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556 results for “Meta Data”
Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones
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Baltic Sea stable isotope ecology meta-data collection
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Data from: The effects of human-altered habitat spatial pattern on frugivory and seed dispersal: a global meta-analysis
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Data for: Developmental plasticity in anurans: meta-analysis reveals effects of larval environments on size at metamorphosis and timing of metamorphosis
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Data from: Tamm Review: a meta-analysis of thinning, prescribed fire, and wildfire effects on subsequent wildfire severity in conifer dominated forests of the Western US
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Data from: A meta-analysis of factors influencing the strength of mate choice copying in animals
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Data from: Connectivity and nutrient enrichment affect the productivity and stability of aquatic meta-ecosystems
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Open Data: FAIR, foul, and meta
<p><strong>Episode Summary: </strong></p> <p>In this episode we are discussing what metadata is, the obstacles to sharing research data, and how Open Science recommendations are being transformed into actions. Our interview guest will be Professor Eva Mendez from Universidad Carlos III in Madrid who is the Chair of the European Open Science Policy Platform.</p> <p><strong>Links:</strong></p> <p><a href="https://www.orion-openscience.eu/publications/training-materials/201808/factsheets">Factsheets (Open Data and Data Management)</a></p> <p><a href="https://uc3m.academia.edu/EvaM%C3%A9ndez/CurriculumVitae">Professor Eva Mendez</a></p> <p><a href="https://ec.europa.eu/research/openscience/index.cfm?pg=open-science-policy-platform">Open Science Policy Platform</a></p> <p><strong>Quotes:</strong></p> <p>'Open doesn't necessarily mean FAIR'</p>
Analysis data for ""Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance""
<p>Analysis data for the manuscript: "Integration of meta-omics data reveals how microbial ecosystems respond to disturbance"</p> <p>Files used with the repository: https://git-r3lab.uni.lu/malte.herold/laots_niche_ecology_analysis/</p> <p>The archive was split into multiple parts for uploading to zenodo which need to be joined in order to extract the files:</p> <pre><code class="language-bash">cat resultsdir_laots.tar.gz.part_* > resultsdir_laots.tar.gz tar xvfz resultsdir_laots.tar.gz</code></pre> <p>Version 2 contains additional files generated in the revision.</p> <p> </p>
Data from: Comparing traditional and Bayesian approaches to ecological meta-analysis
<p>1. Despite the wide application of meta-analysis in ecology, some of the traditional methods used for meta-analysis may not perform well given the type of data characteristic of ecological meta-analyses.</p> <p>2. We reviewed published meta-analyses on the ecological impacts of global climate change, evaluating the number of replicates used in the primary studies (ni) and the number of studies or records (k) that were aggregated to calculate a mean effect size. We used the results of the review in a simulation experiment to assess the performance of conventional frequentist and Bayesian meta-analysis methods for estimating a mean effect size and its uncertainty interval.</p> <p>3. Our literature review showed that ni and k were highly variable, distributions were right-skewed, and were generally small (median ni =5, median k=44). Our simulations show that the choice of method for calculating uncertainty intervals was critical for obtaining appropriate coverage (close to the nominal value of 0.95). When k was low (<40), 95% coverage was achieved by a confidence interval based on the t-distribution that uses an adjusted standard error (the Hartung-Knapp-Sidik-Jonkman, HKSJ), or by a Bayesian credible interval, whereas bootstrap or z-distribution confidence intervals had lower coverage. Despite the importance of the method to calculate the uncertainty interval, 39% of the meta-analyses reviewed did not report the method used, and of the 61% that did, 94% used a potentially problematic method, which may be a consequence of software defaults.</p> <p>4. In general, for a simple random-effects meta-analysis, the performance of the best frequentist and Bayesian methods were similar for the same combinations of factors (k and mean replication), though the Bayesian approaches had higher than nominal (>95%) coverage for the mean effect when k was very low (k<15). Our literature review suggests that many meta-analyses that used z-distribution or bootstrapping confidence intervals may have over-estimated the statistical significance of their results when the number of studies was low; more appropriate methods need to be adopted in ecological meta-analyses.</p>
Data from: A meta-analysis of global avian survival across species and latitude
<p>Tropical birds are thought to be longer lived than many temperate species. We explored the idea of higher survival at tropical latitudes and whether extrinsic climate factors and intrinsic traits helped explain this pattern using a meta-analytical approach. The dataset consists of 949 estimates from 204 studies of avian survival from both New World and Old World biogeographical realms.</p>
Data from: Reptile responses to anthropogenic habitat modification: a global meta-analysis
Aim <p>To determine how reptile populations respond to anthropogenic habitat modification and determine if species traits and environmental factors influence such responses.</p> Location <p>Global.</p> Time period <p>1981–2018.</p> Major taxa studied <p>Squamata.</p> Methods <p>We compiled a database of 56 studies reporting how habitat modification affects reptile abundance, and calculated standardised mean differences in abundance (Hedges' g). We used Bayesian meta-analytical models to test whether responses to habitat modification depended on body size, clutch size, reproductive mode, habitat specialisation, range size, disturbance type, vegetation type, temperature and precipitation.</p> Results <p>Based on 815 effect sizes from 376 species, we found an overall negative effect of habitat modification on reptile abundance (mean Hedges' g = -0.43, 95% credible intervals = -0.61 to -0.26). Reptile abundance was, on average, one-third lower in modified compared to unmodified habitats. Small range sizes and small clutch sizes were associated with more negative responses to habitat modification, although the responses were weak and the credible intervals overlapped zero. We detected no effects of body size, habitat specialisation, reproductive mode (egg-laying or live-bearing), temperature, or precipitation. Some families exhibited more negative responses than others, although overall there was no phylogenetic signal in the data. Mining had the most negative impacts on reptile abundance, followed by agriculture, grazing, plantations and patch size reduction, whereas the mean effect of logging was neutral.</p> Main conclusions <p>Habitat modification is a key cause of reptile population declines, although there is variability in responses both within and between species, families, and vegetation types. The effect of disturbance type appeared to be related to intensity of habitat modification. Ongoing development of environmentally sustainable practices that ameliorate anthropogenic impacts is urgently needed to prevent reptile population declines.</p>
Data from: The costs and benefits of paternal care in fish: a meta-analysis
<p><span><span><span><span><span><span><span><span><span><span><span>Male-only parental care, while rare in most animals, is a widespread strategy within teleost fish. The costs and benefits to males of acting as sole carer are highly variable between fish species making it challenging to determine the selective pressures driving the evolution of male-only care to such a high prevalence. We conducted a phylogenetic meta-analysis to examine the costs and benefits of paternal care across fish species. We found no evidence that providing care negatively affects male condition. In contrast to other taxa, we also found limited evidence that male care has evolved as a strategy to improve offspring survival. Instead, we found that males already caring for a brood are preferred by females and that this preference is strongest in those species in which males work harder to care for larger broods. Thus, in fish, investment in offspring care does not constrain a male's mating success but rather augments it, suggesting that the relatively high prevalence of male-only care in fish may be in part explained by sexual selection through female preference for caring males. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Accelerating homogenization of the global plant–frugivore meta-network
<p>Introductions of species by humans are causing the homogenization of species composition across biogeographic barriers. The ecological and evolutionary consequences of introduced species derive from their effects on networks of species interactions, but we lack a quantitative understanding of the impacts of introduced species on ecological networks and their biogeographic patterns globally. Here we address this data gap by analysing mutualistic seed-dispersal interactions from 410 local networks, encompassing 24,455 unique pairwise interactions between 1,631 animal and 3,208 plant species. We show that species introductions reduce biogeographic compartmentalization of the global meta-network, in which nodes are species and links are interactions observed within any local network. This homogenizing effect extends across spatial scales, decreasing beta diversity among local networks and modularity within networks. The prevalence of introduced interactions is directly related to human environmental modification and is accelerating, having increased sevenfold over the past 75 years. These dynamics alter the coevolutionary environments that mutualists experience, and we find that introduced species disproportionately interact with other introduced species. These processes are likely to amplify biotic homogenization in future ecosystems and may reduce the resilience of ecosystems by allowing perturbations to propagate more quickly and exposing disparate ecosystems to similar drivers. Our results highlight the importance of managing the increasing homogenization of ecological complexity. </p>
Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis
<p><span>Duplicate of </span>10.5061/dryad.6hdr7sqxq</p> <p><span>Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes experience reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, the empirical evidence shows contrasting effects of anthropogenic disturbances on the genetic diversity of species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and more preserved areas (316 paired comparisons) to investigate the genetic responses to different disturbance types. There is a negative effect (effect size: -0.45; 95% CI: -0.61, -0.29) of disturbances on genetic diversity, in which the most detrimental effects are caused by the loss of connectivity and forest cover. The methodological approach can explain part of the heterogeneity among the genetic responses detected by primary studies: (i) studies using the number of effective alleles did not detect genetic erosion, while all other indices, revealed negative responses to disturbances; and (ii) only studies performed with transferred or a combination of transferred and specific microsatellites detected negative responses. The effects on animal populations are more detrimental than in plant populations. Only plant species with shrub life form, self-incompatible reproductive systems, and biotic pollination and seed dispersal, showed negative responses to disturbances. Despite all heterogeneity among studies, there is an overall negative effect of disturbances on the genetic diversity, which indicates that remaining populations inhabiting human-modified landscapes have reduced evolutionary potential and are prone to local extinction.</span></p>
Data from: Parasite infection leads to widespread glucocorticoid hormone increases in vertebrate hosts: a meta-analysis
1. Parasites and pathogens (hereafter parasites) commonly challenge organisms, but the extent to which their infections are physiologically stressful to hosts remains unclear. Importantly, vertebrate hormones, glucocorticoids (GCs), have been reported to increase, decrease, or show no alterations stemming from infections, challenging the generality of parasite-associated GC responses and motivating a search for important moderator variables. 2. We undertook the first meta-analysis of changes in vertebrate GCs following experimental infection with parasites, extracting 146 effect sizes from 42 studies involving 32 host and 32 parasite species to test for general patterns of GC following infection, as well as the influence of moderators. 3. Overall, infection increased GCs relative to preliminary or control levels when the single largest effect sizes from repeated measures studies were examined, suggesting that parasites of vertebrate hosts can be thought of generally as physiological stressors by elevating GCs. 4. When all effect sizes were included along with the moderator of sampling time post-infection (tPI), parasite infection still had a positive effect on host GCs. However, the strength of that effect did not relate consistently to tPI, illustrating temporal differences in GC changes during the course of infection among parasite taxa (e.g., arthropod versus bacterial infections). Other moderator variables examined did not influence GC responses. 5. Studies broadening the range of host and parasite taxa, and sampling during critical time windows, would aid in our understanding of variation in the host stress response and its consequences for fitness of both vertebrate hosts and their parasites. 25-Sep-2019
Data from Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties
<p>Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. <a name="_Hlk9515878">However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships</a>. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapo-transpiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, e.g., shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.</p>
Data from: The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: a global meta-analysis
<p><span>Human activities are primarily responsible for habitat loss and changes in natural environments around the world. It has been suggested that populations inhabiting human-modified landscapes are subject to reduced gene flow, inbreeding depression, and loss of alleles due to genetic drift. However, empirical evidence shows contradictory effects of anthropogenic disturbances on the genetic diversity of terrestrial species. We performed a meta-analysis of 61 studies that compared the genetic diversity of plant and/or animal populations in disturbed and preserved areas (317 paired comparisons) to investigate general responses to different disturbance type. We found significant negative effects of disturbance on genetic diversity (effect size: -0.45), in which the loss of structural connectivity was the most detrimental disturbance type. The choice of the genetic parameter has an influence on the detection of the effect (direction and magnitude), and consequently the studies using number of effective alleles did not detect genetic erosion, while all other indices, especially allelic richness, revealed negative responses to disturbances. Yet, only studies performed with transferred or both transferred and specific microsatellites showed negative responses to disturbances. The general effect was more detrimental in animal than plant populations. Only plant species with biotic pollination and seed dispersal mode, self-incompatible reproductive system, and shrubs showed negative responses to disturbances. Despite all heterogeneity among studies, we found an overall negative effect of disturbance on genetic diversity of terrestrial populations, which suggests that the remaining populations inhabiting anthropogenic landscapes have a reduced evolutionary potential being more prone to local extinction.</span></p>
Data from: Global prevalence and burden of HIV-associated neurocognitive disorder: a meta-analysis
<p>Objectives: We aimed to characterise the prevalence and burden of HAND and assess associated factors in the global population with HIV.</p> <p>Methods: We searched PubMed and Embase for cross-sectional or cohort studies reporting the prevalence of HAND or its subtypes in HIV-infected adult populations from Jan 1, 1996, to May 15, 2020, without language restrictions. Two reviewers independently undertook the study selection, data extraction, and quality assessment. We estimated pooled prevalence of HAND by a random effects model and evaluated its overall burden worldwide.</p> <p>Results: Of 5588 records identified, we included 123 studies involving 35513 participants from 32 countries. The overall prevalence of HAND was 42·6% (95% CI: 39·7-45·5), and did not differ with respect to diagnostic criteria used. The prevalence of asymptomatic neurocognitive impairment (ANI), mild neurocognitive disorder (MND) and HIV-associated dementia (HAD) were 23·5% (20·3-26·8), 13·3% (10·6-16·3) and 5·0% (3·5-6·8) according to the Frascati criteria, respectively. The prevalence of HAND was significantly associated with the level of CD4 nadir, with a prevalence of HAND higher in low CD4 nadir groups (mean/median CD4 nadir <200: 45·2%, 40·5-49·9) versus high CD4 nadir group (mean/median CD4 nadir ≥200: 37·1%, 32·7-41·7). Worldwide, we estimated that there were roughly 16145400 (95% CI 15046300-17244500) cases of HAND in HIV-infected adults, with 72% in sub-Saharan Africa (11571200 cases, 95% CI 9600000-13568000).</p> <p>Conclusions: Our findings suggest that people living with HIV have a high burden of HAND in the ART era, especially in sub-Saharan Africa and Latin America. Earlier initiation of ART and sustained adherence to maintain a high level CD4 cell count and prevent severe immunosuppression is likely to reduce the prevalence and severity of HAND.</p>
Data from: Association between metabolic syndrome components and the risk of developing nephrolithiasis: Bayesian meta-analysis and meta-regression with dose-response analysis
<p>Nephrolithiasis has shifted to be a systemic disease. As opposed to an isolated urinary metabolic problem, it became determined that nephrolithiasis turned into considerably related to link with systemic diseases such as hypertension, obesity, dyslipidemia, and insulin resistance. The interplay between these four factors defines MetS (metabolic syndrome). In this review we aim to clarify the associations of metabolic syndrome and its components to kidney stone incident. Online databases of EMBASE, MEDLINE, and Google Scholar were searched up to October 2020 to identify observational studies examining the association between metabolic syndrome components and kidney stone incident. Bayesian Random-Effects Meta-Analysis and Meta-Regression were performed to observe the association. Linear dose-response analyses were conducted to shape the direction of the association. Data analysis was performed using STATA, and R statistics. This dataset contains supplementary material and figures as additional analysis of the study.</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.