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15 results for “spatial spread”
Ecogeographic drivers of the spatial spread of highly pathogenic avian influenza outbreaks in Europe and North America, 2016–2022
<p>H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterize ecological and environmental predictors of virus spread between geographic regions through constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). Findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the US, H5Nx viruses spread at a greater rate between US-based regions and no evidence demonstrated spread back to any European region. We establish that geographic proximity is a predictor of virus spread between regions, which implies that inter-continental transport across the Atlantic Ocean is relatively rare. Increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and North America during an actively evolving inter-continental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses.</p>
Ecogeographic drivers of the spatial spread of highly pathogenic avian influenza outbreaks in Europe and North America, 2016–2022
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Data from: Spatial spread of the West Africa Ebola epidemic
Controlling Ebola outbreaks and planning an effective response to future emerging diseases are enhanced by understanding the role of geography in transmission. Here we show how epidemic expansion may be predicted by evaluating the relative probability of alternative epidemic paths. We compared multiple candidate models to characterize the spatial network over which the 2013–2015 West Africa epidemic of Ebola virus spread and estimate the effects of geographical covariates on transmission during peak spread. The best model was a generalized gravity model where the probability of transmission between locations depended on distance, population density and international border closures between Guinea, Liberia and Sierra Leone and neighbouring countries. This model out-performed alternative models based on diffusive spread, the force of infection, mobility estimated from cell phone records and other hypothesized patterns of spread. These findings highlight the importance of integrated geography to epidemic expansion and may contribute to identifying both the most vulnerable unaffected areas and locations of maximum intervention value.
Data from: When viruses don't go viral: the importance of host phylogeographic structure in the spatial spread of arenaviruses
Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone's centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon's range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa.
Data from: Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France
Species distribution models (SDM) have often been used to predict the potential ranges of introduced species and prioritize management strategies. However, this approach assumes equilibrium between occurrences and environmental gradients, an assumption which is violated during the invasion process, where many suitable sites are empty because the species has not yet reached them. Here we considered the invasive ladybird Harmonia axyridis as a case study to show the benefits of using a dynamic colonization–extinction model that does not assume equilibrium. We used a multi-year occupancy model incorporating environmental, anthropogenic and neighborhood effects, to identify factors that explained spreading variation of this species in France from 2004, when only a few occupied sites were detected, to 2011. We found that anthropogenic factors (urbanization, agriculture, vineyards, and presence/absence of highways) explained more variation in the diffusion process than environmental factors (winter and summer temperatures, wind-speed, and rainfall). The surface of urbanization was the major anthropogenic factor increasing the probability of colonization. The average summer temperature was the main environmental factor affecting colonization, with a negative effect when high or low. The neighborhood effect revealed that colonization was mostly influenced by contributions coming from a radius of 24 km around the focal cell. The contribution of neighborhood decreases over time, suggesting that H. axyridis is reaching its equilibrium in France. This is confirmed by the small discrepancy observed between the performance of our approach and a SDM approach when predicting a single year occupancy pattern at the end of the study period. Our approach has the advantage of explicitly modelling the state of the biological system during the spatial expansion and identifying colonization constraints. This allows managers to explore the effect of different actions on the system at key moments of the invasion process, hence providing a powerful approach to prioritize management strategies.
Reconstructed spatial resolution and contrast recovery with Bayesian penalized likelihood reconstruction (Q.Clear) for FDG-PET compared to time-of-flight (TOF) with point spread function (PSF)
<p>DICOM data and SPSS datasets with all derived measures (SUV, recovery coefficients, spatial resolution, SNR) that are the basis for the publication.</p>
Data from: When viruses don’t go viral: the importance of host phylogeographic structure in the spatial spread of arenaviruses
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Variation in host home range size decreases rabies vaccination effectiveness by increasing the spatial spread of rabies virus
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Data from: Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France
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Data from: Spatial spread of the West Africa Ebola epidemic
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Data from: Evidence of spatial synchrony in the spread of an invasive forest pest
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Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe
The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on multilocus sequence typing and the Wolbachia surface protein wsp showed that all R. cingulata individuals are infected with wCin2 identical to wCer2 in R. cerasi. In contrast, wCin1, a strain identical to wCer1 in R. cerasi, was present in several European populations of R. cingulata, but not in any individual from the United States. Surveys of R. cingulata from Germany and Hungary indicated that the frequency of wCin1 infection increased dramatically in just a few years with at least two independent horizontal transmission events in Germany and Hungary. This is further corroborated by the analysis of the mitochondrial cytochrome oxidase II gene that showed linkage of wCin1 with two distinct haplotypes in Germany, one of which is also infected with wCin1 in Hungary. In summary, our study provides strong evidence for a very recent interspecific Wolbachia transmission with a subsequent spatial spread in field populations.
Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe
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Data from: The role of geospatial hotspots in the spatial spread of tuberculosis in rural Ethiopia: a mathematical modelling
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The effect of spatial energy spread on sound image size and speech intelligibility [dataset]
<p>This dataset contains the data and supplementary material for the publication titled "The effect of spatial energy spread on sound image size and speech intelligibility" published in the Journal of the Acoustical Society of America.</p> <p>This repository contains the results from the three experiments as well as a figure showing the adaptive tracks of the adaptive procedure and the estimated psychometric functions in experiment 3. The subject identifiers are common across the three experiments.</p> <p><strong>Experiment 1: </strong></p> <p>Factors: <em>Subject/Listener, ambisonics order, audio/stimulus type, spatial location of stimulus, room condition, repetition</em></p> <p>Measured variables: <em>Source image size, source direction (azimuth), source distance</em></p> <p><strong>Experiment 2:</strong></p> <p>Factors: <em>Subject/Listener, ambisonics order, interferer location, room condition</em></p> <p>Measured variable: <em>Speech reception threshold (SRT)</em></p> <p><strong>Experiment 3:</strong></p> <p>Factors: <em>Subject/Listener, ambisonics order, repetition</em></p> <p>Measured variable: <em>Speech reception angle (SRA)</em></p> <p>The figure (exp3_adaptiveTracks.png) shows the adaptive tracks in experiment 3. Each panel shows one of the ambisonics orders. The x-axis is the trial number and the y-axis the separation angle between target and interfering talkers. Each color indicates one subject.</p> <p>The figure (exp3_psychometricFcns.png) shows the estimated psychometric functions in experiment 3. Each panel shows one of the ambisonics orders. The x-axis is the separation angle between target and interfering talkers and the y-axis is the percent correct words. Each color indicates one subject. The black line indicates the median over the subjects and repetitions and the black cross the SRA predicted with this method.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.