49 Works

Diary, letters and poems of Marjory Fleming

Centre for Research in Digital Education Annual Report 2018

Sian Bayne

Centre for Research in Digital Education Annual Report 2020

Sian Bayne

AI3SD Project: Interpretable crystal descriptions across length scales for materials discovery

James Cumby
Most technological devices depend in some way on crystalline inorganic materials, from the perovskite oxides found in the capacitors underpinning phones and computers through to the ceramic materials used to insulate ovens and hobs. Future technologies will require new materials with different properties, but discovering these is a significant challenge; trial and error is simply too complex and time-consuming. An alternative approach is to harness our knowledge of the crystalline structure of existing materials in...

The correlates of intraspecific variation in nest height and nest building duration in the Eurasian blue tit Cyanistes caeruleus

Dagmar Der Weduwen, Katharine Keogan, Jelmer Samplonius, Albert Phillimore & Jack Shutt
Birds build nests primarily as a receptacle to lay their eggs in, but they can also provide secondary benefits including structural support, camouflage, and adjustment of the microclimate surrounding the eggs and offspring. The factors underlying intraspecific variation in nest characteristics are poorly understood. In this study, we aim to identify the environmental factors that predict nest height variation and the duration of nest building in blue tits (Cyanistes caeruleus), evaluating latitude, elevation, temperature, and...

Spatiotemporal variation in drivers of parasitism in a wild wood mouse population

Amy Sweeny, Gregory Albery, Saudamini Venkatesan, Andy Fenton & Amy Pedersen
Host-parasite interactions in nature are driven by a range of factors across several ecological scales, so observed relationships are often context-dependent. Importantly, if these factors vary across space and time, practical sampling limitations can limit or bias inferences, and the relative importance of different drivers can be hard to discern. Here we ask to what degree environmental, host, and within-host influences on parasitism are shaped by spatiotemporal variation. We use a replicated, longitudinal dataset of...

Genetic conservation literature review

Melissa Minter, David O'Brien, Joan Cottrell, Richard Ennos, Jane Hill & Jeanette Hall
Genetic diversity is important for species persistence and Gene Conservation Units (GCUs) have been implemented for forest trees to protect genetic diversity and evolutionary processes in situ. The Convention on Biological Diversity stipulates the protection of genetic diversity as an Aichi target, and so we explore the potential for GCUs to be implemented more widely. Our global systematic review showed that GCUs are currently implemented primarily for plant species of economic importance (109/158 species studied),...

Rare missense functional variants at COL4A1 and COL4A2 in sporadic intracerebral hemorrhage

Jaeyoon Chung, Graham Hamilton, Minsup Kim, Sandro Marini, Bailey Montgomery, Jonathan Henry, Art Cho, Devin Brown, Bradford Worrall, James Meschia, Scott Silliman, Magdy Selim, David Tirschwell, Chelsea Kidwell, Brett Kissela, Steven Greenberg, Anand Viswanathan, Joshua Goldstein, Carl Langefeld, Kristiina Rannikmae, Catherine Sudlow, Neshika Samarasekera, Mark Rodrigues, Rustam Salman, James Prendergast … & Christopher Anderson
Objective To test the genetic contribution of rare missense variants in COL4A1 and COL4A2 in which common variants are genetically associated with sporadic intracerebral hemorrhage (ICH), we performed rare variant analysis in multiple sequencing data for the risk for sporadic ICH. Methods We performed sequencing across 559Kbp at 13q34 including COL4A1 and COL4A2 among 2,133 individuals (1,055 ICH cases; 1,078 controls) in US-based and 1,492 individuals (192 ICH cases; 1,300 controls) from Scotland-based cohorts, followed...

Contributions of genetic and non-genetic sources to variation in cooperative behaviour in a cooperative mammal

Thomas Houslay, Johanna Nielsen & Tim Clutton-Brock
The evolution of cooperative behaviour is a major area of research among evolutionary biologists and behavioural ecologists, yet there are few estimates of its heritability or of its evolutionary potential and long-term studies of identifiable individuals are required to disentangle genetic and non-genetic components of cooperative behaviour. Here we use long-term data on over 1800 individually recognisable wild meerkats (Suricata suricatta) collected over 30 years and a multi-generational genetic pedigree to partition phenotypic variation in...

Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia

Kai Jiang, Xin Tong, Yan-Qian Ding, Zheng-Wei Wang, Li-Yuan Miao, Yue-E Xiao, Wei-Chang Huang, Yong-Hong Hu & Xiao-Yong Chen
This dataset contains one README file and two raw data files on the distribution and genetic data described in the paper: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia. Journal of Biogeography. Ecological niche modeling was employed to predict the potential distribution of M. thunbergii during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were...

A Novel Cognition-Based Guidance System to Improve Surgical Safety

Lauren Kennedy-Metz
Medical errors causing preventable adverse events are the third leading cause of death in the U.S. The role of human cognition in contributing to errors in complex healthcare environments is increasingly being recognized. Many studies have demonstrated a direct relationship between cognitive performance metrics and patient outcomes. Notwithstanding, the role of cognition in improving safety has not received enough attention. Cardiac surgical OR is a high-impact area to improve patient safety and save lives. High...

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...

Nectar values from: Quantifying nectar production by flowering plants in urban and rural landscapes

Nicholas Tew, Jane Memmott, Ian Vaughan, Stephanie Bird, Graham Stone, Simon Potts & Katherine Baldock
Floral resources (nectar and pollen) provide food for insect pollinators but have declined in the countryside due to land use change. Given widespread pollinator loss, it is important that we quantify their food supply to help develop conservation actions. While nectar resources have been measured in rural landscapes, equivalent data are lacking for urban areas, an important knowledge gap as towns and cities often host diverse pollinator populations. We quantified the nectar supply of urban...

Pathogen dynamics across the diversity of ageing

Jessica Clark, Luke McNally & Tom Little
Reproduction, mortality and immune function often change with age, but do not invariably deteriorate. Across the tree of life, there is extensive variation in age-specific performance and changes to key life-history traits. These changes occur on a spectrum from classic senescence, where performance declines with age, to juvenescence, where performance improves with age. Reproduction, mortality and immune function are also important factors influencing the spread of infectious disease, yet there exists no comprehensive investigation into...

Data from: Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus

Alex Twyford
An understanding of genetic structure is essential for answering many questions in population genetics. However, complex population dynamics and scale-dependent processes can make it difficult to detect if there are distinct genetic clusters present in natural populations. Inferring discrete population structure is particularly challenging in the presence of continuous genetic variation such as isolation by distance. Here, we use the plant species Mimulus guttatus as a case study for understanding genetic structure at three spatial...

Who knows, who cares? Untangling ecological knowledge and nature connection among Amazonian colonist farmers

Katarzyna Mikolajczak, Alexander Lees, Jos Barlow, Frazer Sinclair, Oriana Trindade De Almeida, Agnis Souza & Luke Parry
Conservationists often assume that connection with and caring about nature’s wellbeing is strongly linked to ecological knowledge. Existing evidence on the link between ecological knowledge and psychological nature connection is mixed, geographically limited to countries in the Global North, and does not scrutinize potential differences in determinants of ecological knowledge and nature connection. We investigate the relationship between psychological nature connection and ecological knowledge of local bird species and assess their associations with potential drivers,...

Data from: Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

Jim Downie, Andy F. S. Taylor, Glenn Iason, Ben Moore, Jonathan Silvertown, Stephen Cavers & Richard Ennos
1. For successful colonisation of host roots, ectomycorrhizal (EM) fungi must overcome host defence systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defence systems, but it is not yet understood whether variation in these constitutive defences can result in variation in colonisation of hosts by specific fungal species. 2. We planted seedlings from...

Data from: Using singleton densities to detect recent selection in Bos taurus

Matthew Hartfield, Nina Aagaard Poulsen, Bernt Guldbrandtsen & Thomas Bataillon
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the ‘Singleton Density Score’, to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as...

Data from: Sex-specific associations between life history traits and a novel reproductive polymorphism in the Pacific field cricket

Jon Richardson, Justa Heinen-Kay & Marlene Zuk
Associations between heritable polymorphisms and life-history traits, such as development time or reproductive investment, may play an underappreciated role in maintaining polymorphic systems. This is because selection acting on a particular morph could be bolstered or disrupted by correlated changes in life-history or vice versa. In a Hawaiian population of the Pacific field cricket (Teleogryllus oceanicus), a novel mutation (flatwing) on the X-chromosome is responsible for a heritable polymorphism in male wing structure. We used...

Data from: Integrated population models poorly estimate the demographic contribution of immigration

Matthieu Paquet, Jonas Knape, Debora Arlt, Pär Forslund, Tomas Pärt, Øystein Flagstad, Carl G. Jones, Malcolm A. C. Nicoll, Ken Norris, Josephine M. Pemberton, Håkan Sand, Linn Svensson, Vikash Tatayah, Petter Wabakken, Camilla Wikenros, Mikael Åkesson & Matthew Low
Estimating the contribution of demographic parameters to changes in population growth is essential for understanding why populations fluctuate. Integrated Population Models (IPMs) offer a possibility to estimate contributions of additional demographic parameters, for which no data have been explicitly collected: typically immigration. Such parametersare often subsequently highlighted as important drivers of population growth. Yet, accuracy in estimating their temporal variation, and consequently their contribution to changes in population growth rate, has not been investigated. To...

Interference in the shared-stroop task: a comparison of self- and other-monitoring

Martin Pickering, Janet F. McLean & Chiara Gambi
Co-acting participants represent and integrate each other’s actions, even when they are not required to monitor one another. However, monitoring the actions of a partner is an important component of successful interactions, and particularly of linguistic interactions. Moreover, monitoring others may rely on similar mechanisms to those that are involved in self-monitoring. In order to investigate the effect of monitoring on shared linguistic representations, we combined a monitoring task with the shared Stroop task. In...

Benthic silica flux magnitudes and silicon isotopic composition of marine sediment pore waters and solid phase leachates for the Barents Sea (summer 2017-2019)

James PJ Ward, Sian F Henley, Johan C Faust & Felipe Sales de Freitas
This data product comprises 5 files, containing marine sediment pore water and solid phase leachate silicon (Si) isotopic and element concentration data, as well as benthic silica flux magnitudes derived from core incubation experiments and sediment biogenic silica contents. Samples were collected over three cruises of the Changing Arctic Ocean Seafloor (ChAOS) project summer sampling campaigns in the Barents Sea between 2017 and 2019 aboard the RRS James Clark Ross (cruises JR16006, JR17007 and JR18006)....

Centre for Research in Digital Education Annual Report 2021

Sian Bayne

Centre for Research in Digital Education Annual Report 2019

Sian Bayne

Data from: Carry on caring: infected females maintain their parental care despite suffering high mortality

Tom Ratz, Katy Monteith, Pedro Vale & Per Smiseth
Parental care is a key component of an organism’s reproductive strategy that is thought to trade-off with allocation towards immunity. Yet it is unclear how caring parents respond to pathogens: do infected parents reduce care as a sickness behaviour or simply from being ill, or do they prioritise their offspring by maintaining high levels of care? To address this issue, we investigated the consequences of infection by the pathogen Serratia marcescens on mortality, time spent...

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