87 Works

Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations

Euan Furness, Russell Garwood, Philip Mannion & Mark Sutton
It has been widely hypothesised that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the “more individuals” hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently...

Risky decision and happiness task: The Great Brain Experiment smartphone app

Robb B. Rutledge
This resource consists of data from a risky decision and happiness task that was part of The Great Brain Experiment (GBE) smartphone app. Data were collected from 47,067 participants aged 18+ between March 8, 2013 and October 5, 2015. These anonymous unpaid participants completed the task a total of 91,058 times making approximately 2.7 million choices and 1.1 million happiness ratings in total. This resource represents at least 6,000 hours of task data. A subset...

Free energy calculations of noble-gas containing liquid iron and silicate melt

Y Li
Free energy calculations of noble-gas containing liquid iron and silicate melts at 50 GPa (3500 K) and 135 GPa (4200 K). The chemical potentials of noble gases can be obtained from these calculations. The Gibbs free energy of a series of iron and silicate melts with different concentrations of He were calculated. Then the chemical potentials of He can be derived from the concentration dependent Gibbs free energies. The chemical potentials of Ne, Ar, Kr...

Imaging mass cytometry data: Head and neck squamous cell carcinoma tissue section

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, James Arnold, Benedetta Apollonio, Alan Ramsay, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of multiparametric “big data” usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Energy modelling in the UK: The modelling landscape

Neil Strachan & Pei-Hao Li
This paper is the first of four to explore results from UKERC’s Modelling Hub survey. Focusing on the UK energy modelling landscape, these initial findings detail who hosts and runs models, their methodologies and coverage, and their major outputs.

Structural brain network abnormalities and the probability of seizure recurrence after epilepsy surgery: supplementary material

Nishant Sinha, Yujiang Wang, Nádia Moreira Da Silva, Anna Miserocchi, Andrew McEvoy, Jane De Tisi, Sjoerd Vos, Gavin Winston, John Duncan & Peter Taylor
Objective: We assessed pre-operative structural brain networks and clinical characteristics of patients with drug resistant temporal lobe epilepsy (TLE) to identify correlates of post-surgical seizure recurrences. Methods: We examined data from 51 TLE patients who underwent anterior temporal lobe resection (ATLR) and 29 healthy controls. For each patient, using the preoperative structural, diffusion, and post-operative structural MRI, we generated two networks: ‘pre-surgery’ network and ‘surgically-spared’ network. Standardising these networks with respect to controls, we determined...

Iron-Nickel-Sulfide Characterisation and Catalytic Testing Data

Claire Mitchell, David Santos-Carballal, Andrew M Beale, Wilm Jones, Sankar Meenakshisundaram & Nora H De Leeuw
Catalytic data describing the production of formate from the hydrogenation of CO2 using iron-sulfide, iron-nickel-sulphide and nickel-sulfide catalysts prepared with different heat treatments under a range of reaction conditions. Catalyst characterisation of these materials include XRD analysis, giving an understanding of the violarite phase and crystallinity. XPS analysis gains understanding of the iron, nickel and sulphur species, and how sulphide and oxide species change under thermal oxidation. XAS analysis employed is vital to gain more...

REMI-seq analysis of D. discoideum cells treated with Lithium or Valproic acid

Christopher Thompson
A critical aspect of toxicity evaluation is developmental and reproductive toxicity (DART) testing. Traditionally, DART testing has been conducted in vivo in mammalian model systems. New legislation aimed at reducing animal use and the prohibitive costs associated with DART testing, together with a need to understand the genetic pathways underlying developmental toxicity means there is a growing demand for alternative model systems for toxicity evaluation. Here we explore the potential of the eukaryotic social amoeba...

Quantitative assessment of agricultural sustainability reveals divergent priorities among nations

Guolin Yao, Xin Zhang, Srishti Vishwakarma, Carole Dalin, Adam Komarek, David Kanter, Kyle Davis, Kimberly Pfeifer, Jing Zhao, Tan Zou, Paolo D'Odorico, Christian Folberth, Fernando Galeana Rodriguez, Jessica Fanzo, Lorenzo Rosa, William Dennison, Mark Musumba, Amy Heyman & Eric Davidson
Agriculture is fundamental to all three pillars of sustainability, environment, society, and economy. However, the definition of sustainable agriculture and capacities to measure it remain elusive. Independent and transparent measurements of national sustainability are needed to gauge progress, encourage accountability, and inform policy. Here, we developed a Sustainable Agriculture Matrix (SAM) to quantify national performance indicators in agriculture and to investigate the tradeoffs and synergies based on historical data for most countries of the world....

Design of a custom-made device for real-time optical measurement of differential mineral concentrations in 3D scaffolds for bone tissue engineering

Joseph Lovecchio, Valentina Betti, Marilisa Cortesi, Enrico Ravagli, Stefano Severi & Emanuele Giordano
Monitoring bone tissue engineered constructs during their maturation is important to ensure the quality of applied protocols. Several destructive, mainly histochemical, methods are conventionally used to this aim, requiring the sacrifice of the investigated samples. This implies i) to plan several scaffold replicates, ii) expensive and time consuming procedures and iii) to infer the maturity level of a given tissue construct from a cognate replica. To solve these issues, non-destructive techniques such as light spectroscopy-based...

A reassessment of the enigmatic diapsid Paliguana whitei and the early history of Lepidosauromorpha

David Paul Ford, Susan Evans, Jonah Choiniere, Vincent Fernandez & Roger Benson
Lepidosaurs include lizards, snakes, amphisbaenians and the tuatara, comprising a highly speciose evolutionary radiation with widely varying anatomical traits. Their stem-lineage originated by the late middle Permian 259 million years ago, but its early fossil record is poorly documented, obscuring the origins of key anatomical and functional traits of the group. Paliguana whitei, from the Early Triassic of South Africa, is an enigmatic fossil species with potential to provide information on this. However, its anatomy...

How bulk and surface properties of Ti4SiC3, V4SiC3, Nb4SiC3 and Zr4SiC3 tune reactivity: a computational study - data

Matthew Quesne, Nora H De Leeuw & C Richard A Catlow
The bulk and surface properties of early transition metal silicon carbides as well as their activity towards the reduction of CO2 is examined in this first principles DFT study. Data for basal (0001) planes of Ti4C3Si, V4C3Si, Nb4C3Si & Zr4C3Si is stored in one .xlsx file. The first sheet gives formation energies for each silicon carbide as related to the parent monocarbide material. Sheet 2 gives the density of states for each material. Sheet 3...

Data from: Sex differences in costly signalling in rural Western China

Dongzhi Cairang, Erhao Ge & Ruth Mace
Numerous empirical studies suggest that individuals convey their commitment to communities and impart the qualities of being a reliable partner through costly behaviours. We collected religious practices data ranging from daily trivial practices to infrequent grand distant pilgrimages in an agricultural Tibetan village. We predict that 1) villagers who invest more in religious practices are more likely to be nominated as having various prosocial qualities. 2) Investment in grand distant pilgrimages has more efficacy than...

The PURPLE N study: objective and perceived nutritional status in children and adolescents with cerebral palsy

Andras Fogarasi, Elisa Fazzi, Ana R. P. Smorenburg, Maria Mazurkiewicz-Beldzinska, Argirios Dinopoulos, Alena Pobiecka, Dea Schröder-van den Nieuwendijk, Josef Kraus, Hasan Tekgül, Maria Koutsaki, Giovanni Baranello, Simona Bertoli, Elisa Caramaschi, Duccio Maria Cordelli, Ramona De Amicis, Maria Luisa Forchielli, Azzurra Guerra, Althea Lividini, Maddalena Marchiò, Andrea Rossi, Jędrzej Fliciński, Barbara Gurda, Anna Lemska, Agnieszka Matheisel, Zuzanna Niwinska … & Sanem Keskin Yilmaz
To obtain information on characteristics, management, current objective nutritional status and perception of nutritional status of children with cerebral palsy (CP) from healthcare professionals (HCPs) and caregivers. A detailed survey of several items on eight main topics (general characteristics, motor function, comorbidities, therapies, anthropometry, feeding mode and problems and perceived nutritional status) was developed and tested for the study. Correlation between nutritional status and Gross Motor Function Classification System (GMFCS) levels was assessed using continuous...

The closure of the Neotethys in two episodes: first. as a result of Jurassic to Early Cretaceous obduction and second, as a result of Early Palaeocene collision; a comparison of surface geology and tomography (Central Internal Hellenides, Greece)

Rudolph Scherreiks & Camille BouDagher-Fadel
This contribution concerns Neotethys palaeogeography in the Central Internal Hellenides. Neotethys oceanic crust is represented in the Vardar zone of the Hellenides by the ophiolites of the Almopias sub-zone. Contrary to numerous tectonic models in the literature, we show that the Almopias ocean closed in two episodes.

Data from: Meiotic drive does not cause condition-dependent reduction of the sexual ornament in stalk-eyed flies

Sam Finnegan, Matteo Mondani, Kevin Fowler & Andrew Pomiankowski
Meiotic drive systems are associated with low frequency chromosomal inversions. These are expected to accumulate deleterious mutations due to reduced recombination and low effective population size. We test this prediction using the “sex-ratio” (SR) meiotic drive system of the Malaysian stalk-eyed fly Teleopsis dalmanni.SR is associated with a large inversion (or inversions) on the X chromosome. In particular, we study eyespan in males carrying the SR chromosome, as this trait is a highly exaggerated, sexually...

Cerebral small vessel disease and functional outcome prediction after intracerebral haemorrhage

David Werring, Ghil Schwarz & Isabel Hostettler
Background. It is unknown whether adding cerebral small vessel disease (SVD) biomarkers can improve the performance of intracerebral hemorrhage (ICH) outcome predictive scores. Purpose. To determine whether: (1) CT-based SVD biomarkers are associated with 6-month functional outcome after ICH and (2) whether these biomarkers improve the performance of pre-existing ICH score. Methods. We included 864 patients with acute ICH from a multicentre, hospital-based prospective cohort study. We evaluated CT-based SVD biomarkers (white matter hypodensities [WMH];...

Spatial modulation of visual responses arises in cortex with active navigation

, Charu Bai Reddy, Sylvia Schröder, Tomaso Muzzu, Kenneth D. Harris, Aman B. Saleem & Matteo Carandini
During navigation, the visual responses of neurons in mouse primary visual cortex (V1) are modulated by the animal’s spatial position. Here we show that this spatial modulation is similarly present across multiple higher visual areas but negligible in the main thalamic pathway into V1. Similar to hippocampus, spatial modulation in visual cortex strengthens with experience and with active behavior. Active navigation in a familiar environment, therefore, enhances the spatial modulation of visual signals starting in...

Sudden Unexpected Death in Epilepsy: A Personalized Prediction Tool

Ashwani Jha, Cheongeun Oh, Dale Hesdorffer, Beate Diehl, Sasha Devore, Martin Brodie, Torbjörn Tomson, Josemir W. Sander, Thaddeus S. Walczak & Orrin Devinsky
Objective: To develop and validate a tool for individualised prediction of Sudden Unexpected Death in Epilepsy (SUDEP) risk, we re-analysed data from one cohort and three case-control studies undertaken 1980-2005. Methods: We entered 1273 epilepsy cases (287 SUDEP, 986 controls) and 22 clinical predictor variables into a Bayesian logistic regression model. Results: Cross-validated individualized model predictions were superior to baseline models developed from only average population risk or from generalised tonic-clonic seizure frequency (pairwise difference...

Historical analysis of seagrass loss in the United Kingdom

Alix E. Green, Michael A. Chadwick, Richard K.F. Unsworth & Peter J.S. Jones
This dataset includes empirical and qualitative data from a multitude of sources using systematic review methods to provide analysis on seagrass occurrence and loss in the United Kingdom. We document 8,493 ha of recently mapped seagrass in the UK since 1998.

Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods

Katie S. Collins, Roman Klapaukh, James S. Crampton, Michael F. Gazley, C. Ian Schipper, Anton Maksimenko & Benjamin R. Hines
The logarithmic helicospiral has been the most widely accepted model of regularly coiled mollusc form since it was proposed by Moseley (1838) and popularised by Thompson (1942) and Raup (1966). It is based on an explicit assumption that shells are isometric and grow exponentially, and an implicit assumption that the external form of the shell follows the internal shape, which implies that the parameters of the spiral could, theoretically, be reconstructed from the external whorl...

A non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster exhibits antagonistically pleiotropic fitness effects

Michael Jardine, Filip Ruzicka, Charlotte Diffley, Kevin Fowler & Max Reuter
The amount of genetic variation for fitness within populations tends to exceed that expected under mutation-selection-drift balance. Several mechanisms have been proposed to actively maintain polymorphism and account for this discrepancy, including antagonistic pleiotropy (AP), where allelic variants have opposing effects on different components of fitness. Here we identify a non-coding indel polymorphism in the fruitless gene of Drosophila melanogaster and measure survival and reproductive components of fitness in males and females of replicate lines...

A 5.3-million-year history of monsoonal precipitation in northwestern Australia

Jan-Berend Willem Stuut , Patrick De Deckker , Mariem Saavedra-Pellitero , Franck Bassinot , Anna Joy Drury , Maureen Walczak & Kana Nagashima
NIOZ - Royal Netherlands Institute for Sea Research, and Utrecht University, Texel, the Netherlands (1); MARUM – Center for Marine Environmental Sciences, Bremen University, Bremen, Germany (2); Department of Earth Sciences, Faculty of Science, Vrije Universiteit Amsterdam, The Netherlands (3); ANU – Australian National University, Research School of Earth Sciences, Canberra, Australia (4); School of Geography, Earth and Environmental Sciences at University of Birmingham, Edgbaston Birmingham, United Kingdom (5); LSCE - Laboratoire des Sciences du...

Flow cytometry data: healthy donor bone marrow taken during hip surgery

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

Imaging mass cytometry data: Diffuse large B-cell lymphoma lymph node section

Jessica Timms, James Opzoomer, Kevin Blighe, Thanos Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca Ciccarelli, Peter Parker, Michaela Fontenay, Paul Barber, James Arnold & Shahram Kordasti
High dimensional cytometry is an innovative tool for immune monitoring in health and disease, it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here we describe ImmunoCluster (https://github.com/kordastilab/ImmunoCluster) an R package for immune profiling cellular heterogeneity in high dimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by...

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