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151 results for “global meta-analysis”
Fig. 1 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling
Fig. 1. Relative pathogen abundance of four D. nuttalli samples and the phylogenomic analysis of four Rickettsia genomes. (A) Pathogen abundance at the family level. (B) Pathogen abundance at the genus level. (C) The phylogenetic tree of four Rickettsia assemblies. The phylogenetic tree of four Rickettsia assemblies (Rickettsia conorii subsp. raoultii str XinjiangF1, Rickettsia conorii subsp. raoultii str XinjiangF2, Rickettsia conorii subsp. raoultii str XinjiangF3, and Rickettsia conorii subsp. raoultii str XinjiangM1) was built with 28 other publicly available established or proposed Rickettsiales species. The tree was inferred by IQ-TREE based on 277 single-copy orthologs identified by OrthoFinder. Anaplasma phagocytophilum and Ehrlichia ruminantium were two outgroup species.
Fig. 5 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling
Fig. 5. Global potential distribution of D. nuttalli. The red area indicates greater possibilities of suitability for D. nuttalli, while the blue area is less likely to be suitable for D. nuttalli.
Fig. 4 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling
Fig. 4. Geographical distribution of D. nuttalli. D. nuttalli lived mainly between 23◦–53◦ latitude and 76◦–133◦ longitude in the Northern Hemisphere. Triangles represent the locations in prefecture-level regions, while circles represent the distribution locations in county-level regions. The green circles represent points from GBIF, the yellow circles are points from literature, the purple circles represent the points from the field survey and the blue points are points from a reference book. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Global burden of non-tuberculous mycobacteria in the cystic fibrosis population: A systematic review and meta-analysis
<p><span><strong>Background</strong>:</span><span> People living with cystic fibrosis have an increased risk of lung infection with non-tuberculous mycobacteria (NTM), which is reportedly increasing. We conducted a systematic review of the literature to estimate the burden (prevalence and incidence) of non-tuberculous mycobacteria in the cystic fibrosis population. </span></p> <p><span><strong>Methods</strong>: Electronic databases, registries, and grey literature sources were searched for cohort and cross-sectional studies reporting epidemiological measures (incidence and prevalence) of NTM infection or NTM pulmonary disease (NTM-PD) in cystic fibrosis. The last search was conducted in September 2021; we included reports since database creation and registry reports published since 2010. The methodological quality of studies was appraised with the Joanna Briggs Institute tool. A random-effects meta-analysis was conducted to summarize the prevalence of NTM infection, and the remaining results are presented in a narrative synthesis. </span></p> <p><span><strong>Results</strong>: Ninety-five studies were included in this review. All 95 studies reported on NTM infection, and 14 of these also reported on NTM-PD. The pooled estimate for the point prevalence of NTM infection was 7.9% (CI 95%, 5.1–12.0%). In meta-regression, sample size and geographical location of the study modified the estimate. Longitudinal analysis of registry reports showed an increasing trend in NTM infection prevalence between 2010 and 2019. </span></p> <p><span><strong>Conclusions</strong>: The overall prevalence of NTM infection in CF is 7.9% and is increasing over time based on international registry reports. Future studies should report screening frequency, microbial identification methods, and incidence rates of progression from NTM infection to pulmonary disease.</span></p>
Data from: Crop and landscape heterogeneity increase biodiversity in agricultural landscapes: A global review and meta-analysis
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Data from: Responses of insect pollinators to habitat fragmentation: A global meta-analysis
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Pollination deficits and contributions of pollinators in apple production: a global meta-analysis
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Data and code – Effects of climate on salmonid productivity: A global meta-analysis across freshwater ecosystems
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Global burden of non-tuberculous mycobacteria in the cystic fibrosis population: A systematic review and meta-analysis
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Data for a global meta-analysis of passive experimental warming effects on plant traits and community properties
This database contains the data used in a global meta-analysis of warming effects on plants. L0 data are available upon request; they include the raw data from 126 warming experiments. The L1 data are the result of merged L0 data and are cleaned for typos and are standardized names. L1 data contain plant trait and community property measurements in both warmed and ambient conditions. L2 data contain the effect sizes of warming for each study. These data came from 126 warming experiments across the globe.
Explaining global variation in the latitudinal diversity gradient: Meta-analysis confirms known patterns and uncovers new one
This dataset is also available on the Dryad Digital Repository (link: https://doi.org/10.5061/dryad.rg5rd). The code is also available on GitHub (link: https://github.com/nlkinlock/LDGmeta-analysis). This dataset was created to explore patterns in biodiversity across latitude. The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for greater than 200 years. Empirical studies have documented this pattern across many different organisms and locations. In order to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors, a systematic review, followed by a meta-analysis of the resulting dataset, were carried out. This dataset contains a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground‐breaking meta‐analysis of the LDG.
Correlation of native and exotic species richness: a global meta-analysis finds no invasion paradox across scales
This data set is also available on the Dryad Digital repository (link : https://doi.org/10.5061/dryad.59kv753) This dataset was created for investigating the biotic resistance hypothesis, that is, the idea that species‐rich communities are more successful at resisting invasion by exotic species than are species‐poor communities. It has been argued that native–exotic richness relationships (NERR) are negative at small spatial scales and positive at large scales, but evidence for the role of spatial scale on NERR has been contradictory. However, no formal quantitative synthesis had previously examined whether NERR is scale‐dependent across multiple studies, and previous studies on NERR have not distinguished spatial grain and extent, which may drive very different ecological processes Therefore, a global systematic review was carried out to create this dataset, which includes 204 individual cases of observational (non‐experimental) NERRs from 101 publications. Further, the above-mentioned hypotheses were investigated using a hierarchical mixed‐effects meta‐analysis, which showed that NERR was indeed highly scale dependent across studies and increased with the log of grain size. Also, no clear patterns of NERR across different spatial extents were found, suggesting that extent plays a less important role in determining NERR than does grain, although there was a complex interaction between extent and grain size. Almost all studies on NERR were found to have been conducted in North America, western Europe, and a few other regions, with little information on tropical or Arctic regions. NERR was also found to increase northward in temperate regions and vary with longitude. These results were published in the paper titled Correlation of native and exotic species richness: a global meta‐analysis finds no invasion paradox across scales (Peng et al. 2018), which represents the first global quantitative analysis of scale‐based NERR.
Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones
Aim: The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta-analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground-breaking meta-analysis of the LDG, using meta-analysis and meta-regression approaches largely new to the fields of ecology and biogeography. Location: Global. Time period: January 2003–September 2015. Major taxa studied: Bacteria, protists, plants, fungi and animals. Methods: We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed-effects meta-analysis and multiple meta-regression. Additionally, we re-analysed Hillebrand's original dataset using modern methods. Results: We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta-analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta-regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis. Main conclusions: We present evidence of global latitudinal, longitudinal and habitat-based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.
Trophic regulation of soil microbial biomass under nitrogen enrichment: A global meta-analysis
<p>Eutrophication, including nitrogen (N) enrichment, can affect soil microbial communities through changes in trophic interactions. However, a knowledge gap still exists about how plant resources ('bottom-up effects') and microbial predators ('top-down effects') regulate the impacts of N enrichment on microbial biomass at the global scale.</p> <p>To address this knowledge gap, we conducted a global meta-analysis using 2885 paired observations from 217 publications to evaluate the regulatory effects of plant biomass and soil nematodes on soil microbial biomass under N enrichment across terrestrial ecosystems.</p> <p>We found that the effects of N enrichment on soil microbial biomass strongly varied across ecosystems. N enrichment decreased the soil microbial biomass of natural grasslands and forests due to soil acidification and the subsequent losses of predatory and microbivorous nematodes stimulating microbial growth. By contrast, N enrichment increased the microbial biomass of managed croplands mainly via increasing plant biomass production. The short-term of N enrichment (experimental duration ≤ 5 years) could reduce microbial biomass via decreasing nematode abundance across diverse ecosystems, whereas the long-term of N enrichment (experimental duration > 5 years) mainly promoted microbial biomass via increasing plant biomass.</p> <p>These findings highlight the critical roles of microbial predators and plant input in shaping microbial responses to N enrichment, which are highly dependent on ecosystem type and the period of N enrichment. Earth system models that predict soil microbial biomass and their linkages to soil functioning should consider the variations in plant biomass and soil nematodes under future scenarios of N deposition.</p>
A global meta-analysis of yield-scaled N2O emissions and its mitigation efforts for maize, wheat, and rice
<p>Maintaining or even increasing crop yields while reducing nitrous oxide (N<sub>2</sub>O) emissions is necessary to reconcile food security and climate change, while the metric of yield-scaled N<sub>2</sub>O emission (i.e., N<sub>2</sub>O emissions per unit of crop yield) is at present poorly understood. Here we conducted a global meta-analysis with more than 6000 observations to explore the variation patterns and controlling factors of yield-scaled N<sub>2</sub>O emissions for maize, wheat, and rice and associated potential mitigation options. Our results showed that the average yield-scaled N<sub>2</sub>O emissions across all available data followed the order wheat (322 g N Mg<sup>-1</sup>, with the 95% confidence interval (CI): 301-346) > maize (211 g N Mg<sup>-1</sup>, CI: 198-225) > rice (153 g N Mg<sup>-1</sup>, CI: 144-163). Yield-scaled N<sub>2</sub>O emissions for individual crops were generally higher in tropical or subtropical zones than in temperate zones, and also showed a trend towards lower intensities from low to high latitudes. This global variation was better explained by climatic and edaphic factors than by N fertilizer management, while their combined effect predicted more than 70% of the variance. Furthermore, our analysis showed a significant decrease in yield-scaled N<sub>2</sub>O emissions with increasing N use efficiency or in N<sub>2</sub>O emissions for production systems with cereal yields > 10 Mg ha<sup>-1</sup> (maize), 6.6 Mg ha<sup>-1</sup> (wheat) or 6.8 Mg ha<sup>-1</sup> (rice), respectively. This highlights that N use efficiency indicators can be used as valuable proxies for reconciling trade-offs between crop production and N<sub>2</sub>O mitigation. For all three major staple crops, reducing N fertilization by up to 30%, optimizing the timing and placement of fertilizer application or using enhanced-efficiency N fertilizers significantly reduced yield-scaled N<sub>2</sub>O emissions at similar or even higher cereal yields. Our data-driven assessment provides some key guidance for developing effective and targeted mitigation and adaptation strategies for the sustainable intensification of cereal production.</p>
Phosphorus Limitation Directly and Indirectly Constrains Tree Photosynthesis and Productivity: Evidence from a Global Meta-Analysis
<p>These dataset contains the source data and the correposnding code for the paper explained above.</p>
Data from: The effects of human-altered habitat spatial pattern on frugivory and seed dispersal: a global meta-analysis
<p>Seed dispersal by frugivorous animals is important for plant mobility, regeneration, and persistence. Human-caused landscape change is thought to disrupt seed dispersal, but evidence is scarce. We performed a comprehensive meta-analysis on the effects of habitat spatial pattern on frugivory and seed dispersal. We found 233 effects from 71 studies. At a patch or local scale, altered habitat spatial pattern was measured as declining patch size, increasing patch isolation, or habitat edge (vs. interior). At a landscape scale it was measured as declining amount of habitat, increasing mean patch isolation, increasing number of patches, or increasing habitat edge in the landscape.</p> <p>We found overall negative effects of altered habitat spatial pattern on: (i) the quantity of frugivory or seed dispersal, (ii) the number of species involved in a plant-frugivore interaction, and (iii) seed dispersal distance. Moderator variable analysis was only possible for the first of these. It revealed negative responses of the quantity of frugivory or seed dispersal to habitat loss at both the local scale (declining patch size), and the landscape scale (declining habitat amount), but little evidence for a response to habitat edge at either scale. In addition, altered habitat spatial pattern reduced the quantity of frugivory or seed dispersal more strongly in temperate than tropical areas. Finally, the few-recorded effects of landscape-scale fragmentation per se (increasing patch density or edge density) on the quantity of frugivory or seed dispersal were mixed and weak. Our meta-analysis reinforces the notion that habitat loss is a major threat to frugivory and seed dispersal by animals, and reveals an insufficiency of studies of the effects of habitat fragmentation per se. Thus, based on the current literature, we conclude that maintaining and increasing habitat amount is vital for maintaining seed dispersal by frugivorous animals.</p>
When Do Cover Crops Reduce Nitrate Leaching? A Global Meta-Analysis
<p>The document includes the dataset extracted from peer-reviewed publications on the effect of cover crops on nitrate leaching. The results and report corresponding to this dataset have been published as a review article entitled: " When Do Cover Crops Reduce Nitrate Leaching? A Global Meta-Analysis" <strong>DOI: </strong>10.1111/gcb.16269 in the Global Change Biology journal.</p>
Multiple global changes drive grassland productivity and stability: A meta-analysis
<p><span>Temporal stability of primary productivity is the key to stable provisioning of ecosystem services to human beings. Yet, the effects of various global changes on grassland stability remain ambiguous. </span></p> <p><span>Here, we conducted a comprehensive meta-analysis based on 1,070 multi-year paired observations from 173 studies, to examine the impacts of various global changes on productivity, community stability and plant diversity of grasslands on a global scale. The global change drivers include nitrogen (N) addition, phosphorus (P) addition, N & P addition, precipitation increase, precipitation decrease, elevated CO2, and warming. </span></p> <p><span>Global change drivers generally had stronger impacts on grassland productivity than on temporal stability, except for precipitation changes. Community temporal stability was reduced by N addition, N & P addition, and precipitation decrease, but was increased by precipitation increase and remained unchanged under P addition, elevated CO2, and warming. In addition, species richness decreased under N addition, N & P addition, and precipitation decrease. At the plant functional group level, N & P addition reduced grasses' stability and precipitation increase enhanced forbs' stability.</span></p> <p><span>Nutrient additions decreased community stability via increasing the inter-annual variation more than the mean of primary productivity, while precipitation changes mainly affected community temporal stability via changing mean productivity. The negative impacts of global change drivers (i.e. N & P addition, warming) on community temporal stability increased with the degree of species loss, but decreased with increasing stability of grasses. Moreover, the negative impacts of nutrient addition and precipitation decrease on community stability was lessened while the positive effect of precipitation increase on community stability was enhanced in grasslands with higher historical precipitation variability, greater soil fertility, and longer experimental duration.</span></p> <p><span><strong>Synthesis</strong>.</span><span> Our findings demonstrate that N-based nutrient additions and drought destabilise grassland productivity, while precipitation increase enhances community stability. Impacts of global changes on community productivity and stability are mediated by species richness, plant functional group, site-specific environmental conditions (i.e. climate, soil), and experimental duration, which deserve more attention in grassland management practices under future global change scenarios.</span></p>
Impacts of pastures and forestry plantations on herpetofauna: a global meta-analysis
<p class="MsoListParagraphCxSpFirst"><span>1.</span><span> </span><span>The establishment of pastures and forestry plantations has increased globally to meet growing demands for meat and wood products. <a name="_Hlk108096120"></a>Pasture and plantation expansion often drives deforestation, which causes homogenization of biotic communities and is a major driver of the global extinction crisis. A core question is how the severity of losses varies between pastures and plantations, and in turn, how geographical location and plantation management characteristics moderate these impacts.</span></p> <p class="MsoListParagraphCxSpMiddle">2.<span> </span><span>Focusing on herpetofauna (amphibians and reptiles) as the most endangered vertebrate group, we performed a global synthesis using 41 scientific articles that reported species richness or abundance in pastures and forestry plantations relative to natural forest in 191 case studies among 19 countries. </span></p> <p class="MsoListParagraphCxSpMiddle">3.<span> </span><span>We found a severe negative effect of pasture and a less negative effect of forestry plantations on species richness and abundance of herpetofauna.</span> <span>Within plantations, species richness and total abundance were more negatively impacted in amphibians than reptiles, in the tropics, when planting exotic tree species, monocultures, large or commercial plantations, and when clearing understory vegetation. Yet mixed, old, small, or </span>conservation plantations and those permitting recovery of understory vegetation had no negative impacts relative to the reference natural forest.</p> <p class="MsoListParagraphCxSpLast">4.<span> </span><em><span>Synthesis and applications</span></em><span>. The loss of herpetofauna species richness and abundance underscores the importance of h</span>alting ongoing tropical deforestation for pasture and intensive forestry plantations. The potential for <span>a</span>ppropriately managed f<span>orestry plantations to support biodiversity in regions lacking forest cover, including via replacement of anthropogenic pastures, </span>suggests that such plantations have an important role <span>under global reforestation agendas.</span></p> <p> </p>
ScienceDex guides
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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.