Fixed or random? On the reliability of mixed‐effects models for a small number of levels in grouping variables

Biological data are often intrinsically hierarchical (e.g., species from different genera, plants within different mountain regions), which made mixed-effects models a common analysis tool in ecology and evolution because they can account for the non-independence. Many questions around their practical applications are solved but one is still debated: Should we treat a grouping variable with a low number of levels as a random or fixed effect? In such situations, the variance estimate of the random effect can be imprecise, but it is unknown if this affects statistical power and type I error rates of the fixed effects of interest. Here, we analyzed the consequences of treating a grouping variable with 2–8 levels as fixed or random effect in correctly specified and alternative models (under- or overparametrized models). We calculated type I error rates and statistical power for all-model specifications and quantified the influences of study design on these quantities. We found no influence of model choice on type I error rate and power on the population-level effect (slope) for random intercept-only models. However, with varying intercepts and slopes in the data-generating process, using a random slope and intercept model, and switching to a fixed-effects model, in case of a singular fit, avoids overconfidence in the results. Additionally, the number and difference between levels strongly influences power and type I error. We conclude that inferring the correct random-effect structure is of great importance to obtain correct type I error rates. We encourage to start with a mixed-effects model independent of the number of levels in the grouping variable and switch to a fixed-effects model only in case of a singular fit. With these recommendations, we allow for more informative choices about study design and data analysis and make ecological inference with mixed-effects models more robust for small number of levels

Factores asociados a la no realización de examen citopatológico en São Leopoldo, Rio Grande do Sul, Brasil, 2015: estudio transversal de base poblacional

Objetivo: estimar a prevalência de exame citopatológico não realizado nos últimos três anos e de nunca realizado em mulheres, e analisar fatores associados. Métodos: estudo transversal, com mulheres de 20 a 69 anos de idade, em São Leopoldo, RS, Brasil, em 2015; calcularam-se as razões de prevalência (RP) por regressão de Poisson. Resultados: entre 919 mulheres, a prevalência de exame atrasado foi 17,8% (intervalo de confiança de 95% [IC95%15,4;20,3), e de nunca realizado, 8,1% (IC95%6,3;9,8); na análise ajustada, o aumento na prevalência de exame atrasado mostrou-se associado à classe econômica D/E (RP=2,1 - IC95%1,3;3,5), idade de 20-29 anos (RP=3,2 - IC95%2,1;4,9) e nenhuma consulta realizada (RP=3,0 - IC95%2,1;4,1); nunca ter realizado exame associou-se com classe econômica D/E (RP=2,6 - IC95%1,4;5,0), idade de 20-29 anos (RP=24,1 - IC95%6,4;90,9) e nenhuma consulta (RP=2,9 - IC95%1,7;4,8). Conclusão: a cobertura de exame foi alta e com iniquidade.Objective: to estimate the prevalence of Pap tests not performed in the last three years and never performed in women and to analyze associated factors. Methods: this was a cross-sectional study with women aged 20 to 69 years living in São Leopoldo, RS, Brazil, in 2015; prevalence ratios (PR) were calculated using Poisson regression. Results: among 919 women, prevalence of delayed testing was 17.8% (95% confidence interval [95%CI]15.4;20.3) and never tested prevalence was 8.1% (95%CI6.3%;9.8%); in the adjusted analysis, the increase in the prevalence of delayed testing was associated with economic class D/E (PR=2.1 – 95%CI1.3;3.5), being aged 20-29 years (PR=3.2 – 95%CI2.1;4.9) and not having had a medical appointment (PR=3.0 – 95%CI2.1;4.1); never having tested was associated with economic class D/E (PR=2.6 – 95%CI1.4;5.0), being aged 20-29 years (PR=24.1 – 95%CI6.4;90.9), and not having had a medical appointment (PR=2.9 – 95%CI1.7;4.8). Conclusion: coverage of the test was high but characterized by social inequality.Objetivo: estimar la prevalencia de examen en mujeres, no realizado en los últimos tres años y de nunca realizado, y analizar factores asociados. Métodos: estudio transversal con mujeres de 20 a 69 años de edad de São Leopoldo, RS, Brasil, en 2015; se calcularon las razones de prevalencia (RP) por la regresión de Poisson. Resultados: entre 919 mujeres, la prevalencia de examen retrasado fue 17,8% (intervalo de confianza del 95% [IC95%]15,4;20,3) y de nunca realizado fue del 8,1% (IC95%6,3;9,8); en el análisis ajustado, el aumento en la prevalencia de examen retrasado se asoció con clase económica D/E (RP=2,1 – IC95%1,3;3,5), a edad entre 20-29 años (RP=3,2 – IC95%2,1;4,9) y ninguna consulta (RP=3,0 – IC95%2,1;4,1); nunca haber realizado examen se asoció con clase D/E (RP=2,6 – IC95%1,4;5,0), a 20- 29 años de edad (RP=24,1 – IC95%6,4;90,9) y ninguna consulta (RP=2,9 – IC95%1,7;4,8). Conclusión: la cobertura de examen fue alta y con inequidad

Latitudinal patterns in stabilizing density dependence of forest communities

Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10,11,12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): Study protocol for a randomized controlled trial

Background: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). Methods/Design: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH(2)O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure <= 30 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. Discussion: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration method.Hospital do Coracao (HCor) as part of the Program 'Hospitais de Excelencia a Servico do SUS (PROADI-SUS)'Brazilian Ministry of Healt

Embracing variability: the use of mixed effects models in Ecology

A ecologia é uma ciência que se preocupa constantemente em testar hipóteses ou mesmo entender processos ecológicos a partir de padrões em dados, os quais são na maioria das vezes descritos com uso de ferramentas estatísticas. Modelos mistos são cada vez mais usados em ecologia devido à natureza hierárquica da maioria dos dados ecológicos e são modelos especialmente úteis em se particionar fontes de variabilidade. Modelos mistos podem fornecer respostas quantitativas que descrevem que fração de um padrão em particular é explicada por diferentes mecanismos: o \"quanto\" em vez de \"qual\". Essa mudança de perspectiva pode se muito útil em ecologia tanto para entender contribuição relativa de processos ecológicos, quanto descrever melhor padrões globais de variabilidade. Nesta tese, eu emprego e advogo pelo uso de modelos mistos em perguntas ecológicas bem distintas, mas com um arcabouço analítico comum: partição de variabilidade em modelos mistos. No primeiro capítulo, buscamos entender como a matriz (não habitat) modula a contribuição relativa de processos de montagem de comunidades (filtro ambiental e deriva) de aves florestais com a de perda de habitat em paisagens fragmentadas. Para modelar a ocorrência das aves, usamos um modelo misto com associação entre os atributos das espécies e a cobertura florestal como efeitos fixos e diversos componentes aleatórios para medir força relativa de certos processos. Encontramos que o filtro ambiental por perda de habitat é o processo dominante e pode ser relaxado ou reforçado dependendo da qualidade da matriz, evidenciando que esta tem um forte impacto na modulação dos processos de montagem da comunidade. No segundo capítulo, desenvolvemos e aplicamos um framework conceitual e analítico através da partição de variâncias de um modelo misto para atribuir a variabilidade em taxas vitais de árvores devido a variações espaciais, temporais, entre espécies e suas interações. Aplicamos o framework no crescimento, mortalidade e recrutamento de 21 florestas globalmente distribuídas cobrindo mais de 2,9 milhões de árvores de aproximadamente 6,5 mil espécies. A proposta de decomposição da variação das taxas vitais de árvores tem um alto potencial para identificar os mecanismos estruturantes da dinâmica florestal, pois destaca os caminhos mais promissores para pesquisas futuras, aumentando a compreensão das contribuições relativas dos grupos de mecanismos para a demografia e diversidade florestal. Junto às ferramentas de partição de variâncias, destacamos nesta tese o grande potencial dos modelos mistos em conectar inferência estatística e ecológica, incorporando a variabilidade como fonte de informações diversas e de qualidade tanto para entender contribuição relativa de processos ecológicos, quanto descrever padrões mais detalhados em sistemas ecológicos complexos.Ecology is a science that is constantly concerned with testing hypotheses or even understanding ecological processes from patterns in data, which are mostly described using statistical tools. Mixed-effects models are increasingly used in ecology given the hierarchical nature of most ecological data and are especially useful in partitioning sources of variability. Mixed-effects models can provide quantitative answers that describe what fraction of a particular pattern is explained by different mechanisms: the \"how much\" rather than the \"which\". This shift in perspective can prove very useful in ecology both to understand relative contribution of ecological processes, and to better describe global patterns of variability. In this thesis, I employ and advocate for the use of mixed-effects models in very different ecological questions, but with a common analytical framework: variability partitioning in mixed-effects models. In the first chapter, we seek to understand how matrix (non-habitat) modulates the relative contribution of community assembly processes (environmental filter and drift) of forest birds due to habitat loss in fragmented landscapes. To model bird occurrence, we used a mixed-effect model with association between species attributes and forest cover as fixed effects and several random components to measure relative strength of certain processes. We found that the environmental filter by habitat loss is the dominant process and can be relaxed or strengthened depending on matrix quality, evidencing that the matrix has a strong impact on modulating community assembly processes. In the second chapter, we develop and apply a conceptual and analytical framework through variance partitioning of a mixed-effect model to attribute variability in tree vital rates due to differences among species, space, and time, and their interactions. We apply the framework to growth, mortality, and recruitment rates of 21 globally distributed forests covering over 2.9 million trees of approximately 6,500 species. Our framework has a high potential for identifying the structuring mechanisms of forest dynamics, as it highlights the most promising avenues for future research by increasing understanding of the relative contributions of groups of mechanisms to forest demography and diversity. Along with variance partitioning tools, we highlight in this thesis the great potential of mixed-effects models in connecting statistical and ecological inference, incorporating variability as a diverse and good source of information both to understand the relative contribution of ecological processes and to describe more detailed patterns in complex ecological systems

Determination of Macro- and Microelements in the Inflorescences of Banana Tree Using ICP OES: Evaluation of the Daily Recommendations of Intake for Humans

The inflorescence of Musa paradisiaca, known as “banana heart” is a structure that includes flowers and bracts of banana, commonly used as food source worldwide. The aims of this study were (1) to determine the mineral components of Musa paradisiaca and (2) to compare the obtained results with previously reported data of Recommendation Dietary Allowances (RDAs) and edible plant permissible limits set by FAO/WHO. The samples were digested using microwave-assisted equipment, while elemental contents were determined by inductively coupled plasma optical emission spectroscopy (ICP OES). Metal (Mg, Ca, Cr, Ni, Cu, Fe, and Zn) and nonmetal (S and P) contents were detected. According to RDA, the inflorescences could be excellent sources of Mg, P, Cr, Cu, Zn, and Fe for females, males, and pregnant women, all age 31–50 y, as well as children (4–8 y). Bracts are good source of Zn for male and pregnant women and good source of Fe for children. All the samples contained considerable amounts of Mg, Ca, P, Ni, Cu, Zn, and Fe, which were quite low to induce deleterious effects (UL). FAO/WHO limits for edible plants have not yet been established for S, P, Mg, and Ca, but Ni and Zn are below of those limit values. However, Cr and Cu concentrations are higher than the values established for edible plants and may pose a threat to human health. Farmers should be encouraged by government agencies, not only for sustainability of production but also to ensure the storage and trade of banana tree inflorescence

A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus

Abstract The cattle tick Rhipicephalus microplus is a hematophagous ectoparasite that causes important economic losses in livestock. Different species of ticks harbor a symbiont bacterium of the genus Coxiella. It was showed that a Coxiella endosymbiont from R. microplus (CERM) is a vertically transmitted mutualist symbiont, comprising 98% of the 16S rRNA sequences in both eggs and larvae. Sequencing of the bacterial genome revealed genes for biosynthetic pathways for several vitamins and key metabolic cofactors that may provide a nutritional complement to the tick host. The CERM was abundant in ovary and Malpighian tubule of fully engorged female. Tetracycline treatment of either the tick or the vertebrate host reduced levels of bacteria in progeny in 74% for eggs and 90% for larvae without major impact neither on the reproductive fitness of the adult female or on embryo development. However, CERM proved to be essential for the tick to reach the adult life stage, as under antibiotic treatment no tick was able to progress beyond the metanymph stage. Data presented here suggest that interference in the symbiotic CERM-R. microplus relationship may be useful to the development of alternative control methods, highlighting the interdependence between ticks and their endosymbionts