Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
126
datasets available to search
ShareScore release 0.9.0
Dataset results
126 results for “disease emergence”
Data from: Forecasting potential emergence of zoonotic diseases in Southeast Asia: network analysis identifies key rodent hosts
1. Within complex ecological systems, identifying animal species likely to play a key role in the emergence of infectious zoonotic diseases remains a major challenge. One approach consists of using information on current ecological and parasitological similarities among host species in order to predict the most likely pathways for future pathogen spillover. 2. Using field data acquired from 15 sympatric rodent species in various habitats in Thailand, Cambodia and Laos, we built networks based on shared parasites (17 helminth and 15 microparasite species) and shared habitats among rodent species and humans. We investigated the architectures of bipartite and unipartite networks using modularity, subgroups partitioning or node centrality, to assess the relative epidemiological importance of particular rodent species. 3. Our results showed that Rattus tanezumi, Bandicota savilei and R. exulans were consistently found to be members of subgroups that included humans in unipartite and bipartite networks on zoonotic agents and shared habitats. High values of centrality in shared zoonotic agents were found for the same three rodent species, whereas high values of shared habitats were observed for two of them. Although phylogenetically related rodent species likely shared both habitats and parasites, a lack of habitat specialisation was associated with increased zoonotic parasite sharing. 4. Our results emphasize the disproportionate importance of these three rodent species, through their high degree of connectivity with humans, which may represent a high risk for direct zoonotic spillover. Moreover, due to its high centrality in habitats, R. tanezumi may also play a key role as a bridge host. 5. The recent discovery of new arenaviruses in rodents in Southeast Asia, with associated disease in humans in Cambodia, provides an opportunity to test this empirically. The three rodent species identified using our network approach are some of the potential maintenance hosts for these new emerging arenaviruses. 6. Synthesis and applications. Our results on rodents and their pathogens in Southeast Asia show that network analysis has a high potential to improve the surveillance of emerging zoonotic pathogens by targeting key host species and potential "emerging' pathogen–rodent interactions in complex and heterogeneous landscapes.
wild_expression: gene expression data on wildlife hosts of emerging infectious diseases
<p>Publicly accessible data and code supporting the manuscript:</p> <p>"Host gene expression in wildlife disease: making sense of species-level responses"</p>
Literature search on worldwide surveillance systems targeting transboundary zoonotic and emerging diseases
<p>Surveillance systems for zoonotic and transboundary emerging pathogens that are structured following the holistic principles of joint work efforts from the human health, animal health and environmental health sectors are reviewed to provide a summary of one-health based surveillance systems existing worldwide. A systematic search of available literature was undertaken across various biomedical and scientific literature databases (from 2000 to 2022) and were selected using inclusion/exclusion criteria to filter references presenting systematic surveillance systems applicable to transmissible, transboundary, and zoonotic diseases operating under the One Health approach. A standardized data model and vocabulary were used to extract and classify key information to characterize target surveillance systems. 996 studies were obtained after research (589 after duplicates’ elimination) for inclusion in this review and information was extracted using a data model, which were reduced to 79 items once inclusion and exclusion criteria were applied. From these articles, 80 additional items were found within references.</p>
Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease
<p>Demographic factors are fundamental in shaping infectious disease dynamics. Aspects of populations that create structure, like age and sex, can affect patterns of transmission, infection intensity and population outcomes. However, studies rarely link these processes from individual to population-scale effects. Moreover, the mechanisms underlying demographic differences in disease are frequently unclear. Here, we explore sex-biased infections for a multi-host fungal disease of bats, white-nose syndrome, and link disease-associated mortality between sexes, the distortion of sex ratios, and the potential mechanisms underlying sex differences in infection. We collected data on host traits, infection intensity, and survival of five bat species at 42 sites across seven years. We found females were more infected than males for all five species. Females also had lower apparent survival over winter and accounted for a smaller proportion of populations over time. Notably, female-biased infections were evident by early hibernation and likely driven by sex-based differences in autumn mating behavior. Male bats were more active during autumn which likely reduced replication of the cool-growing fungus. Higher disease impacts in female bats may have cascading effects on bat populations beyond the hibernation season by limiting recruitment and increasing the risk of Allee effects.</p>
Emergency Evaluation of Convalescent Plasma for Ebola Viral Disease (EVD) in Guinea
ClinicalTrials.gov study NCT02342171. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Wildfire alters the disturbance impacts of an emerging infectious disease via changes to host occurrence and demographic structure
Open the record for dataset details and reuse information.
Putative resistance and tolerance mechanisms have little impact on disease progression for an emerging salamander pathogen
Open the record for dataset details and reuse information.
Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease
Open the record for dataset details and reuse information.
Data from: Forecasting potential emergence of zoonotic diseases in Southeast Asia: network analysis identifies key rodent hosts
Open the record for dataset details and reuse information.
A method for characterizing disease emergence curves from paired pathogen detection and serology data
Open the record for dataset details and reuse information.
Data from: Activity patterns during the mating season predict sex-biased infections in an emerging fungal disease
Open the record for dataset details and reuse information.
Experimental evidence of warming-induced disease emergence and its prediction by a trait-based mechanistic model
<p>Predicting the effects of seasonality and climate change on the emergence and spread of infectious disease remains difficult, in part because of poorly understood connections between warming and the mechanisms driving disease. Trait-based mechanistic models combined with thermal performance curves arising from the Metabolic Theory of Ecology (MTE) have been highlighted as a promising approach going forward; however, this framework has not been tested under controlled experimental conditions that isolate the role of gradual temporal warming on disease dynamics and emergence. Here, we provide experimental evidence that a slowly warming host – parasite system can be pushed through a critical transition into an epidemic state. We then show that a trait-based mechanistic model with MTE functional forms can predict the critical temperature for disease emergence, subsequent disease dynamics through time, and final infection prevalence in an experimentally warmed system of <i>Daphnia </i>and a microsporidian parasite. Our results serve as a proof of principle that trait-based mechanistic models using MTE sub-functions can predict warming-induced disease emergence in data-rich systems – a critical step towards generalizing the approach to other systems.</p>
Data from: Megafauna decline have reduced pathogen dispersal which may have increased emergent infectious diseases
<p>The Late Quaternary extinctions of megafauna (defined as animal species > 44.5 kg) reduced the dispersal of seeds and nutrients, and likely also microbes and parasites. Here we use body-mass based scaling and range maps for extinct and extant mammal species to show that these extinctions led to an almost seven-fold reduction in the movement of gut-transported microbes, such as Escherichia coli (3.3–0.5 km 2 d − 1 ). Similarly, the extinctions led to a seven-fold reduction in the mean home ranges of vector-borne pathogens (7.8–1.1km 2 ). To understand the impact of this, we created an individualbased model where an order of magnitude decrease in home range increased maximum aggregated microbial mutations 4-fold after 20 000 yr. We hypothesize that pathogen speciation and hence endemism increased with isolation, as global dispersal distances decreased through a mechanism similar to the theory of island biogeography. To investigate if such an effect could be found, we analysed where 145 zoonotic diseases have emerged in human populations and found quantitative estimates of reduced dispersal of ectoparasites and fecal pathogens significantly improved our ability to predict the locations of outbreaks (increasing variance explained by 8%). There are limitations to this analysis which we discuss in detail, but if further studies support these results, they broadly suggest that reduced pathogen dispersal following megafauna extinctions may have increased the emergence of zoonotic pathogens moving into human populations.</p>
Data from: Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population
The emergence rate of new plant diseases is increasing due to novel introductions, climate change, and changes in vector populations, posing risks to agricultural sustainability. Assessing and managing future disease risks depends on understanding the causes of contemporary and historical emergence events. Since the mid-1990s, potato growers in the western United States, Mexico, and Central America have experienced severe yield loss from Zebra Chip disease and have responded by increasing insecticide use to suppress populations of the insect vector, the potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae). Despite the severe nature of Zebra Chip outbreaks, the causes of emergence remain unknown. We tested the hypotheses that 1) B. cockerelli occupancy has increased over the last century in California and 2) such increases are related to climate change, specifically warmer winters. We compiled a dataset of 87,000 museum specimen occurrence records across the order Hemiptera collected between 1900 and 2014. We then analyzed changes in B. cockerelli distribution using a hierarchical occupancy model using changes in background species lists to correct for collecting effort. We found evidence that B. cockerelli occupancy has increased over the last century. However, these changes appear to be unrelated to climate changes, at least at the scale of our analysis. To the extent that species occupancy is related to abundance, our analysis provides the first quantitative support for the hypothesis that B. cockerelli population abundance has increased, but further work is needed to link B. cockerelli population dynamics to Zebra Chip epidemics. Finally, we demonstrate how this historical macro-ecological approach provides a general framework for comparative risk assessment of future pest and insect vector outbreaks.
Directional control of neurite outgrowth: emerging technologies for Parkinson's Disease using magnetic nanoparticles and magnetic field gradients
<p>Data set for publication '<strong>Directional control of neurite outgrowth: emerging technologies for Parkinson’s Disease using magnetic nanoparticles and magnetic field gradients'</strong></p> <p><strong>Journal of The Royal Society Interface</strong></p> <p><strong>2022</strong></p>
Supplementary material 7 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
Coefficient estimate for each variable of maple basal area computed for different radius and their 95% credible intervals in brackets for models predicting the number of spores detected per week
Supplementary material 3 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
Standard curve and its correlation coefficient to determine the limit of detection for the real-time PCR assay in ten-folded DNA solutions of C. corticale mycelium (a) and total number of spores in the qPCR reaction (b)
Supplementary material 5 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
Zero-centred histogram of the residuals between simulated data and predictions of the model with the distance to the closest disease report as a predictor of the number of Cryptostroma corticale spores detected in aerobiological samples
Supplementary material 4 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
Zero-centred histogram of the residuals between simulated data and predictions of the model with the water balance (P-ETP) in the vegetative season (April-August) of the year preceding disease report as a predictor of the standardized record rate of the SBD
Supplementary material 6 from: Muller E, Dvořák M, Marçais B, Caeiro E, Clot B, Desprez-Loustau M-L, Gedda B, Lundén K, Migliorini D, Oliver G, Ramos AP, Rigling D, Rybníček O, Santini A, Schneider S, Stenlid J, Tedeschini E, Aguayo J, Gomez-Gallego M (2023) Conditions of emergence of the Sooty Bark Disease and aerobiology of Cryptostroma corticale in Europe. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 319-347. https://doi.org/10.3897/neobiota.84.90549
Zero-centred histogram of the residuals between simulated data and predictions of the model with the total sycamore maple basal area in a radius of 50 km from the sampler as a predictor of the number of Cryptostroma corticale spores detected in aerobiological samples
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.