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opencc-zeroMay 2020View details →

Data from: City sicker? a meta-analysis of wildlife health and urbanization

Urban development can alter resource availability, land use, and community composition, in turn influencing wildlife health. Generalizable relationships between wildlife health and urbanization have yet to be quantified, and could vary across health metrics and animal taxonomy. We present a phylogenetic meta-analysis of 516 records spanning 81 wildlife species from 106 studies comparing the toxicant loads, parasitism, body condition, or stress of urban and non-urban wildlife populations in 30 countries. We find a significantly negative relationship between urbanization and wildlife health, driven by higher toxicant loads and greater parasitism by parasites transmitted through close contact. Invertebrates and amphibians were particularly affected, with higher toxicant loads and physiological stress in urban populations as compared to their non-urban counterparts. We also found strong geographic and taxonomic bias in research effort, highlighting future research needs. Our results suggest urban wildlife experience several health risks with potential threats to conservation.

Bayesian diagnostic meta-analysis dataset of pelvic examination in pelvic inflammatory disease

Pelvic inflammatory disease (PID) is not merely a transient sexually transmitted disease. It can lead to chronic pain, ectopic pregnancy, and infertility. Although the Centers for Disease Control and Prevention have established minimum diagnostic criteria, including pelvic examination, the diagnostic value of pelvic tenderness has recently garnered controversy. Our meta-analysis aimed to confirm whether pelvic examination can help diagnose PID among at-risk women. Design A Bayesian meta-analysis of studies reporting diagnostic data of patients at risk for PID. Setting We searched MEDLINE, EMBASE, CENTRAL, CINAHL, Google, and Google Scholar for eligible articles. Participants Female patients at risk for PID. Main results The literature search produced 5,395 articles. After quality assessment, 16 studies and their 4,083 participants were eligible for synthesis on pelvic tenderness.

opencc-zeroOct 2020View details →

Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver

The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response. Weight loss and alleviation of insulin resistance were consistently associated with improvement in NAFLD. Multiple drug classes that do not affect weight in humans caused weight loss in animals. Other study design variables, such as age of animals and dietary composition, influenced the magnitude of treatment effect. Publication bias may have increased effect estimates by 37-79%. These findings help to explain the challenge of reproducibility and translation within the field of metabolism.

opencc-zeroDec 2018View details →

Data from: A meta-analysis of plant interaction networks reveals competitive hierarchies as well as facilitation and intransitivity

The extent to which competitive interactions and niche differentiation structure communities has been highly controversial. To quantify evidence for key features of plant community structure, I recharacterized published data from interaction experiments as networks of competitive and facilitative interactions. I measured the network structure of 31 woody and herbaceous communities, including the intensity, distribution, and diversity of interactions at the species-pair and community level to determine the generality of competition, winner-loser relationships, and unequal interaction allocation. I developed novel methodology using meta-analysis to incorporate interaction uncertainty into estimates of structural metrics among independent networks. Plant communities were competitive, but intraspecific interactions were sometimes more intense than interspecific interactions. On the whole, interactions were imbalanced and communities were transitive. However, facilitation, balanced interactions, and intransitivity were common in individual communities. Synthesizing network metrics using meta-analysis is an original approach with which to generalize community structure in a systematic way.

opencc-zeroNov 2020View details →

Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems

If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value - notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and non-crop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested. We synthesized the results of 102 studies, comprising 2,004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ~20% for non-crop hosts and by ~50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.

opencc-by-4.0Dec 2020View details →

The influence of thin as compared to thick peri-implant soft tissues on esthetic outcomes. A systematic review and meta-analysis.

Dataset for all analyses in the paper.

opencc-zeroDec 2020View details →

Influence of polymorphisms in the vascular endothelial growth factor gene on allograft rejection after kidney transplantation: a meta-analysis

Purpose Reported associations of allograft rejection in kidney transplant patients with VEGF single nucleotide polymorphisms (SNPs) have been inconsistent between studies, which prompted a meta-analysis to obtain more precise estimates. Methods Using the PICO elements, kidney transplant patients (P) were compared by genotype data between rejectors (I) and non-rejectors (C) in order to determine the risk of allograft rejection (O) attributed to the VEGF SNPs. Literature search of four databases yielded seven articles. To calculate risks for allograft rejection, four SNPs were examined. Meta-analysis treatments included outlier and subgroup analyses, the latter was based on ethnicity (Indians/Caucasians) and rejection type (acute/chronic). Multiple comparisons were corrected with the Bonferroni test. Results Five highly significant outcomes (Pa < 0.01) survived Bonferroni correction, one of which showed reduced risk for the var allele (OR 0.61, 95% CI 0.45-0.82). The remaining four indicated increased risk for the wt allele where the chronic rejection (OR 2.10, 95% CI 1.36-3.24) and Indian (OR 1.44, 95% CI 1.13-1.84) subgroups were accorded susceptibility status. Conclusions Risk associations for renal allograft rejection were increased and reduced on account of the wt and var alleles, respectively. These findings could render the VEGF polymorphisms useful in the clinical genetics of kidney transplantation.

opencc-zeroDec 2020View details →

Data from: Large-scale meta-analysis on rheumatoid arthritis across East Asian and European populations

Objective: Nearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly polygenic genetic architecture of RA. Here, we performed the largest-ever trans-ancestral meta-analysis with the aim to identify new RA loci and to better understand RA biology underlying genetic associations. Methods: Genome-wide RA association summary statistics in three large case-control collections consisting of 311,292 individuals of Korean, Japanese, and European populations were used in an inverse-variance-weighted fixed-effects meta-analysis. Several computational analyses using public omics resources were conducted to prioritize causal variants and genes, RA variant-implicating features (tissues, pathways, and transcription factors), and potentially repurposable drugs for RA treatment. Results: We identified 11 new RA susceptibility loci that explained 6.9% and 1.8% of the SNP-based heritability in East Asians and Europeans, respectively, and confirmed 71 known non-HLA susceptibility loci, identifying 90 independent association signals. The RA variants were preferentially located in binding sites of various transcription factors and in cell type-specific transcription-activation histone marks that simultaneously highlighted the importance of CD4+ T-cell activation and the potential role of non-immune organs in RA pathogenesis. A total of 615 plausible effector genes, based on gene-based associations, expression-associated variants, and chromatin interaction, included targets of drugs approved for RA treatments and potentially repurposable drugs approved for other indications. Conclusion: Our findings provide useful insights regarding RA genetic etiology and variant-driven RA pathogenesis.

opencc-zeroDec 2020View details →

Meta-analysis on pulse disturbances reveals differences in functional and compositional recovery across ecosystems

Most ecosystems are affected by anthropogenic or natural pulse disturbances, which alter the community composition and functioning for a limited period of time. Whether and how quickly communities recover from such pulses is central to our understanding of biodiversity dynamics and ecosystem organization, but also to nature conservation and management. Here, we present a meta-analysis of 508 (semi-)natural field experiments globally distributed across marine, terrestrial and freshwater ecosystems. We found recovery to be significant yet incomplete. At the end of the experiments, disturbed treatments resembled controls again when considering abundance (94%), biomass (82%), and univariate diversity measures (88%). Most disturbed treatments did not further depart from control after the pulse, indicating that few studies showed novel trajectories induced by the pulse. Only multivariate community composition on average showed little recovery: disturbed species composition remained dissimilar to the control throughout the experiment. Still, when experiments showed a higher compositional stability, they tended to also show higher functional stability. Recovery was more complete when systems had high resistance, whereas resilience and resistance were negatively correlated. The overall results were highly consistent across studies, but significant differences between ecosystems and organism groups appeared. Future research on disturbances should aim to understand these differences, but also fill obvious gaps in the empirical assessments for regions (especially the tropics), ecosystems and organisms. In summary, we provide general evidence that (semi-)natural communities can recover from pulse disturbances, but compositional aspects are more vulnerable to long-lasting effects of pulse disturbance than the emergent functions associated to them.

Local adaptation to biotic interactions: a meta-analysis across latitudes

Adaptation to local conditions can increase species' geographic distributions and rates of diversification, but which components of the environment commonly drive local adaptation—particularly the importance of biotic interactions—is unclear. Biotic interactions should drive local adaptation when they impose consistent divergent selection; if this is common we expect transplant experiments to detect more frequent and stronger local adaptation when biotic interactions are left intact. We tested this hypothesis using a meta-analysis of transplant experiments from >125 studies (mostly on plants). Overall, local adaptation was common and biotic interactions affected fitness. Nevertheless, local adaptation was neither more common nor stronger when biotic interactions were left intact, either between experimental treatments within studies (control vs. biotic interactions experimentally manipulated) or between studies that used natural vs. biotically-altered transplant environments. However, the effect of ameliorating negative interactions varied with latitude, suggesting that interactions may promote local adaptation more often in tropical vs. temperate ecosystems, though few tropical studies were available to test this. Our results suggest that biotic interactions often fail to drive local adaptation even though they strongly affect fitness, perhaps because temperate biotic environments are unpredictable at the spatiotemporal scales required for local adaptation.

Data from: Individual differences in behaviour explain variation in survival: a meta-analysis

Research focusing on among-individual differences in behaviour ("animal personality") has been blooming for over a decade. One of the central theories explaining the maintenance of such behavioural variation posits that individuals expressing greater "risky" behaviours should suffer higher mortality. Here, for the first time, we synthesize the existing empirical evidence for this key prediction. Our results did not support this prediction as there was no directional relationship between riskier behaviour and greater mortality; however there was a significant absolute relationship between behaviour and survival. In total, behaviour explained a significant, but small, portion (5.8%) of the variance in survival. We also found that risky (versus "shy") behavioural types live significantly longer in the wild, but not in the laboratory. This suggests that individuals expressing risky behaviours might be of overall higher quality but the lack of predation pressure and resource restrictions mask this effect in laboratory environments. Our work implies that individual differences in behaviour explain important differences in survival but not in the direction predicted by theory. Importantly, this suggests that the models predicting survival trade-offs may need revision and/or empiricists may need to reconsider their proxies of risky behaviours when testing such theory.

opencc-zeroJan 2020View details →

Diapause is not selected as a bet-hedging strategy in insects: a meta-analysis of reaction norm shapes

Many organisms escape from lethal climatological conditions by entering a resistant resting stage called diapause, and it is essential that this strategy remains optimally timed with seasonal change. Climate change therefore exerts selection pressure on phenology, which is expected to cause the evolution of mean diapause timing, but also phenotypic plasticity and bet-hedging strategies. Especially the latter as a strategy to cope with unpredictability is so far little considered in the context of climate change, and it is unknown whether it can readily evolve. Contemporary patterns of phenological strategies across a geographic range may provide information about their evolvability. We thus extracted 458 diapause reaction norms from 60 studies. First, we correlated mean diapause timing with mean winter onset. Then we partitioned the reaction norm variance into a temporal component (phenotypic plasticity) and among-offspring variance (diversified bet-hedging) and correlated this variance composition with predictability of winter onset. Contrary to our expectation, mean diapause timing correlated only weakly with mean winter onset, as populations at high latitudes failed to track early onsets. Variance among offspring was also limited and correlated only weakly with environmental predictability, indicating little scope for bet-hedging. We conclude that constraints may limit the evolution of phenology in a rapidly changing climate.

opencc-zeroJun 2021View details →

Latitudinal gradient in the intensity of biotic interactions in terrestrial ecosystems: Sources of variation and differences from the diversity gradient revealed by meta-analysis

The Latitudinal Biotic Interaction Hypothesis (LBIH) states that the intensity of biotic interactions increases from high to low latitudes. This hypothesis, which may partly explain latitudinal gradients in biodiversity, remains hotly debated, largely due to variable outcomes of published studies. We used meta-analysis to identify the scope of the LBIH in terrestrial ecosystems. For this purpose, we explored the sources of variation in the strength of latitudinal changes in herbivory, carnivory, and parasitism (119 publications) and compared these gradients with gradients in the diversity of the respective groups of animals (102 publications). Overall, both herbivory and carnivory decreased towards the poles, while parasitism increased. The latitudinal gradient in herbivory and carnivory was threefold stronger above 50–60º than at lower latitudes and was significant due to interactions involving ectothermic consumers, studies using standardized prey (i.e. prey lacking local anti-predator adaptations) and studies aimed at testing LBIH. The poleward decrease in biodiversity did not differ between ectothermic and endothermic animals or among climate zones and was four-fold stronger than decrease in herbivory and carnivory. The discovered differences between the gradients in biotic interactions and biodiversity suggest that these two global macroecological patterns are likely shaped by different factors.

Occupational exposure to silica and risk of heart disease: a systematic review with meta-analysis

Objective To search for evidence of the relationship between occupational silica exposure and heart disease. Design A systematic review and meta-analysis. Background Growing evidences suggest a connection between occupational silica exposure and heart disease; however, the link between them is less clear. Data sources PubMed, ScienceDirect, Springer and EMBASE were searched for articles published between 1 January 1995 and 20 June 2019. Articles that investigated the effects of occupational silica exposure on heart disease risk were considered. Study selection We included cohort studies, including prospective, retrospective and retro-prospective studies. Data extraction and synthesis We extracted data by using a piloted data collection form and conducted random-effects meta-analysis and exposure-response analyses. The meta-relative risk (meta-RR), a measure of the average ratio of heart disease rates for those with and without silica exposure, was used as an inverse variance-weighted average of relative risks from the individual studies. The Newcastle-Ottawa Quality assessment Scale about cohort studies was used for study quality assessment. Outcome measure We calculated heart disease risks of pulmonary heart disease, ischaemic heart disease and other heart diseases. Results Twenty cohort articles were included. Results suggest a significant increase of overall heart disease risk (meta-RR = 1.08, 95% CI = 1.03, 1.13). Stronger evidences of association with pulmonary heart disease were found through both categories of heart disease risk estimate (meta-RR = 1.24, 95% CI = 1.08, 1.43) and exposure-response analyses (meta-RR = 1.39, 95% CI = 1.19, 1.62). Moreover, our subgroup analyses revealed that the statistical heterogeneity among studies could be attributed mainly to the diversities of reference group, occupation and study quality score. Conclusions Silica-exposed workers have increased risk of overall heart disease, especially pulmonary heart disease. While further research is needed to better clarify the relationship between occupational silica exposure and ischaemic heart disease.

opencc-zeroDec 2016View details →

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.

opencc-zeroApr 2020View details →

Effects of nutrient limitation on the synthesis of N-Rich phytoplankton toxins: a meta-analysis

Eutrophication has played a major role in the worldwide increase of harmful algal blooms (HABs). Higher input of key nutrients, such as nitrogen (N) and phosphorus (P), can stimulate the growth of harmful algal species in freshwater, estuarine, and coastal marine ecosystems. Some HAB-forming taxa, particularly several cyanobacteria and dinoflagellate species, are harmful through the production of N-rich toxins that have detrimental effects on the environment and human health. Here, we test how changes in nutrient availability affect N-rich toxin synthesis in cyanobacteria and dinoflagellates using a meta-analysis approach. Overall, N-rich toxin content showed an increase with P limitation, while it tended to decrease with N limitation, but we also observed substantial variation in responses both within and across genera and toxin groups. For instance, in response to N limitation, microcystin content varied from a 297% decrease up to a 273% increase, and paralytic shellfish poisoning (PSP) toxin content varied from a 204% decrease to an 82% increase. Cylindrospermopsin, produced by N2-fixing cyanobacteria, showed no clear direction in response to nutrient limitation, and cellular contents of this compound may thus vary independently of nutrient fluctuations. Our results confirm earlier reported stoichiometric regulation of N-rich phytoplankton toxins, showing increased toxin content with an increase in cellular N:P ratios, and vice versa. Thus, changes in N-rich toxin content largely follow the changes in relative cellular N content. Consequently, although nutrient limitation may limit bloom biomass and thereby bloom toxicity, our results warn that P limitation can cause accumulation of cellular toxins and thus lead to unexpected increases in bloom toxicity.

opencc-zeroDec 2023View details →

A meta-analysis reveals increases in soil organic carbon following the restoration and recovery of croplands in Southwest China

In China, the Grain for Green Program (GGP) is an ambitious project to convert croplands into natural vegetation, but exactly how changes in vegetation translate into changes in soil organic carbon remains less clear. Here we conducted a meta-analysis using 734 observations to explore the effects of land recovery on the soil organic carbon and nutrients in 4 provinces in Southwest China. Following GGP, the soil organic carbon content (SOCc) and soil organic carbon storage (SOCs) increased by 33.73% and 22.39%, respectively. Likewise, soil nitrogen increased, while phosphorus decreased. Outcomes were heterogeneous, however, depending on variation in soil and environmental characteristics. Both the regional land use and cover change indicated by landscape type transfer matrix and net primary production from 2000 to 2020 further confirmed that GGP promoted the forest area (2.95%) and regional mean net primary production (52.94%). Our findings suggest that GGP could enhance soil and vegetation carbon sequestration in Southwest China and help to develop carbon neutral strategy.

opencc-by-4.0Dec 2016View details →

Supplementary material for "Patient portal adoption rates: a systematic literature review and meta-analysis"

The attached file contains the searches used to review the literature and identify papers evaluating usage, usability and influence on decision making of patient portals (Supplementary Table 1). Supplementary Table 2 and Supplementary Table 3 contains references and individual studies characteristics of included studies.

opencc-by-4.0Dec 2016View details →

Supplementary material for "Patient portal adoption rates: a systematic literature review and meta-analysis"