184 Works

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...

2010 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2015 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2016 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms

Hans Recknagel, Arne Jacobs, Pawel Herzyk & Kathryn R. Elmer
Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction site associated DNA sequencing (RAD sequencing or RADseq) has become an established method for SNP genotyping on Illumina sequencing platforms. Here, we developed a protocol and adapters for double-digest RAD sequencing for Ion Torrent (Life Technologies; Ion Proton,...

Data from: Effects of interspecific coexistence on laying date and clutch size in two closely related species of hole‐nesting birds

Anders Pape Møller, Javier Balbontin, André A. Dhondt, Vladimir Remeš, Frank Adriaensen, Clotilde Biard, Jordi Camprodon, Mariusz Cichoń, Blandine Doligez, Anna Dubiec, Marcel Eens, Tapio Eeva, Anne E. Goodenough, Andrew G. Gosler, Lars Gustafsson, Philipp Heeb, Shelley A. Hinsley, Staffan Jacob, Rimvydas Juškaitis, Toni Laaksonen, Bernard Leclercq, Bruno Massa, Tomasz D. Mazgajski, Rudi G. Nager, Jan-Åke Nilsson … & Ruedi G. Nager
Coexistence between great tits Parus major and blue tits Cyanistes caeruleus, but also other hole‐nesting taxa, constitutes a classic example of species co‐occurrence resulting in potential interference and exploitation competition for food and for breeding and roosting sites. However, the spatial and temporal variations in coexistence and its consequences for competition remain poorly understood. We used an extensive database on reproduction in nest boxes by great and blue tits based on 87 study plots across...

Data from: Can variation in standard metabolic rate explain context-dependent performance of farmed salmon offspring?

Grethe Robertsen, Donald Reid, Sigurd Einum, Tonje Aronsen, Ian A. Fleming, Line E. Sundt-Hansen, Sten Karlsson, Eli Kvingedal, Ola Ugedal & Kjetil Hindar
Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self-maintenance) during domestication. Furthermore, fitness related advantages of phenotypic traits associated with both high SMR and...

Data from: Evolution on the move: specialization on widespread resources associated with rapid range expansion in response to climate change

Jon R. Bridle, James Buckley, Edward J. Bodsworth & Chris D. Thomas
Generalist species and phenotypes are expected to perform best under rapid environmental change. In contrast to this view that generalists will inherit the Earth, we find that increased specialisation on a single host plant is associated with the recent climate-driven range expansion of the UK Brown Argus butterfly. Field assays of female host plant preference across the UK reveal a diversity of adaptations to host plants in long-established parts of the range, whereas butterflies in...

Data from: Among-sibling differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank

Tim Burton, Mia O. Hoogenboom, Nicholas D. Beevers, John D. Armstrong & Neil B. Metcalfe
We investigated whether among-sibling differences in the phenotypes of juvenile fish were systematically related to the position in the egg mass where each individual developed during oogenesis. We sampled eggs from the front, middle and rear thirds of the egg mass in female brown trout of known dominance rank. In the resulting juveniles, we then measured traits that are related to individual fitness: body size, social status and standard metabolic rate (SMR). When controlling for...

Data from: Vitamins, stress and growth: the availability of antioxidants in early life influences the expression of cryptic genetic variation

Sin-Yeon Kim, José C. Noguera, Andrea Tato, Alberto Velando & S.-Y. Kim
Environmental inputs during early development can shape the expression of phenotypes, which has long-lasting consequences in physiology and life history of an organism. Here, we study whether experimentally manipulated availability of dietary antioxidants, vitamins C and E, influences the expression of genetic variance for antioxidant defence, endocrine signal and body mass in yellow-legged gull chicks using quantitative genetic models based on full siblings. Our experimental study in a natural population reveals that the expression of...

Data from: Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation

James P. J. Hall, Huanhuan Wang & J. David Barry
A main determinant of prolonged Trypanosoma brucei infection, and hence transmission and success of the parasite, is the interplay between host acquired immunity and antigenic variation of the parasite variant surface glycoprotein (VSG) coat. About 0.1% of trypanosome divisions produce a switch to a different VSG through differential expression of an archive of hundreds of silent VSG genes and pseudogenes, but the patterns and extent of the trypanosome diversity phenotype, particularly in chronic infection, are...

Data from: Eye coding mechanisms in early human face event-related potentials

Guillaume A. Rousselet, Robin A. A. Ince, Nicola J. Van Rijsbergen & Philippe G. Schyns
In humans, the N170 event-related potential (ERP) is an integrated measure of cortical activity that varies in amplitude and latency across trials. Researchers often conjecture that N170 variations reflect cortical mechanisms of stimulus coding for recognition. Here, to settle the conjecture and understand cortical information processing mechanisms, we unraveled the coding function of N170 latency and amplitude variations in possibly the simplest socially important natural visual task: face detection. On each experimental trial, 16 observers...

Data from: Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species

Johanna L. Baily, Guillaume Méric, Sion Bayliss, Geoffrey Foster, Simon E. Moss, Eleanor Watson, Ben Pascoe, Jane Mikhail, Robert J. Goldstone, Romain Pizzi, David G. E. Smith, Kim Willoughby, Alisa J. Hall, Mark P. Dagleish, Samuel K. Sheppard & Ailsa J. Hall
Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal bacterial pathogens, of anthropic origin, to spread to marine wildlife in coastal areas. The common zoonotic bacterium Campylobacter was isolated from grey seals (Halichoerus grypus), an important sentinel species for environmental pollution, and compared to isolates from wild birds, agricultural sources and clinical samples to...

Data from: Parasitism in early life: environmental conditions shape intra-brood variation in responses to infection

Hanna M. V. Granroth-Wilding, Sarah J. Burthe, Sue Lewis, Thomas E. Reed, Katherine A. Herborn, Mark A. Newell, Emi A. Takahashi, Francis Daunt & Emma J. A. Cunningham
Parasites play key ecological and evolutionary roles through the costs they impose on their host. In wild populations, the effect of parasitism is likely to vary considerably with environmental conditions, which may affect the availability of resources to hosts for defense. However, the interaction between parasitism and prevailing conditions is rarely quantified. In addition to environmental variation acting on hosts, individuals are likely to vary in their response to parasitism, and the combined effect of...

Data from: Why do frog and toad forelimbs suddenly (but asynchronously) appear every time metamorphosis is near?

Luigi Zechini, Alison Lilley, J. Roger Downie & Patrick T. Walsh
1. The internal development and the emergence of the forelimbs at metamorphosis is a defining feature of anuran amphibians (frogs and toads). However, although forelimb emergence is considered sudden, it is rarely synchronous. Any asynchrony may or may not exacerbate the increased drag that is predicted to occur with the emergence of the forelimbs at metamorphic climax. 2. Despite the impact forelimb emergence is hypothesized to have on individual survival and life-history evolution, the degree...

Data from: Are molecular markers useful predictors of adaptive potential?

Elizabeth A. Mittell, Shinichi Nakagawa & Jarrod D. Hadfield
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By...

Data from: 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador

Luis Enrique Hernandez Castro, Marta Paterno, Anita G. Villacís, Björn Andersson, Jaime A. Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A. Yumiseva, Mario J. Grijalva, Martin S. Llewellyn & Luis E. Hernandez-Castro
Background: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some...

Data from: Pulse of inflammatory proteins in the pregnant uterus of European polecats (Mustela putorius) leading to the time of implantation

Heli Lindeberg, Richard J.S. Burchmore, Malcolm W. Kennedy & Richard J. S. Burchmore
Uterine secretory proteins protect the uterus and conceptuses against infection, facilitate implantation, control cellular damage resulting from implantation, and supply pre-implantation embryos with nutrients. Unlike in humans, the early conceptus of the European polecat (Mustela putorius; ferret) grows and develops free in the uterus until implanting at about 12 days after mating. We found that the proteins appearing in polecat uteri changed dramatically with time leading to implantation. Several of these proteins have also been...

Data from: Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

Kevin J. Parsons, Young H. Son, Amelie Crespel, Davide Thambithurai, Shaun Killen, Matthew P. Harris & R. Craig Albertson
Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have...

Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland

Adrian Allen, Jimena Guerrero, Andrew Byrne, John Lavery, Eleanor Presho, Emily Courcier, James O'Keeffe, Ursula Fogarty, Richard Delahay, Gavin Wilson, Chris Newman, Christina Buesching, Matthew Silk, Denise O'Meara, Robin Skuce, Roman Biek & Robbie A. McDonald
The colonization of Ireland by mammals, has been the subject of extensive study using genetic methods, and forms a central problem in understanding the phylo-geography of European mammals after the Last Glacial Maximum. Ireland exhibits a de-pauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger (Meles meles) have found conflicting microsatellite and...

Data from: Environmental conditions shape the temporal pattern of investment in reproduction and survival

Valeria Marasco, Winnie Boner, Kate Griffiths, Britt Heidinger & Pat Monaghan
The relationship between environmental stress exposure and ageing is likely to vary with stressor severity, life history stage, and the time scale over which effects are measured. Such factors could influence whether stress exposure accelerates or slows the ageing process, but their interactions have not previously been experimentally investigated. We found that experimental exposure of zebra finches to mildly challenging environmental circumstances from young to old adulthood, which increased exposure to stress hormones, reduced breeding...

Data from: Continent-level drivers of African pyrodiversity

Gareth P. Hempson, Catherine L. Parr, Sally Archibald, T. Michael Anderson, Colin J. Courtney Mustaphi, Andrew P. Dobson, Jason E. Donaldson, Thomas A. Morrison, James Probert & Colin M. Beale
Pyrodiversity, which describes fire variability over space and time, is believed to increase habitat heterogeneity and thereby promote biodiversity. However, to date there is no standardised metric for quantifying pyrodiversity, and so broad geographic patterns and drivers of pyrodiversity remain unexplored. We present the first generalizable method to quantify pyrodiversity, and use it to address the fundamental questions of what drives pyrodiversity, which fire attributes constrain pyrodiversity under different conditions, and whether pyrodiversity is spatial...

Diet and temperature modify the relationship between energy use and ATP production to influence behaviour in zebrafish (Danio rerio)

Amélie Le Roy, Geoffrey Mazué, Neil Metcalfe & Frank Seebacher
Food availability and temperature influence energetics of animals, and can alter behavioural responses such as foraging and spontaneous activity. Food availability, however, is not necessarily a good indictator of energy (ATP) available for cellular processes. The efficiency of energy transduction from food-derived substrate to ATP in mitochondria can change with environmental context. Our aim was to determine whether the interaction between food availability and temperature affects mitochondrial efficiency and behaviour in zebrafish (Danio rerio). We...

Survey data of scientists on knowledge exchange in critical zone and geoscience

Y. Zheng, L.A Naylor, S. Waldron & D.M. Oliver
Survey data on knowledge exchange experience of both Chinese and British scientists working on critical zone and more broadly on geoscience. Data are drawn from questionnaire surveys to explore the knowledge management methods used in their environmental research. Data are anonymised social survey data from questionnaires. The data were generated during the NERC grant 'The transmissive critical zone: understanding the karst hydrology-biogeochemical interface for sustainable management' reference NE/N007425/1 undertaken as part of the NERC Using...

Literature review of knowledge management across the environment-policy interface in China

Y. Zheng, L.A. Naylor, S. Waldron & D.M. Oliver
Data from literature search systematically conducted using two widely-used academic databases: Web of Science™ (WoS) and Scopus . Data include the annual amount of KM publication in China and across the world, in WoS, the total amount of knowledge management (KM) publication during the searched years for each country (top 20), in Scopus, the total amount of KM publication during the searched years for each country (top 20), information about the retained KM publication for...

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