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1,123 results for “Meta-analysis”
Elemental and biochemical nutrient limitation of zooplankton: A meta-analysis
<p>Primary consumers in aquatic ecosystems are frequently limited by the quality of their food, often expressed as phytoplankton elemental and biochemical composition. However, effects of these food quality indicators vary across studies, and we lack an integrated understanding of how elemental (e.g., nitrogen, phosphorus) and biochemical (e.g., fatty acid, sterol) limitations interactively influence aquatic food webs. Here we present results of a meta-analysis using >100 experimental studies, confirming that limitation by N, P, fatty acids, and sterols all have significant negative effects on zooplankton performance. However, effects varied by grazer response (growth versus reproduction), specific manipulation, and across taxa. While P limitation had greater effects on zooplankton growth than fatty acids overall, P and fatty acid limitation had equal effects on reproduction. Furthermore, we show that: nutrient co-limitation in zooplankton is strong; effects of essential fatty acid limitation depend on P availability; indirect effects induced by P limitation exceed direct effects of mineral P limitation; and effects of nutrient amendments using laboratory phytoplankton isolates exceed those using natural field communities. Our meta-analysis reconciles contrasting views about the role of various food quality indicators, and their interactions, for zooplankton performance, and provides a mechanistic understanding of trophic transfer in aquatic environments.</p>
Meta-analysis reveals challenges and gaps for genome-to-phenome research underpinning plant drought response.
<p>Data used to identify species occurring in hyperarid environments for analyses described in "Meta-analysis reveals challenges and gaps for genome-to-phenome research underpinning plant drought response." The "PlantsLackingHumanUse_PrelimQCd_Data.csv" contains data for all plants queried, while "HyperArid_Occurrences.csv" contains the subset of data corresponding to plants occurring in hyperarid environments.</p>
Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver: processed data
<p>The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 43 public mouse liver tissue timeseries totaling 805 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, with around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies. This revealed the extent of asymmetric and multimodal genes.<br> <br> This supplemental file provides preprocessed RNA-seq quantifications of all reviewed datasets, as well as results of multiple analyses.</p>
Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects
<p>Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the idea that substantial sex differences in plastic responses could be interpreted as resulting from sex-specific life-history optimization, whereas similarity among the sexes should rather be seen as evidence of an essential role of physiological constraints. In this study, we performed a meta-analysis of sex-specific thermal responses in insect development times, using data on 161 species with comprehensive phylogenetic and ecological coverage. As a reference for judging the magnitude of sex-specificity in thermal plasticity, we compared the magnitude of sex differences in plastic responses to temperature with those in response to diet. We show that sex-specific responses of development times to temperature variation are broadly similar. We also found no strong evidence for sex-specificity in thermal responses to depend on the magnitude or direction of sex differences in development time. Sex differences in temperature-induced plastic responses were systematically less pronounced than sex differences in responses induced by variations in larval diet. Our results point to the existence of substantial constraints on the evolvability of thermal reaction norms in insects as the most likely explanation. If confirmed, the low evolvability of thermal response is an essential aspect to consider in predicting evolutionary responses to climate warming.</p>
Optimized summary-statistic-based single-cell meta-analysis. Input files
<p>This dataset contains information about the input files used in the Optimized summary-statistic-based single-cell meta-analysis research project. </p> <p> </p>
Dataset related to article: QUALITY ASSESSMENT OF THE MRI-RADIOMICS STUDIES FOR MGMT PROMOTER METHYLATION PREDICTION IN GLIOMA: A SYSTEMATIC REVIEW AND META-ANALYSIS
<p><strong><span>This table contains the raw data used to generate the heatmap illustrated in Fig 2. Each row of the table shows the distribution of the scores achieved by the studies for a domain. Colors from red to green denote progressive increase from minimum to maximum score obtainable for each domain.</span></strong></p>
Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."
<div> <p>All data and R code for</p> <p><strong>Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to <em>Daphnia</em> - a meta-analysis. <em>Microplastics and Nanoplastics</em>. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>)</strong></p> <p><em>Abstract</em></p> <p>Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus <em>Daphnia</em>. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in <em>Daphnia</em> spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.</p> </div>
Figure 7 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 7. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) weed germination/emergence, (B) seedling radicle/root length, (C) plant height, and (D) leaf area when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.
Figure 3 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 3. Overall water-stress effects on germination/emergence of grass and broadleaf weeds (top) and six weed families—Asteraceae, Fabaceae, Convolvulaceae, Amaranthaceae, Rubiaceae, and Poaceae (bottom). The vertical black dashed line represents zero effect. The black dots are overall mean effect sizes, and the black lines are 99% confidence intervals (CIs).The values in parentheses are the number of observations followed by the number of studies for each pair-wise comparison. The mean effect sizes were considered significantly different when their 99% CIs did not include zero.
Figure 4 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 4. The log response ratio for germination and seedling radicle length of broadleaf (green dots/line) and grass (red dots/line) weed species as a function of water-stress intensity. Water stress increased as solution osmotic potential (ψsolution) decreased and vice versa.The subgroups for germination are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −0.8, −0.8 to −1.0, −1.0 to −1.4, and <−1.4 MPa, while the subgroups for radicle length are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −1.0, and <−1.0 MPa. Only ψsolution-based studies were used in this analysis. For each subgroup, the solid dots and lines represent mean effect sizes and their corresponding 99% confidence intervals (CIs).The mean effect sizes were considered significantly different when their 99% CIs did not include zero. Similarly, the water-stress effects were significantly different for each subgroup and among weed types only when their 99% CIs did not overlap with one another. The fitted lines represent a four-parameter logistic regression model, and the coefficients of the models are presented in Table 2.
Figure 1 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 1. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses; Page and McKenzie 2021) flow diagram highlighting the selection procedure of 86 scientific published papers included in the meta-analysis.
Figure 8 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 8. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) branches/tillers per plant, (B) leaves per plant, (C) inflorescences per plant, (D) seeds per plant, (E) total biomass, (F) root biomass, (G) shoot biomass, and (H) root:shoot ratio, when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.
Figure 6 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 6. Density plots depicting the distribution of the individual effect sizes for all 12 response variables considered in this meta-analysis: (A) weed seed germination/emergence; (B) radicle/root length, plant height, and leaf area; (C) branches/tillers per plant, leaves per plant, inflorescences per plant, and seeds per plant; and (D) total biomass, root biomass, shoot biomass, and root:shoot ratio.
Figure 2 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 2. Overall water-stress effects on weed germination/emergence, growth characteristics, and seed production. The vertical black dashed line represents zero effect. The black dots are overall mean effect sizes, and the black lines are 95% confidence intervals (CIs). The values in parentheses are the number of observations followed by the number of studies for each pair-wise comparison. The mean effect sizes were considered significantly different when their 95% CIs did not include zero.
Figure 5 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis
Figure 5. The log response ratio for weed growth characteristics (plant height, leaf area, branches/tillers per plant, leaves per plant,root biomass, shoot biomass, and root:shoot ratio) and seed production (inflorescences per plant and seeds per plant) as a function of water-stress intensity. Water stress increased as soil moisture (% field capacity) decreased and vice versa. The green and red dots represent broadleaf and grass weed species, respectively. The solid black points and the lines represent mean effect sizes and their 99% confidence intervals (CIs) for low (>60%), moderate (30%–60%), and severe (<30% field capacity) water-stress subgroups. The mean effect sizes were considered significantly different when their 99% CIs did not include zero. Similarly, the water-stress effects were significantly different for each subgroup and among weed types only when their 99% CIs did not overlap with one another.
Figure 3 in Does narrow row spacing suppress weeds and increase yields in corn and soybean? A meta-analysis
Figure 3. The overall effect of narrow row spacing (<76 cm) on weed density, weed biomass,weed control,weed seed production,and crop yield.The vertical black dashed line indicates zero effect. The black dots represent mean effect sizes (log of response ratios [lnðRRÞ]), and the black lines represent their respective 95% confidence intervals (CIs). The numbers in parentheses indicate the number of observations followed by the number of studies for each effect size. The effect sizes were considered significantly different when their 95% CIs did not overlap or contain zero.
Figure 6 in Does narrow row spacing suppress weeds and increase yields in corn and soybean? A meta-analysis
Figure 6. The effect of narrow row spacing (<76 cm) on crop yield as explained by subgroups of the crop, tillage, weed type, weed management method, herbicide application frequency, and time. The vertical black dashed line indicates zero effect. The black dots represent mean effect sizes (log of response ratios [lnðRRÞ]) for each subgroup, and the black lines represent their respective 99% confidence intervals (CIs). The numbers in parentheses indicate the number of observations followed by the number of studies for each effect size. The effect sizes were considered significantly different when their 99% CIs did not overlap or contain zero.
Figure 2. A in Does narrow row spacing suppress weeds and increase yields in corn and soybean? A meta-analysis
Figure 2. A map of the states in the midwestern and eastern United States showing experimental sites for the 35 corn and soybean narrow row spacing studies included in the meta-analysis.
Figure 5 in Does narrow row spacing suppress weeds and increase yields in corn and soybean? A meta-analysis
Figure 5. The individual effect sizes (natural log of response ratios [lnðRRÞ]) of (A) weed density, (B) weed biomass,(C) weed control, (D) weed seed production, and (E) crop yield as a function of crop row spacing. The green and red dots represent individual effect sizes for corn and soybean, respectively. The horizontal black dashed line represents zero effect,while the vertical black line represents 76-cm row spacing (control).The black bold line shows the relationship between individual effect sizes and crop row spacing,which is given as R (Pearson's correlation) with a P-value. The gray-shaded area represents 95% confidence intervals (CIs) of the linear relationship.
Figure 8 in Does narrow row spacing suppress weeds and increase yields in corn and soybean? A meta-analysis
Figure 8. Sensitivity analysis showing the variation in overall effect sizes (log of response ratios [ln(RR)]) (mean ± 95% confidence intervals [CIs]) of narrow row spacing effects on (A) weed density, (B) weed biomass, (C) weed control, (D) weed seed production, and (E) crop yield when any specific study was excluded from the analysis. The vertical red solid and dashed lines represent the mean ± 95% CIs, respectively, of overall effect sizes with all the studies included in the analysis.
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.