on the improvement of the cognitive function in patients with maintenance hemodialysis. In the present study, we randomly assigned patients undergoing hemodialysis who had the Montreal Cognitive Assessment (MoCA) score lower than 26 to treatment group (n = 25, thiamin 90 mg/day combined with folic acid 30 mg/day) or control group (n = 25, nonintervention). All subjects were followed up for 96...

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...

Cholesterol depletion sensitizes gallbladder cancer to cisplatin by impairing DNA damage response

Yonglong Zhang, Yanfeng Liu, Jinlin Duan, Hui Wang, Yuchen Zhang, Ke Qiao & Jian Wang
Gallbladder cancer (GBC) is the common malignancy of the bile tract system with extremely poor clinical outcomes, owing to its metastatic property and intrinsic resistance to the first-line drugs. Although it is well-established that cholesterol abnormity contributes to gallstone formation, a leading risk factor for GBC, the link of cholesterol homeostasis with GBC has not been investigated. The present study systematically examined the genes implicated in cholesterol homeostasis, and revealed altered gene expressions of de...

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...

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...

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...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Oxford
  • Central South University
  • Capital Medical University
  • Zhejiang University
  • Air Force Medical University
  • Huazhong University of Science and Technology
  • Shanghai Jiao Tong University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Wuhan University
  • Tongji University