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1,200 results for “Meta analysis”
Tree germination sensitivity to increasing temperatures: a global meta-analysis across biomes, species and populations.
<p>The dataset contains the files used for the meta-analysis on the role of temperature increases on the germination of tree species from different biomes around the world.</p> <p>This meta-analysis is accepted for publication in Global Ecology and Biography (MS reference number: GEB-2024-0273.R1 ; Article DOI: 10.1111/geb.13921).</p> <p>Files S6 and S7 gather data of germination percentage and time, respectively, at population scale. File S5 is a summary of the publications used as data sources for the meta-analysis. The whole dataset comprises 50 papers addressing 63 species and 250 populations, it covers boreal, temperate, Mediterranean and tropical-subtropical biomes, and a time period between 1996 and 2024.</p>
Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue
<p>Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. </p> <p>Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.</p> <p>Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:</p> <pre>umap_embeddings_Fig2A.Rdata<br>cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata<br>organoid_egad_results_ranked_6_26_24_Fig3D.Rdata<br>fetal_egad_results_ranked_6_26_24_Fig3D.Rdata<br>org_eigenvec_matrices_SuppFig3CD.Rdata</pre> <p><br>The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp</p>
Data from: Independent and interactive effects of plant genotype and environment on plant traits and insect herbivore performance: a meta-analysis with Salicaceae
1. Ecological research has increasingly highlighted the importance of intraspecific variation in shaping the structure and function of communities and ecosystems. Indeed, the effects of intraspecific variation can match or exceed those of interspecific variation. Previous reviews of intraspecific variation in plant traits across heterogeneous environments have focused primarily on mean phenotypic effects. We propose that a richer and fuller understanding of the ecological causes and consequences of intraspecific variation would be provided by partitioning trait variance into its subcomponents (genetic, environment, genotype by environment interaction). 2. We used a meta-analysis of 352 sets of genetic, environment, and genotype by environment (GxE) variation estimates from 72 studies of Salicaceae to compare these sources of variation across plant traits (growth, foliar nitrogen, defense compounds), insect herbivore performance metrics (e.g., survival, growth, fecundity), and environmental conditions (e.g., soil nutrients, water, defoliation). 3. Our findings revealed that variation in levels of defense compounds (both condensed tannins and salicinoids) and insect herbivore performance were primarily genetically determined, while variation in plant growth and foliar nitrogen were more environmentally determined. 4. Plasticity in plant growth, foliar nitrogen levels, and insect herbivore performance varied substantially across different sites (year x location), and nutrient, water, and carbon dioxide environments. Plasticity was lowest for chemical defense traits and all traits in contrasting ozone and defoliation environments. 5. Our quantitative review also revealed several gaps in the literature, including a need for surveying more mature plants (>2 years-old), a wider variety of insect herbivore species (e.g., leaf-modifiers, specialist insects), and underrepresented environmental treatments (e.g., competition, defoliation, disease, light, water). This work will help to assess how the patterns within this meta-analysis may or may not be confined within particular parameters (e.g., plant maturity). 6. Findings from this analysis further highlight the importance of and patterns within intraspecific variation in shaping the evolvability and plasticity of traits and in governing plant-insect interactions.
Data from: Systemic thyroid hormone status during levothyroxine therapy in hypothyroidism: a systematic review and meta-analysis
CONTEXT: The standard of care for overt hypothyroidism is levothyroxine at doses that normalize serum TSH levels. Whether this approach universally restores thyroid hormone signaling is unknown. OBJECTIVE: To review studies of overt hypothyroidism in which participants were treated with levothyroxine to normalize serum TSH levels and measured other objective markers of thyroid hormone signaling. DESIGN: Databases were searched for studies that reported objective markers of thyroid hormone signaling (serum low-density lipoprotein (LDL), total cholesterol (TC), sex hormone-binding globulin (SHBG), creatine kinase and/or ferritin levels; cognition, energy expenditure, and/or renal function) in levothyroxine monotherapy for overt, primary hypothyroidism among nonpregnant adults with normal serum TSH levels. For studies with LDL, TC and SHBG outcomes, data were pooled using random effects meta-analysis. RESULTS: A total of 99 studies met inclusion criteria, including 65 that reported serum cholesterol data. Meta-analysis showed that levothyroxine-treated hypothyroid participants with normal serum TSH levels had 3.31 ± 1.64 mg/dL higher serum LDL levels (p=0.044) and 9.60 ± 3.55 mg/dL higher serum TC levels (p=0.007) compared to controls. In studies that did not concomitantly assess healthy controls, serum LDL levels were 138.3 ± 4.6 mg/dL (p<0.001) and serum TC levels were 209.6 ± 3.4 mg/dL (p<0.001). Meta-analysis of 2 studies showed no significant difference between SHBG levels of levothyroxine-treated participants and controls. CONCLUSIONS: In studies that utilized levothyroxine monotherapy at doses that normalized the serum TSH for overt, primary hypothyroidism, not all systemic biological markers of thyroid hormone signaling were normalized, including serum LDL and TC levels.
Modeling System Behaviour from Log Analysis Using Meta-Heuristic Search
<p>Dataset used to perform the experiments in our paper on <em>Modeling System Behaviour from Log Analysis Using Meta-Heuristic Search </em>(BSc. thesis, 2021).</p>
Drought has negative consequences on aphid fitness and plant vigour: insights from a meta-analysis
<p>1. Aphids are abundant in natural and managed vegetation, supporting a diverse community of organisms and causing damage to agricultural crops. Due to a changing climate, periods of drought are anticipated to increase, and the potential consequences of this for aphid-plant interactions are unclear.</p> <p>2. Using a meta-analysis and synthesis approach, we aimed to advance understanding of how increased drought incidence will affect this ecologically and economically important insect group, and to characterise any potential underlying mechanisms. We used qualitative and quantitative synthesis techniques to determine whether drought stress has a negative, positive, or null effect on aphid fitness and examined these effects in relation to 1) aphid biology, 2) geographical region, 3) host plant biology.</p> <p>3. Across all studies, aphid fitness is typically reduced under drought. Subgroup analysis detected no difference in relation to aphid biology, geographical region, or the aphid-plant combination, indicating the negative effect of drought on aphids is potentially universal. Furthermore, drought stress had a negative impact on plant vigour and increased plant concentrations of defensive chemicals, suggesting the observed response of aphids is associated with reduced plant vigour and increased chemical defence in drought-stressed plants.</p> <p>4. We propose a conceptual model to predict drought effects on aphid fitness in relation to plant vigour and defence to stimulate further research.</p>
Decline in telomere length with increasing age across non‐human vertebrates: a meta‐analysis
<p>The prediction that telomere length (TL) shortens with increasing age is a major element in considering the role of telomeres as a key player in evolution. While telomere attrition is found in humans both <i>in vitro</i> and <i>in vivo</i>, the increasing number of studies reporting diverse age-specific patterns of TL challenges the hypothesis of a universal decline of TL with increasing age. Here we performed a meta-analysis to estimate the relationship between TL and age across 175 estimates encompassing 98 species of vertebrates. We found that, on average, TL does decline with increasing age during adulthood. However, this decline was weak and variable across vertebrate classes, and we also found evidence for a publication bias that might weaken our current evidence of decreasing TL with increasing age. We found no evidence for a faster decline in TL with increasing age when considering the juvenile stage (from birth to age at first reproduction) compared to the adult stage. Heterogeneity in TL ageing rates was explained by the method used to measure telomeres: detectable TL declines with increasing age were found only among studies using TRF with in-gel hybridisation and qFISH methods, but not in studies using qPCR and Southern blot-based TRF methods. While we confirmed that TL declines with increasing age in most adult vertebrates, our results identify an influence of telomere measurement methodology, which highlights the need to examine more thoroughly the effect of the method of measurement on TL estimates.</p>
Non-native species outperform natives in coastal marine ecosystems subjected to warming and freshening events - A meta-analysis of coastal marine native and non-native species responses to experimentally manipulated climatic events
<p><b>Aims</b>: Contemporary climate change and biological invasions are two main drivers of biodiversity redistribution. Interactive effects between these drivers have been reported in a number of study systems, yet results are conflicting. Some studies find that future climate change facilitates the spread and success of non-native species, especially those with broad physiological tolerances. Other studies conclude that non-natives are vulnerable to current and future changes in climatic conditions. Given that most studies have focused on terrestrial species, here we contribute to this debate by analysing responses of coastal native and non-native fauna and flora to key climate-related stressors namely increased temperature (warming) and decreased salinity (freshening).</p> <p><b>Location: </b>Global.</p> <p><b>Time period: </b>2002 – 2019.</p> <p><b>Major taxa studied: </b>Marine benthic<b> </b>macrophytes and invertebrates.</p> <p><b>Methods</b>: We conducted a meta-analysis of results from experiments investigating the performance (e.g., growth, survival and reproduction) of sessile and sedentary species from benthic marine communities to warming and freshening.</p> <p><b>Results</b>: We found evidence of positive responses to elevated temperature across a range of biological processes on non-native species, whereas the performance of native species declined. Similarly, decreased salinity negatively affected the biological processes of native species, but non-natives<span> showed no positive or negative overall response to freshening</span>.</p> <p><b>Main conclusions:</b> Our study showed that non-native species outperform natives under a wide variety of warming and freshening conditions. The growth and reproduction of non-natives are enhanced by warmer temperatures, and thus ocean warming is expected to facilitate future spread and success of non-native species. Increased freshening, however, <span>will likely have a negative impact in the future in both native and non-native species and thus is expected to be a driver of significant change in coastal marine ecosystems. Our</span> comprehensive literature search revealed the need of more <span>studies </span>focusing on s<span>alinity changes and highlighted the need to expand our understanding of climate change drivers beyond warming.</span></p>
Effectiveness of lateral bone augmentation prior to implant placement: a systematic review and meta-analysis
<p>Dataset for all analyses performed in the paper.</p>
Complications of biliary stenting versus T-tube insertion after common bile duct exploration: A systematic review and meta-analysis
<p><strong>Complications of biliary stenting versus T-tube insertion after common bile duct exploration: A systematic review and meta-analysis</strong></p>
Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture
<p><span>The heritability of susceptibility to tuberculosis disease (TB) has been well recognized. Over one-hundred genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicates. We established the International Tuberculosis Host Genetics Consortium (ITHGC) to perform a multi-ancestry meta-analysis of GWAS including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h<sup>2</sup>=26.3% 95% CI 23.7–29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p < 5x10<sup>-8</sup>) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value = 5.2x10<sup>-9</sup>). These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressures. </span></p>
Soil microbial biomass C, N in biocrust: A meta-analysis
<p><span>The biological soil crust (biocrust) has many crucial ecological functions in dryland ecosystems. </span><span>Differentiation</span><span> of soil microbial biomass in different ecosystems' biocrust under various climatic and soil conditions remains unknown, restricting our knowledge of biocrust microbiomes regulating terrestrial carbon and nitrogen cycling globally. We selected 255 paired observations from 45 global study sites for meta-analysis to quantify the effect of biocrust type, soil texture, and ecosystem type on soil microbial biomass in biocrust and identify the underlying impact factors. The results showed that</span> <span>biocrust had significantly higher soil microbial carbon and nitrogen contents (SMBC and SMBN, respectively) than bare (non-crust) soil (<em>P</em> < 0.05). Biocrust also significantly increased total nitrogen (TN) (143.68%), soil organic carbon (SOC) and TN ratio (C: N) (9.93%), and soil water content (SWC) (60.18%), and decreased pH (0.72%) (<em>P</em> < 0.05). Overall, the SMBC significantly differed between biocrust type, ecosystem type, and soil texture (<em>P</em> < 0.05). Compared with other biocrust types, lichen crust had the strongest positive effect on SMBC (822.48%). Grassland ecosystems had stronger positive effects on SMBC in biocrust than forest ecosystems, and sand and sandy loam soils had higher SMBC in biocrust than loam soils. Notably, altitude drives the positive effects of biocrust on SMBN and the negative effects of biocrust on SMBC and SMBC and SMBN ratio (SMBC: SMBN). Mean annual temperature (MAT) positively affected SMBC based on regression analysis. Further analysis revealed that SMBC and SMBN positively correlated with SOC, C: N, SWC, and urease activity and negatively correlated with pH. The random forest analysis confirmed that SOC, C: N, and altitude could be considered determinants of SMBC, SMBN, and SMBC: SMBN, respectively. Climatic factors and soil nutrients differently affected soil microbial biomass C, N and their ratio in biocrust. The high contribution of lichen crust to SMBC should be incorporated into regional and global models to predict the effects of climate change on soil carbon budgets in ecosystems worldwide.</span></p>
Nitrification, denitrification, and related functional genes under elevated CO2: a meta-analysis in terrestrial ecosystems
<p>This file encompasses the data that support the findings of the study entitled "Nitrification, denitrification, and related functional genes under elevated CO<sub>2</sub>: a meta-analysis in terrestrial ecosystems" by Robin Gineyts and Audrey Niboyet in Global Change Biology.</p>
Breast self-examination practice and its determinants among women in Indonesia: A systematic review, meta-analysis, and meta-regression
<p>Breast self-examination practice and its determinants among women in Indonesia: A systematic review, meta-analysis, and meta-regression</p>
Microbial necromass in cropland soils: A global meta-analysis of management effects
<p>The data support the article "Microbial necromass in cropland soils: A glogal meta-analysis of management effects" published in Global Change Biology.</p>
Data for "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis"
<p>This dataset was used to make tables and figures for the study entitled "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis", which was submitted to Global Change Biology in October 2022. It contains a meta-analysis database focusing on the effects of warming on soil C storage, root biomass and soil respiration.</p>
Data for: When does early-life telomere length predict survival? A case study and meta-analysis
<p>Suboptimal conditions during development can shorten telomeres, the protective DNA caps on the end of chromosomes. Shorter early-life telomere length (TL) can indicate reduced somatic maintenance, leading to lower survival and shorter lifespan. However, despite some clear evidence, not all studies show a relationship between early-life TL and survival or lifespan, which may be due to differences in biology or study design (e.g., survival period measured). In superb fairy-wrens (<em>Malurus cyaneus</em>), we assessed whether early-life TL predicts mortality across different life-history stages (fledgling, juvenile, adult). However, in contrast to a similar study on a congener, early-life TL did not predict mortality across any life stage in this species. We then performed a meta-analysis including 32 effect sizes from 23 studies (15 birds and 3 mammals) to quantify the effect of early-life TL on mortality whilst taking into consideration potential sources of biological and methodological variation. Overall, the effect of early-life TL on mortality was significant, corresponding to a 15% reduction in mortality risk with each standard deviation increase in TL. However, the effect became weaker when correcting for publication bias. Contrary to our predictions, there was no evidence that effects of early-life TL on mortality varied with species lifespan or the period over which survival was measured. However, negative effects of early-life TL on mortality risk were pervasive throughout life. These results imply that effects of early-life TL on mortality are more likely context-dependent rather than age-dependent, although substantial power and publication bias issues highlight the need for more research.</p>
Interactive effects of elevated temperature and drought on plant carbon metabolism: A meta‐analysis
<p><span>Elevated temperature (</span><span><em>T<sub>e</sub></em></span><span>) and drought often co-occur and interactively affect plant carbon (C) metabolism and thus the ecosystem C cycling, but the magnitude of their interaction is unclear, making the projection of global change impacts challenging. Here, we compiled 107 journal articles in which temperature and water availability were jointly manipulated and performed a meta-analysis of interactive effects of <em>T<sub>e</sub></em> and drought on leaf photosynthesis (</span><span>A<sub>growth</sub></span><span>) and respiration (</span><span>R<sub>growth</sub></span><span>) at growth temperature, nonstructural carbohydrates and biomass of plants, and their dependencies on experimental and biological moderators (e.g., treatment intensity, plant functional type). Our results showed that, overall, there was no significant interaction of </span><span><em>T<sub>e</sub></em></span><span> and drought on A<sub>growth</sub>. </span><span><em>T<sub>e</sub></em></span><span> accelerated R<sub>growth</sub> under well-watered conditions rather than under drought conditions. The </span><span><em>T<sub>e</sub></em></span><span> × </span><span>drought interaction on leaf soluble sugar and starch concentrations were neutral and negative, respectively. The effect of </span><span><em>T<sub>e</sub></em></span><span> and drought on plant biomass displayed a negative interaction, with </span><span><em>T<sub>e</sub></em></span><span> deteriorating the drought impacts. Drought induced an increase in root-to-shoot ratio at ambient temperature but not at </span><span><em>T<sub>e</sub></em></span><span>. The magnitudes of </span><span><em>T<sub>e</sub></em></span><span> and drought negatively modulated the </span><span><em>T<sub>e</sub></em></span><span> drought interactions on </span><span>A<sub>growth</sub></span><span>. Root biomass of woody plants was more vulnerable to drought than that of herbaceous plants at ambient temperature, but this difference diminished at </span><span><em>T<sub>e</sub></em></span><span>. Perennial herbs exhibited a stronger amplifying effect of </span><span><em>T<sub>e</sub></em></span><span> on plant biomass in response to drought than did annual herbs. </span><span><em>T<sub>e</sub></em></span><span> exacerbated the responses of </span><span>A<sub>growth</sub></span><span> and stomatal conductance to drought for evergreen broadleaf trees rather than for deciduous broadleaf and evergreen coniferous trees. A negative </span><span><em>T<sub>e</sub></em></span> <span>×</span><span> drought interaction on plant biomass was observed on the species level rather than on the community level. Collectively, our findings provide a mechanistic understanding of the interactive effects of </span><span><em>T<sub>e</sub></em></span><span> and drought on plant C metabolism, which would improve the prediction of climate change impacts.</span></p>
Data obtained by systematic review (codified data and meta-data) for: Influence of upwelling on coral reef benthic communities: a systematic review and meta-analysis
<p>Highly competitive coral reef benthic communities are acutely sensitive to changes in environmental parameters such as temperature and nutrient concentrations. Physical oceanographic processes that induce upwelling therefore act as drivers of community structure on tropical reefs. How upwelling impacts coral communities, however, is not fully understood; upwelling may provide a natural buffer against climate impacts and could potentially enhance the efficacy of spatial management and reef conservation efforts. This study employed a systematic review to assess existing literature linking upwelling with reef community structure, and a meta-analysis to quantify upwelling impact on the percentage cover of coral reef benthic groups. We show that upwelling has context-dependant effects on the cover of hard coral and fleshy macroalgae, with effect size and direction varying with depth, region and remoteness. Fleshy macroalgae was found to increase by 110% on inhabited reefs yet decrease by 56% around one well-studied remote island in response to upwelling. Hard coral cover was not significantly impacted by upwelling on inhabited reefs but increased by 150% when direct human pressures were absent. By synthesising existing evidence, this review facilitates adaptive and nuanced reef management which considers the influence of upwelling on reef assemblages.</p>
High temperature frequently increases facilitation between aquatic foundation species: A global meta-analysis of interaction experiments between angiosperms, seaweeds, and bivalves
<ol> <li><span>Many studies have quantified ecological impacts of individual foundation species (FS). However, emerging data suggest that FS often co-occur, potentially inhibiting or facilitating one another, thereby causing indirect, cascading effects on surrounding communities. Furthermore, global warming is accelerating, but little is known about how interactions between co-occurring FS vary with temperature. </span></li> <li><span>Shallow aquatic sedimentary systems are often dominated by three types of FS: slower-growing clonal angiosperms, faster-growing solitary seaweeds, and shell-forming filter- and deposit-feeding bivalves. Here, we tested the impacts of one FS on another by analyzing manipulative interaction experiments from 148 papers with a global meta-analysis.</span></li> <li> <span>We calculated </span><span>1,942 (non-independent) Hedges' <em>g</em> effect sizes,</span> <span>from 11,652 extracted values over performance responses, such as abundances, growths or survival of FS, and their associated standard deviations and replication levels. Standard aggregation procedures generated 511 independent Hedges' <em>g</em> that was classified into six types of reciprocal impacts between FS. </span> </li> <li><span>We found that (i) seaweeds had consistent negative impacts on angiosperms across performance responses, organismal sizes, experimental approaches, and ecosystem types; (ii) angiosperms and bivalves generally had positive impacts on each other (e.g., positive effects of angiosperms on bivalves were consistent across organismal sizes and experimental approaches, but angiosperm effects on bivalve growth and bivalve effect on angiosperm abundance were not significant); (iii) bivalves positively affected seaweeds (particularly on growth responses); (iv) there were generally no net effects of seaweeds on bivalves (except for positive effect on growth) or angiosperms on seaweeds (except for positive effect on 'other processes'); and (v) bivalve interactions with other FS were typically more positive at higher temperatures, but angiosperm-seaweed interactions were not moderated by temperature.</span></li> <li> <em><span>Synthesis</span></em><span>: Despite variations in experimental and spatiotemporal conditions, the stronger positive interactions at higher temperatures suggest that facilitation, particularly involving bivalves, may become more important in a future warmer world. Importantly, addressing research gaps, such as the scarcity of FS interaction experiments from tropical and freshwater systems and for less studied species, as well as testing for density-dependent effects, could better inform aquatic ecosystem conservation and restoration efforts and broaden our knowledge of FS interactions in the Anthropocene.</span> </li> </ol>
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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.