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lme4: Linear mixed-effects models using Eigen and S4
... Within this environment, R statistical software with packages tidyverse, epitools, lme4, and marginaleffects and will be used for data handling and analysis. [36][37][38][39][40] Statistical methods: We will analyse the effect a single high-dose of glucocorticoids in two ways; 1) a crude, unadjusted analysis, 2) a pre-defined model adjusted for important pre-exposure variables using stabilised inverse probability of treatment weighting (SIPTW). 10,41 1) The crude analyses of binary outcomes (i.e., persistent opioid/NSAID/paracetamol use) are conducted with the Fischer's exact test and reported as relative and absolute risk differences with 95% confidence intervals (calculated assuming binomial distribution). ...
... First, we will apply a logistic mixed-effects model, using the lme4 package 39 Each unit is given weight by the inverse probability of being in their respective arm (treatment/control). That is, patients in the treatment arm are assigned weights as (propensity score) -1 , while controls are assigned (1 -propensity score) -1 . ...
Background: Persistent postsurgical pain and opioid use after primary total hip and knee arthroplasty (THA and TKA) have major consequences for the patient and for society. High-dose perioperative treatment with glucocorticoids reduces inflammation and acute pain, both of which are associated with persistent postsurgical pain. We therefore hypothesise that routine treatment with glucocorticoids reduces the number of patients with persistent opioid use.
Objective: To determine if perioperative glucocorticoids for primary THA or TKA surgery, relative to no glucocorticoids, decreases the number of patients taking opioids in the period from 3 to 12 months after surgery.
Design: Target trial emulation trial with data from Danish national registries.
Setting: All departments of orthopaedic surgery in Denmark, from 1 January 2010 to 31 December 2020.
Participants: Patients with primary osteoarthritis undergoing primary THA or TKA, excluding presurgical users of glucocorticoids or insulin because these patients do not always receive the intervention.
Intervention: A single high-dose glucocorticoids (≥125 mg methylprednisolone or ≥24 mg dexamethasone) after induction of anaesthesia.
Comparator: No glucocorticoids during surgery.
Allocation: Patients operated at departments where treatment with high-dose glucocorticoids was standard of care at the time of surgery constitute the treatment arm, while patients operated at departments where high-dose glucocorticoids was not used serve as controls. Thus, all patients will be analysed according to their allocation, regardless of whether they received the treatment or not.
Main outcome measures: The primary outcome is number of persistent opioid users, defined as patients who redeem a prescription within at least two of the last three quarters during the first postsurgical year. The primary safety outcome is number of days alive and out of hospital within 90 days after surgery.
Expectations: These results will provide important evidence for or against the use of perioperative glucocorticoids in total hip and knee arthroplasty.
... Significant differences between phylum contributions to total community growth were determined also with an analysis of variance using the packages car [74] and emmeans [75] to determine pairwise contrasts between phyla across treatments and the two sites. In R, a linear mixed effects model and variance partitioning analysis was used to determine the variance in bacterial growth rate associated with individual amplicon sequence variant (ASV), warming treatment, and site using the lme4 package [76]. The model was coded as follows for each site data: lmer(RGR~1 + (1|temp_trt) + (1 | ASV), data = pertube.persite. ...
... Flux time series data were plotted in R using the package ggplot2 [79]. We performed linear mixed effects model in the package lme4 [76], using plot id and day as random effects to account for the repeated measures in each plot. For fixed effects, we used the main effects of treatment and site, and their interaction. ...
Ice-free terrestrial environments of the western Antarctic Peninsula are expanding and subject to colonization by new microorganisms and plants, which control biogeochemical cycling. Measuring growth rates of microbial populations and ecosystem carbon flux is critical for understanding how terrestrial ecosystems in Antarctica will respond to future warming. We implemented a field warming experiment in early (bare soil; +2 °C) and late (peat moss-dominated; +1.2 °C) successional glacier forefield sites on the western Antarctica Peninsula. We used quantitative stable isotope probing with H 2 ¹⁸ O using intact cores in situ to determine growth rate responses of bacterial taxa to short-term (1 month) warming. Warming increased the growth rates of bacterial communities at both sites, even doubling the number of taxa exhibiting significant growth at the early site. Growth responses varied among taxa. Despite that warming induced a similar response for bacterial relative growth rates overall, the warming effect on ecosystem carbon fluxes was stronger at the early successional site—likely driven by increased activity of autotrophs which switched the ecosystem from a carbon source to a carbon sink. At the late-successional site, warming caused a significant increase in growth rate of many Alphaproteobacteria , but a weaker and opposite gross ecosystem productivity response that decreased the carbon sink—indicating that the carbon flux rates were driven more strongly by the plant communities. Such changes to bacterial growth and ecosystem carbon cycling suggest that the terrestrial Antarctic Peninsula can respond fast to increases in temperature, which can have repercussions for long-term elemental cycling and carbon storage.
... The first analysis employed four linear mixed-effects models in R (R Core Team, 2023) using the lme4 package (Bates et al., 2023). Normalized F1, F2, F3, and duration (ms) comprised the dependent variables. ...
While many studies have previously conducted direct comparisons between results obtained from frequentist and Bayesian models, our research introduces a novel perspective by examining these models in the context of a small dataset comprising phonetic data. Specifically, we employed mixed-effects models and Bayesian regression models to explore differences between monolingual and bilingual populations in the acoustic values of produced vowels. Our findings revealed that Bayesian hypothesis testing exhibited superior accuracy in identifying evidence for differences compared to the posthoc test, which tended to underestimate the existence of such differences. These results align with a substantial body of previous research highlighting the advantages of Bayesian over frequentist models, thereby emphasizing the need for methodological reform. In conclusion, our study supports the assertion that Bayesian models are more suitable for investigating differences in small datasets of phonetic and/or linguistic data, suggesting that researchers in these fields may find greater reliability in utilizing such models for their analyses.
... To investigate whether infants' looking time response to changes in object identity and location was influenced by the presence of eye contact, we compared the fit of two generalized linear mixed models (GLMMs) with gamma distribution using likelihood ratio tests: a full model and a reduced model. We fitted the models using the R-package lme4 version 1.1-32 (Bates et al., 2020). We used GLMMs with a non-normal distribution to account for the right-skewed distribution of the looking time data (Lo & Andrews, 2015, for more details see section S1 in the Supplemental Materials). ...
Sharing joint visual attention to an object with another person biases infants to encode qualitatively different object properties compared to a parallel attention situation lacking interpersonal sharedness. This study investigated whether merely observing joint attention amongst others shows the same effect. In Experiment 1 (first-party replication experiment), N = 36 9-month-old German infants were presented with a violation-of-expectation task during which they saw an adult looking either in the direction of the infant (eye contact) or to the side (no eye contact) before and after looking at an object. Following an occlusion phase, infants saw one of three different outcomes: the same object reappeared at the same screen position (no change), the same object reappeared at a novel position (location change), or a novel object appeared at the same position (identity change). We found that infants looked longer at identity change outcomes (vs. no changes) in the “eye contact” condition compared to the “no eye contact” condition. In contrast, infants’ response to location changes was not influenced by the presence of eye contact. In Experiment 2, we found the same result pattern in a matched third-party design, in which another sample of N = 36 9-month-old German infants saw two adults establishing eye contact (or no eye contact) before alternating their gaze between an object and their partner without ever looking at the infant. These findings indicate that infants learn similarly from interacting with others and observing others interact, suggesting that infant cultural learning extends beyond infant-directed interactions.
... We calculated the neighbouring tree species diversity and phylogenetic diversity using 'vegan' (Oksanen et al., 2019) and 'picante' (Kembel et al., 2010) packages, respectively. GLMMs were fitted using the 'lme4' package (Bates et al., 2013). All analyses were performed in R 4.1.2 ...
Insect herbivory plays a critical role in the regulation of plant populations and community structures. Although the strength of insect herbivory varies with neighbouring tree diversity and identity, it is not clear to what extent insect guilds and leaf traits of host plants mediate the relationships, particularly in diverse natural forests.
In this study, we measured leaf herbivory by chewing and mining insect herbivores in 442 saplings of nine species of deciduous trees in a warm‐temperate montane forest. We censused neighbouring trees and measured five leaf traits known to influence herbivory (i.e. specific leaf area‐SLA, thickness, carbon: nitrogen ratio‐C:N ratio, sodium‐Na and silicon‐Si content) on a subset of saplings.
Only herbivory by leaf‐mining insects was influenced by the identity and diversity of neighbouring trees. Specifically, the incidence of leaf‐miners decreased with the phylogenetic diversity of neighbouring trees and increased with conspecific adult density in the vicinity of focal trees. Furthermore, leaf mining herbivory was positively correlated with the amount of Si in the leaves of focal saplings, and leaf chewing herbivory decreased with increasing C:N ratio in the leaves. In contrast to our hypothesis, the leaf traits of focal saplings did not serve as a functional link between tree diversity and insect herbivory.
Synthesis : Overall, this study highlights the importance of considering the specialisation of insect herbivores in understanding the impacts of the diversity and identity of neighbouring trees on the strength of insect herbivory.
... All analyses were conducted in R (R Core Team, 2021) and the following packages: afex (Singmann et al., 2023), beepr (Bååth & Dobbyn, 2018), brms (Bürkner et al., 2020), broom (Robinson et al., 2023), broom.mixed (Bolker & Robinson, 2022), car (Fox et al., 2023), cowplot (Wilke, 2020), faux (DeBruine et al., 2023), foreign (R Core Team et al., 2023), ggeffects (Lüdecke et al., 2023), lavaan (Rosseel et al., 2020), lme4 (Bates et al., 2020), MASS (Ripley et al., 2023), MBESS (Kelley, 2021), and tidyverse (Wickham & RStudio, 2019). The R code is available at https://osf.io/ektfd/. ...
While working memory capacity is associated with superior performance on a number of tasks, could it paradoxically sometimes be associated with suboptimal performance? Corbin et al. (2010, Judgment and Decision Making 5(2), 110–115) found that, in a between-subjects design, higher WMC is associated with a larger risky-choice framing effect, traditionally conceived of as a departure from rational principles. Such surprising findings are of potentially great theoretical importance; yet the original study was underpowered. In this registered report, we aimed to replicate and extend the original findings, by conducting an online experiment among 425 North Americans. To extend the findings beyond the specific single tasks used in the original study, we used three WMC tasks with different processing components and six framing problems involving human lives. In a close replication, the frame significantly interacted with neither the Ospan short absolute score nor the Ospan short partial score in predicting ratings on the disease-framing problem. Similarly, in an extended replication, a composite WMC score did not significantly interact with the frame in predicting ratings on three framing problems involving human lives. The Bayes factors showed that the data were 3 to 10 times more likely under the null hypothesis of no interaction between WMC and frame. Taken together, these findings show an absence of association between the between-subjects risky-choice framing effect and WMC. This outcome is compatible with four out of the six theoretical accounts we considered, and is uniquely predicted by the default-interventionist dual-process account and the pragmatic inference account. Further research can more rigorously pit conflicting predictions of these accounts against each other.
... Se utilizaron modelos lineales mixtos, con el paquete "lme4" (Bates et al., 2022) para analizar los efectos de las razas (Parda Alpina y Saanen) época (lluviosa y seca), horarios (mañana, mediodía y tarde), así como la interacción entre estos efectos y el animal como efecto aleatorio para las variables fisiológicas y productivas. La normalidad de los errores residuales en los modelos adoptados se probó utilizando la prueba de Shapiro-Wilks (1965), Anderson-Darling (1954) y el gráfico de cuantil-cuantil normal ('qqnorm{stats}') y el histograma ('hist{stats}'). ...
... Analyses were performed in R using the packages 'raster' (Hijmans and Etten 2014), 'rgdal' (Bivand et al., 2018), 'sf ' (Pebesma, 2018), 'dunn.test' (Dinno, 2017), 'lme4' (Bates et al., 2015), 'BHPMF' (https://github.com/fisw10/BHP-MF), 'plyr' (Wickham, 2011) and 'hypervolume' (Blonder et al., 2022). ...
Among the characteristics of alien plant species that are likely to influence invasion success, those that capture variation in relation to distribution and environmental requirements in their native range are of special interest. Similarly, traits such as maximum height, specifc leaf area (SLA) and seed dry mass, related respectively to vegetative growth, resource use strategy, and reproductive effort and dispersal ability, have been found to vary
with invasiveness. Australian Acacia species (‘wattles’) present an exceptional natural experiment for identifying traits linked with invasiveness, while applying the source-area framework and controlling for the environmental conditions within the native range. We combine large-scale data sets of the distribution and functional traits of wattles with high-resolution climate surfaces to re-examine the effect of range size, environmental niche breadths and functional traits in determining invasion status (not introduced, casual, naturalized, or invasive) in wattles. We extracted occurrence records of 1036 wattle species (96% of all species in the genus) in Australia from the Atlas of Living Australia. For each species, we calculated the range size through the minimum convex polygon, and environmental niche breadths by matching occurrence records with WorldClim long-term average climate conditions. We extracted trait values from AusTraits and gap-filled when certain values were not known. We compared the obtained values, grouping wattle species by their introduction (not introduced vs introduced species) and invasion statuses, and calculated functional hypervolumes for each of
the groups and overlaps between pairs of them. We found the performance of introduced wattle species to be profoundly influenced by their historical environment; species with broader distributions and climate niche breadths in their native range were more likely to become invasive. Trait strategies for wattles that enhance invasion consisted of maximizing plant height to promote competitive ability, displaying medium-to-high SLA values for enhanced photosynthetic activity and relative growth rate, and intermediate values of seed mass for successful establishment and sufficient seed output and dispersal.
... Following Jescheniak and Levelt, we analysed the experimental trials, where the word and the picture matched and participants responded yes (2604 trials in total). We evaluated the effects of word frequency on response times using linear mixed effects models (Baayen, Davidson, & Bates, 2008) using the lmer function of the lme4 package (version 1.1-26; Bates, Maechler, Bolker, & Walker, 2021) in RStudio (version 1.2.5042). Response times were predicted by Frequency (reference level: low vs. high), which was contrast coded (− 0.5, 0.5) and centered. ...
... As an exploratory analysis, we ran a linear mixed-effects model to investigate whether changes in autistic traits over time are associated with certain metabolites. Models were fit using the lme4 package [45]. Linear mixed-effects models contain numerous positive features, including modeling of random effects and handling of missing time points. ...
Autism Spectrum Disorder (ASD) is a diverse neurodevelopmental condition. Gene–environmental interactions in early stages of life might alter metabolic pathways, possibly contributing to ASD pathophysiology. Metabolomics may serve as a tool to identify underlying metabolic mechanisms contributing to ASD phenotype and could help to unravel its complex etiology. In a population-based, prospective cohort study among 783 mother–child pairs, cord blood serum concentrations of amino acids, non-esterified fatty acids, phospholipids, and carnitines were obtained using liquid chromatography coupled with tandem mass spectrometry. Autistic traits were measured at the children’s ages of 6 (n = 716) and 13 (n = 648) years using the parent-reported Social Responsiveness Scale. Lower cord blood concentrations of SM.C.39.2 and NEFA16:1/16:0 were associated with higher autistic traits among 6-year-old children, adjusted for sex and age at outcome. After more stringent adjustment for confounders, no significant associations of cord blood metabolites and autistic traits at ages 6 and 13 were detected. Differences in lipid metabolism (SM and NEFA) might be involved in ASD-related pathways and are worth further investigation.
... The R 2 was used to evaluate the magnitude of the MTAs effects. For each traits, the best linear unbiased predictor (BLUP) values were calculated using entry mean scores over different environments using the lme4 package (Bates et al. 2015). ...
Arabinoxylan (AX) and resistant starch (RS) are essential components of dietary fiber, that affect the nutritional value, health benefits, and end-use quality of wheat. Fully understanding their genetic basis is crucial for enhancing wheat quality through marker-assisted selection or other means. In this study, a genome-wide association study of AX-related traits i.e., total-arabinoxylan (TAX), water-extractable arabinoxylan (WEAX), and water un-extractable arabinoxylan (WUAX) of whole wheat flour (WWF) and refined wheat flour (RWF), as well as RS content was conducted using 205 elite wheat varieties (lines) with a composite map (24,355 SNPs) constructed with 90 K single nucleotide polymorphism (SNP) arrays. The broad-sense heritability (H2) of RS was 48.50%, whereas that of AX-related traits ranged from 55.66 to 77.23%. A total of 115 loci for RS and AX related traits, comprising 322 marker-trait associations (MTAs), were identified on all 21 chromosomes across four environments, explaining 5.52–12.40% of the phenotypic variance. Among them, 19 stable loci were significant in two or more environments, including one for RWF-TAX, six for RWF-WEAX, four for RWF-WUAX, three for WWF-TAX, two for WWF-WUAX, and three for RS. Furthermore, 17 co-located chromosomal regions related to the measured traits were stably detected in multiple environments. These findings may be used for further research and to improve wheat quality in wheat breeding programs.
... We conducted multilevel regression analysis (mixedeffect models) in R 4.1.0 using the 'lme4' package [38] to investigate the relationships between leisure walking behaviour and the streetscape indicators of green in the neighbourhood of a participant. We set the leisure walking hours per week as the dependent variable, and each of five neighbourhood indicators of green (green visibility of the whole range or four green visibility zones separated by latitude) as the independent variable in the regression analysis. ...
Background
It has been pointed out that eye-level greenery streetscape promotes leisure walking which is known to be a health -positive physical activity. Most previous studies have focused on the total amount of greenery in the eye-level streetscape to investigate its association with walking behaviour. While it is acknowledged that taller trees contribute to greener environments, providing enhanced physical and psychological comfort compared to lawns and shrubs, the examination of streetscape metrics specifically focused on greenery height remains largely unexplored. Therefore, this study examined the relationship between objective indicators of street greenery categorized by height from a pedestrian viewpoint and leisure walking time.
Methods
We created streetscape indices of street greenery using Google Street View Images at 50-m intervals in an urban area in Sendai City, Japan. The indices were classified into four ranges according to the latitude of the virtual hemisphere centred on the viewer. We then investigated their relationship to self-reported leisure walking.
Results
Positive associations were identified between the street greenery in higher positions and leisure walking time, while there was no significant association between the greenery in lower positions.
Conclusion
The findings indicated that streets with rich greenery in high positions may promote residents’ leisure walking, indicating that greenery in higher positions contributes to thermally comfortable and aesthetic streetscapes, thus promoting leisure walking. Increasing the amount of greenery in higher positions may encourage residents to increase the time spent leisure walking.
... We examined for collinearity among predictors with variance inflation factors but in every case, we found VIF to be lower than 5 (range 1.2 -3.7; see Table 2). All analyses were performed in R (R Core Team 2013); linear mixed-effect models were performed with package lme4 (Bates et al. 2023) and lmerTest (Kuznetsova et al. 2017). ...
Biogeographic rules illustrate linkages between selective pressures and morphological traits among species that occur along broad environmental (usually latitudinal) gradients. Most research on such rules consists of observational studies, lacking any forms of experimental control. Species invasions, especially those consisting of multiple, independent introductions, present a form of natural experiment by which these rules can be more rigorously assessed. Here, we investigate whether the morphological traits of both native and non-native invasive populations of Monk Parakeet, a widespread invasive parrot distributed in North America, follow Allen’s, Bergmann’s, and Gloger’s rules. Furthermore, we go beyond correlations between latitude and morphological traits, and investigate specific climatic variables pertaining to prevailing precipitation and temperature conditions for their effects on morphology. Analyzing morphological measurements from 148 study skins from North and South America, we found statistical support for latitudinal effects on body mass consistent with predictions from Bergmann’s rule, but no support for Allen’s rule as no effects of latitude on bill length were detected once we corrected it for body size. Our findings show that areas with warmer winters and higher precipitation were associated with smaller specimens with larger wings. We also found areas with higher minimum precipitation were associated with specimens with larger bills relative to body size, a pattern potentially related with feeding resources. We observed no relationship between plumage luminance and latitude or climatic variables, suggesting that monk parakeets do not adhere to Gloger’s rule.
... We compared the LMM from the lme4 R package 42,43 and the generalized linear mixed models with L1-penalization from the glmmLasso R package 44 . The glmmLasso models allow for further feature selection by reducing the weight of irrelevant features to zero 45 . ...
Drug development for mood disorders can greatly benefit from the development of robust, reliable, and objective biomarkers. The incorporation of smartphones and wearable devices in clinical trials provide a unique opportunity to monitor behavior in a non-invasive manner. The objective of this study is to identify the correlations between remotely monitored self-reported assessments and objectively measured activities with depression severity assessments often applied in clinical trials. 30 unipolar depressed patients and 29 age- and gender-matched healthy controls were enrolled in this study. Each participant’s daily physiological, physical, and social activity were monitored using a smartphone-based application (CHDR MORE™) for 3 weeks continuously. Self-reported depression anxiety stress scale-21 (DASS-21) and positive and negative affect schedule (PANAS) were administered via smartphone weekly and daily respectively. The structured interview guide for the Hamilton depression scale and inventory of depressive symptomatology–clinical rated (SIGHD-IDSC) was administered in-clinic weekly. Nested cross-validated linear mixed-effects models were used to identify the correlation between the CHDR MORE™ features with the weekly in-clinic SIGHD-IDSC scores. The SIGHD-IDSC regression model demonstrated an explained variance (R²) of 0.80, and a Root Mean Square Error (RMSE) of ± 15 points. The SIGHD-IDSC total scores were positively correlated with the DASS and mean steps-per-minute, and negatively correlated with the travel duration. Unobtrusive, remotely monitored behavior and self-reported outcomes are correlated with depression severity. While these features cannot replace the SIGHD-IDSC for estimating depression severity, it can serve as a complementary approach for assessing depression and drug effects outside the clinic.
... PERMANOVA was performed using the adonis2 function from the vegan package (Oksanen et al. 2019). LMMs were performed using the lmer function, and GLMMs were performed by using the glmer function from the lme4 package (Bates et al. 2013). We checked for overdispersion by using the testDispersion function from the DHARMa package (Hartig and Lohse 2020). ...
The colony performance of social insects is supported by an efficient allocation of tasks among workers in the colony. The division of labor among ant workers is linked to age and caste polyethism, however, only a few studies have shown the relationship between workers’ behavioral variation and task performance. In this study, we investigated the task syndrome by testing the relationship between behavioral traits with task performance and location switching (switching the performance of tasks from inside to outside the nest) in the same-age workers of Camponotus vagus ants. We also investigated the division of labor in workers with and without location switching by checking if each caste is characterized by specific behavioral traits or tasks. Moreover, we checked whether the difference in the worker’s body size and its lifespan can influence task performance. Our results support the existence of task syndrome in ant workers by showing how individuals with specific behavioral traits are more likely to perform specific tasks within the colony. Moreover, the time of location switching was correlated with the tasks performed by the workers ( brood care , selfgrooming and walking ) and their behavioral traits ( aggressiveness and total distance ). In addition, worker size and lifespan are shown to influence task performance by the workers. Altogether, our study underpins the relationship between the behavioral traits and the task allocation and performance of workers within an ant colony.
... Latency was log-transformed to better meet the assumptions of the model. For the model with number of attacks as the dependent variable, we ran a generalized linear mixed-effects model (GLMM) with logit link functions as implemented in the glmer functions in the lme4 package [43]. Since the variance increased quadratically with the mean, the number of attacks was modeled under a type II negative binomial distribution. ...
Over recent decades, substantial research has focused on fish cognitive evolution to increase our understanding of the evolution of the enormous diversity of cognitive abilities that exists in fishes. One important but understudied aspect of cognitive evolution is sexual dimorphism in cognitive abilities. Sex-specific variation in brain region morphology has been proposed to be an important mechanism in this context. However, it is also common to find sex-specific variation in behavior and cognition without associated differences in brain morphology among the sexes. The telencephalon is the major cognitive center in the vertebrate brain and variation in telencephalon size has been associated with variation in cognition. Here, we utilize recently developed guppy artificial selection lines with ca. 10% differences in relative telencephalon size to investigate whether similar responses to selection of the size of this region may affect cognitive abilities differently in males and females. To that end, we compared two ecologically relevant aspects of cognition, detour learning and binary spatial discrimination. We tested the significance of the interaction between telencephalon size and sex, and we found no sex-specific effects of evolutionary increases in telencephalon size in the cognitive abilities tested. This study indicates that no clear cognitive sex-specific effects occur in response to rapid selection of telencephalon size. We suggest that future research on sexual dimorphism in cognitive abilities in fish could use various cognitive tests and examine telencephalic sub-regions to gain a more comprehensive understanding of their evolution.
... All analyses from the subsequent sections were run in R software 4.2.2 (R Development Core Team 2022), using the packages 'lme4' (Bates et al. 2022), 'lmerTest' (Kuznetsova et al. 2020), 'pscl' (Jackman 2020) and 'car' (Fox et al. 2022), and the performance of such linear models was assessed using the package 'performance' (Lüdecke et al. 2023). To achieve normality of model residuals and error variance homoscedasticity, ESR, EMI, WBC, H/L ratio, number of polychromatic erythrocytes, total number of erythrocytic nuclear abnormalities and number of micronuclei in erythrocytes were log-transformed. ...
The utility of fresh green material in avian nests is still not fully understood. Potential explanations include the effects of plants’ volatile compounds on parasite reduction (nest protection hypothesis) or direct beneficial effects on nestling condition (drug hypothesis). We used correlative data collected during 2020 and 2021 in a Mediterranean population of blue tits (Cyanistes caeruleus) as well as experimental data (aromatic nest content manipulation) to assess the effects of aromatic plant use on nestling physiological condition and survival, nest-dwelling ectoparasitic pressure and its relationship with breeding parameters. We found that aromatic plants were disproportionally used in relation to their abundance in the environment and that their use was positively related to egg mass (but only in 2020). Blowflies and facultative parasitic mites were more frequent in nests with aromatics compared to nests without aromatics, but obligatory parasitic mites were less abundant in nests with aromatics. However, no effects of aromatic plants were observed on nestling haemoglobin levels nor erythrocyte sedimentation rate or other physiological health metrics, but the heterophil to lymphocyte ratio was higher in nests with the highest quantity of aromatics. The artificial addition of mint reduced the flea abundance, but 7-day old nestlings showed significantly lower colour saturation and brightness in the mouth flange. Nestling survival to fledging was not related to aromatic plant use. Therefore, our results partially support a beneficial effect of aromatic plants in blue tit nests because some ectoparasite groups were reduced. Immediate effects on nestling physiology or survival could not be established.
Significance statement
Some avian species place fresh aromatic plant material in their nests, and several non-mutually exclusive hypotheses have been proposed to explain its potential functions. In this study, we use both correlational and experimental data from a blue tit population to test two hypotheses, namely the ‘nest protection hypothesis’ and the ‘drug hypothesis’. The first one proposes that aromatic plants have direct repellent effects against ectoparasites, while the latter poses that these plant components benefit nestling condition through the stimulation of some components of the immune system. Our results suggest that some ectoparasites, such as fleas and obligatory parasitic mites, were less abundant in nests where aromatic plants were artificially or naturally added, respectively, but no relationships were detected with nestling physiology or survival, which could be partially explained by our small sample size. Our study partially supports a beneficial effect of aromatic plants in avian nests.
... Generalized linear mixed models (GLMMs) were conducted using the lme4 package (Bates et al., 2014). Biotope type was included as a fixed parameter in all models and plantation estate as a random parameter to account for spatial autocorrelation (Fig. 2). ...
Studies examining changes in functional diversity and trait composition for soil arthropods are limited yet crucial for understanding the effects of land-use change. To determine whether plantation forestry drives functional homogenization of soil biota, we compared the taxonomic and functional diversity of ants and springtails between natural (indigenous forests and grasslands) and transformed (Eucalyptus plantations) biotopes. The prevalence of morphological and ecological traits in natural vs. transformed biotopes was also assessed. The study was conducted in two environmentally contrasting regions: high elevation areas with clay soils and coastal areas with sandy soils, in KwaZulu-Natal, South Africa. Surprisingly, the Eucalyptus compartments generally had similar levels of taxonomic and functional diversity as indigenous forests and/or grasslands. However, there were shifts in traits between the three biotopes, with each biotope supporting arthropods with traits suited to the environmental conditions in the biotope. Some traits were representative of the natural biotopes, and others of the plantation compartments. As a functionally diverse component of soil biodiversity is present in the plantations , it is indicative that these plantations have seemingly high levels of ecosystem stability and functioning. Arthropod traits compatible with the different environments appear to allow them to persist in high diversity across the landscape mosaic. These results suggest that enhancing landscape heterogeneity in a production landscape increases taxonomic and functional diversity of soil arthropods by creating a large-scale, spatial mosaic of complementary conditions for species with different habitat requirements.
... We fit generalized linear mixed models (GLMM) to the data to test for statistical significance in the chili fence's ability to deter elephants from entering crop fields compared to its control using the lme4 package in R (Bates et al., 2015). Fence type was set as a fixed effect, and trial (the experimental period), block, and interaction between trial and block were set as random effects to account for potential variances. ...
As human–elephant coexistence is challenged across Africa and Asia, conservationists seek methods to mitigate elephant crop raiding. Farmers rely on their crops for sustenance, and crop raiding events can destroy harvests. To mitigate these conflicts, deterrent fences continue to be developed. Modern deterrent techniques incorporate improved understanding of elephant biology, including their reliance on chemical signals. The construction of deterrent fences with cloths soaked in chili pepper extracts with high Scoville heat units (SHU) and used engine oil has become widespread but with variable effectiveness. However, the active levels of capsaicinoids in these mixtures and the rate of degradation of these compounds remain largely unexplored. In Kenya, our field experiments found that chili fences performed less effectively than desired possibly due to environmental conditions. In the lab, we evaluated SHU from chili peppers in three preparation recipes (vodka, water, and oil) and found that mixing with oil was crucial for increased solubility. We simulated a chili fence in the lab and detected no significant SHU loss over 7 days, which has positive implications for fence maintenance. Continuous exploration of the applications of chemical ecology to major conservation issues such as crop raiding can benefit humans and wildlife globally.
... Subsequently, to investigate whether region variation was responsible for generating most of the variability in the formant model, we ran eight separate linear mixed models [57] in R (v. 4.1.2 [58]). ...
Variation in formant frequencies has been shown to affect social interactions and sexual competition in a range of avian species. Yet, the anatomical bases of this variation are poorly understood. Here, we investigated the morphological correlates of formants production in the vocal apparatus of African penguins. We modelled the geometry of the supra-syringeal vocal tract of 20 specimens to generate a population of virtual vocal tracts with varying dimensions. We then estimated the acoustic response of these virtual vocal tracts and extracted the centre frequency of the first four predicted formants. We demonstrate that: (i) variation in length and cross-sectional area of vocal tracts strongly affects the formant pattern, (ii) the tracheal region determines most of this variation, and (iii) the skeletal size of penguins does not correlate with the trachea length and consequently has relatively little effect on formants. We conclude that in African penguins, while the variation in vocal tract geometry generates variation in resonant frequencies supporting the discrimination of conspecifics, such variation does not provide information on the emitter's body size. Overall, our findings advance our understanding of the role of formant frequencies in bird vocal communication.
... The R package mostly used for LME is lme4 (Bates et al., 2022), often accessed through the lmerTest package (Kuznetsova et al., 2022), which provides p-values. We will need a new input file in long format, which contains all the information from Table 1. ...
In this tutorial, we provide guidelines for conducting linear mixed effects (LME) analysis for simple designs. First, we discuss how LME analyses compare to traditional t-tests, ANOVAs and linear regression when participants are the only random variable. Then we extend the discussion to studies in which researchers want to generalize across both participants and stimuli, to ensure that statistically significant effects are not due to a few of the stimuli used. For each analysis, we analyze a small toy dataset and provide information on conducting the analysis in R and in jamovi. We also summarize which standardized effect sizes can be calculated with the existing software. We hope the tutorial gives readers a good foundation for using LME analysis for the designs discussed and for extending it to more complex designs.
... GLMMs were performed using glmer and glmer.nb functions of the 'lme4' package (Bates and Maechler, 2013). The emmeans function ('emmeans' package) was used for sequential post-hoc comparisons among factor levels when performing LMM and GLMM analyses (Lenth, 2020). ...
Wood-pastures harbor critical natural and social values and are among the most ancient land use forms of
Europe. The crucial conservation value of these silvopastoral systems is generally contributed to their characteristic
landscape elements, the solitary trees, which provide microhabitats for a variety of organisms. However,
by accommodating four habitat types (grasslands, solitary trees, forests, and forest edges) on a relatively small
spatial scale, wood-pastures might host functionally and compositionally distinct arthropod communities, thus
enhancing the landscape-level biodiversity. To test this, we assessed the fine-scale microclimatic conditions of
the four different habitat types of three wood-pastures and investigated the effects of these conditions on ant
activity and community organization patterns. Besides microclimate, niche breadths (quantified by fourdimensional
niche hypervolumes), niche overlaps, and interspecific interactions were also considered to assess
the importance of interspecific competition in shaping the studied ant communities. The four habitat types
showed notable differences in the previous aspects, which resulted in different patterns of ant activity and
community organization. Posing ideal conditions (high solar irradiance and temperatures above 25 ◦C) for ant
activity, the grasslands were monopolized by usually 2–3 dominant species with large hypervolumes, while the subordinates mostly occurred under environmental extremities. Despite their vicinity to the grasslands, solitary
trees showed a different pattern, where in total 8 subordinate species associated with specific microclimates were
present. The forest edges hosted the most species-rich communities, with 18 species in total, where interspecific
interactions played a major role in shaping the activity patterns. A similar result was obtained for forests,
although the mild environmental conditions of these habitat types resulted in low overall ant activity. Our results
unveil that by posing various microclimatic and structural conditions, wood-pastures enable the coexistence of
four ecologically and functionally distinct communities, which makes them ideal targets for biodiversity
conservation.
... Mixed-effects modeling was the primary statistical modeling method. All models were fitted using the lme4 package (Bates et al., 2022; version 1.1-30) in R (R Core Team, 2021; version 4.2.1). The reported p-values were provided by the lmerTest package (Kuznetsova et al., 2020; version 3.1-3). ...
Clearly enunciated speech (relative to conversational, plain speech) involves articulatory and acoustic modifications that enhance auditory–visual (AV) segmental intelligibility. However, little research has explored clear-speech effects on the perception of suprasegmental properties such as lexical tone, particularly involving visual (facial) perception. Since tone production does not primarily rely on vocal tract configurations, tones may be less visually distinctive. Questions thus arise as to whether clear speech can enhance visual tone intelligibility, and if so, whether any intelligibility gain can be attributable to tone-specific category-enhancing (code-based) clear-speech cues or tone-general saliency-enhancing (signal-based) cues. The present study addresses these questions by examining the identification of clear and plain Mandarin tones with visual-only, auditory-only, and AV input modalities by native (Mandarin) and nonnative (English) perceivers. Results show that code-based visual and acoustic clear tone modifications, although limited, affect both native and nonnative intelligibility, with category-enhancing cues increasing intelligibility and category-blurring cues decreasing intelligibility. In contrast, signal-based cues, which are extensively available, do not benefit native intelligibility, although they contribute to nonnative intelligibility gain. These findings demonstrate that linguistically relevant visual tonal cues are existent. In clear speech, such tone category-enhancing cues are incorporated with saliency-enhancing cues across AV modalities for intelligibility improvements.
Human activities and infrastructures can disturb wildlife and alter their behaviour by triggering anti-predator responses such as changes in time allocation to different behaviours. For instance, disturbance sources like traffic can cause significant variation in allocation of time to vigilance and foraging behaviours , which can be used as sensitive measures of the effects of human disturbance on animals. Such changes may ultimately result in physiological and ecological costs for the species. We used a unique opportunity to obtain direct behavioural observations of European wildcats, Felis silvestris, in the Can-tabrian Mountains (northwest Spain) to investigate how different sources of anthropogenic disturbance influence time allocation of wildcats to specific behaviours. We also analysed how traffic affects hunting and vigilance time budgets as well as hunting success. We found that wildcats allocated more time to being alert and less time to hunting, feeding and moving in the presence of humans than in undisturbed situations. Wildcats also allocated more time to hunting when traffic levels were high, near roads and further from villages. Similarly, they dedicated more time to vigilance behaviours while feeding in the presence of moving vehicles. Finally, hunting success in the presence of vehicles seemed to decrease more for female wildcats than for males although this effect was not significant. In conclusion, humans and traffic influence the behaviour of wildcats inhabiting pastoral anthropogenic landscapes, although it is difficult to know to what extent such changes may translate into demographic effects.
Quantifying the rate of metabolic energy expenditure (Ṁ) of varied aerobic exercise modalities is important for optimizing fueling and performance and maintaining safety in military personnel operating in extreme conditions. However, although equations exist for estimating oxygen uptake during running, surprisingly, there are no general equations that estimate Ṁ. Our purpose was to generate a general equation for estimating Ṁ during level running in healthy, military-age (18-44 years) women and men. We compiled indirect calorimetry data collected during treadmill running from 3 types of sources: original individual subject data (n 5 45), published individual subject data (30 studies; n 5 421), and published group mean data (20 studies, n 5 619). Linear and quadratic equations were fit on the aggregated data set using a mixed-effects modeling approach. A chi-squared (x 2) difference test was conducted to determine whether the more complex quadratic equation was justified (p , 0.05). Our primary indicator of model goodness-of-fit was the root-mean-square deviation (RMSD). We also examined whether individual characteristics (age, height, body mass, and maximal oxygen uptake [VȮ 2max ]) could minimize prediction errors. The compiled data set exhibited considerable variability in Ṁ (14.54 6 3.52 W·kg 21), respiratory exchange ratios (0.89 6 0.06), and running speeds (3.50 6 0.86 m·s 21). The quadratic regression equation had reduced residual sum of squares compared with the linear fit (x 2 , 3,484; p , 0.001), with higher combined accuracy and precision (RMSD, 1.31 vs. 1.33 W·kg 21). Age (p 5 0.034), height (p 5 0.026), and body mass (p 5 0.019) were associated with the magnitude of under and overestimation, which was not the case for VȮ 2max (p 5 0.898). The newly derived running energy expenditure estimation (RE3) model accurately predicts level running Ṁ at speeds from 1.78 to 5.70 m·s 21 in healthy, military-age women and men. Users can rely on the following equations for improved predictions of running Ṁ as a function of running speed (S, m·s 21) in either watts (W·kg 21 5 4.43 + 1.51·S + 0.37·S 2) or kilocalories per minute (kcal·kg 21 ·min 21 5 308.8 + 105.2·S + 25.58·S 2).
The prevalence of avian influenza viruses (AIVs) is commonly found to increase dramatically from farms to live bird markets (LBMs). Viral transmission dynamics along marketing chains is, however, poorly understood. To address this gap, we implemented a field experiment altering chicken supply to an LBM in Chattogram, Bangladesh. Chickens traded along altered (intervention) and conventional (control) marketing chains were tested for AIVs. Upon arrival at the LBM, the odds of detecting AIVs did not differ between control and intervention groups. However, 12 hours later, intervention group odds were lower, particularly for broiler chickens, indicating that viral shedding in LBM resulted partly from infections during transport and trade. Curtailing AIV prevalence in LBMs requires mitigating risk in marketing chain nodes preceding chickens’ delivery at LBMs.
Article Summary Line
The high prevalence of avian influenza viruses in marketed chickens cannot be solely attributed to viral transmission within live bird markets but is also influenced by infections occurring prior to the chickens’ supply to these markets.
Over the past decades, the Western workforce has experienced two notable demographic shifts: there has been an increase in the percentage of women occupying leadership roles and the workforce is aging. Considering these two trends in unison, it would be intuitive that the future workforce will be defined by an increasingly age and gender-diverse group of leaders. However, although the general percentage of female leaders has increased, this percentage decreases sharply in upper leadership and executive roles. The current theory on barriers to female leadership ascension contains conflicting propositions and has largely examined gender issues in isolation from other factors (i.e., age stereotypes). We aim to create consensus across the literature on age and gender-based leader prototypes by investigating intersectional role-congruity bias as a predictor of barriers to career advancement for age and gender-diverse individuals. We integrate fundamental propositions from role congruity theory within an intersectional framework to examine the joint influence that age- and gender-based agentic-communal role norms exert on leadership evaluations. Through the application of experimental vignette methodology across two studies ( N 1 = 163, N 2 = 466), our results suggest that (a) the positive effect of age on leadership prototypicality is attenuated for women, (b) traditional biases associated with female leadership are dependent upon age, and (c) male leaders receive a consistent and age-dependent bonus in ratings when displaying gender atypical communal behaviors. Implications for practice and research are discussed.
The escalating industrial and artisanal extraction of natural resources in the Amazon Basin has centered it into the spotlight of global environmental concern. This study deals with the environmental problems of heavy metals pollution and biomagnification, which stem from mining, agricultural, petrochemical, and industrial discharges. We conducted an extensive investigation, analyzing 360 fish specimens representing 58 species, to assess the concentrations of 11 metals (Al, As, Cd, Cr, Cu, He, Mn, Ni, Pb, Zn, and Hg) along the Ecuadorian sections of the Napo and Pastaza watersheds. Stable isotope analyses (δ15N and δ13C) were employed to determine their trophic positions and potential biomagnification risks. Sampling was carried out during two distinct hydrological seasons to capture seasonal variations in metal concentrations. Furthermore, we estimated species-specific daily heavy metal intake levels. The results of our study revealed that 15 fish species and 53 individual specimens exhibited heavy metal concentrations surpassing recommended standards, with elevated levels of Al, As, and Hg posing significant risks to human consumers with daily intakes of 0.46 kg/day. Notably, our investigation unveiled concerning trends, including increased metal concentrations, Hg biomagnification within fish populations from the Pastaza watershed, and an association between smaller fish size and higher metal content. This study provides a crucial baseline for monitoring future environmental changes and understanding the persistent impacts of heavy metal pollution in the Ecuadorian Amazon region and the broader Western Amazon. It underscores the urgent need for sustainable environmental management practices to mitigate the escalating threat to these vital ecosystems.
Mass bleaching events and local anthropogenic influences have changed the benthic communities of many coral reefs with pronounced spatial differences that are linked to resilience patterns. The Gulf of Thailand is an under-investigated region with only few existing datasets containing long-term developments of coral reef communities using the same method at fixed sites. We thus analyzed benthic community data from seven reefs surrounding the island of Koh Phangan collected between 2014 and 2022. Findings revealed that the average live hard coral cover around Koh Phangan increased from 37% to 55% over the observation period, while turf algae cover decreased from 52% to 29%, indicating some recovery of local reefs. This corresponds to a mean increased rate of coral cover by 2.2% per year. The increase in live hard coral cover was mainly driven by plate-like corals, which quadrupled in proportion over the last decade from 7% to 28% while branching corals decreased in proportion from 9% to 2%. Furthermore, the hard coral genus richness increased, indicating an increased hard coral diversity. While in other reefs, increasing live hard coral cover is often attributed to fast-growing, branching coral species, considered more susceptible to bleaching and other disturbances, the reefs around Koh Phangan recovered mainly via growth of plate-like corals, particularly of the genus Montipora . Although plate-like morphologies are not necessarily more bleaching tolerant, they are important for supporting reef fish abundance and structural complexity on reefs, aiding reef recovery and sturdiness. Hence, our findings indicate that the intensity of local stressors around Kho Phangan allows reef recovery driven by some hard coral species.
Little is known about the effect of pre‐reading exposure on collocational learning. This study used eye‐tracking and offline measures (form recall and recognition) to explore the effectiveness of pre‐reading study and reading exposure on the processing and learning of novel collocations. Three learning conditions were evaluated: reading‐only (target items were simply embedded in sentences), study‐only (explicit learning of target items), and pre‐reading study plus reading (explicit learning of target items followed by reading). Pre‐reading study plus reading was the most effective learning condition, while reading‐only was more effective than study‐only. More specifically, studying collocations before reading led to increased attention when encountering the same collocation in subsequent reading. Furthermore, greater attention, in the pre‐reading study phase, as indicated by fixations, was associated with larger collocational gains.
A mandatory tomato-free period (TFP) was implemented in the state of Goiás, Brazil, in 2007 to help manage diseases caused by whitefly-transmitted begomoviruses. The impact of the TFP was examined in five locations across three states in Central Brazil from 2013-2016. Surveys revealed significant differences in begomovirus disease incidence among locations, i.e., low in Guaíra-TFP and Patos de Minas-TFP, moderate-high in Itaberaí-TFP and Morrinhos-TFP, and high in the non-TFP (NTFP) control, Cristalina-NTFP. PCR tests and DNA sequencing were used to validate the symptoms, and showed that all collected symptomatic plant samples were infected with tomato severe rugose virus (ToSRV), a common indigenous bipartite begomovirus. Early season surveys (20-40 days after transplants [DAT]) in Itaberaí-TFP and Morrinhos-TFP revealed significantly less begomovirus disease in fields established sooner after the TFP (0-2 months) compared with incidences in (i) equivalent early-planted fields in the Cristalina-NTFP control; and (ii) in fields established longer after the end of the TFP (>2-5 months). Whitefly infestation of crops was detected year-round in all locations and years, and all tested adults were classified in the Bemisia tabaci MEAM1 cryptic species. Infestation levels were significantly higher during the summer, but did not vary significantly among locations. Results of monthly monitoring of adult whiteflies for general begomovirus and ToSRV detection was positively correlated, and was an indicator of disease incidence in the field. Notably, ToSRV was not detected in whiteflies collected from non-tomato plants during the TFP, and there was a longer lag period before detection in whiteflies collected from processing tomatoes for Itaberaí-TFP and Morrinhos-TFP compared with Cristalina-NTFP. Taken together with the low levels of ToSRV infection detected in potential non-tomato reservoir hosts at all locations, our results revealed low levels of primary inoculum during the TFP. Thus, even in a complex agroecosystem with year-round whitefly infestation of crops, the TFP was beneficial because of delayed and reduced begomovirus disease pressure during a critical stage of plant development (first month) and for favoring low levels of primary inoculum. Thus, we concluded that the TFP should be part of a regional IPM program targeting ToSRV in Brazil.
Beneficial Microorganisms for Corals (BMCs), or probiotics, enhance coral resilience against stressors in laboratory trials, being the only sustainable treatment currently explored to retain threatened native corals. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. To elucidate this, we inoculated BMCs on Pocillopora verrucosa colonies in situ in the Red Sea for three months. BMCs significantly influenced the coral microbiome, while those of the surrounding seawater and sediment appeared unchanged. The inoculated genera Halomonas and Pseudoalteromonas were significantly enriched in probiotic-treated corals. Furthermore, probiotic treatment correlated with an increase in beneficial groups (e.g., Ruegeria and Limosilactobacillus ), while potential coral pathogens, like Vibrio , decreased in abundance. Notably, treated and non-treated corals remained healthy throughout the experiment. Our data indicate the feasibility of using probiotics in real-world conservation efforts through beneficial restructuring of the coral microbiome without off-target changes in the surrounding environment.
Mercury (Hg) is a toxic contaminant that has been mobilized and distributed worldwide and is a threat to many wildlife species. Amphibians are facing unprecedented global declines due to many threats including contaminants. While the biphasic life history of many amphibians creates a potential nexus for methylmercury (MeHg) exposure in aquatic habitats and subsequent health effects, the broad-scale distribution of MeHg exposure in amphibians remains unknown. We used nonlethal sampling to assess MeHg
bioaccumulation in 3,241 juvenile and adult amphibians during 2017−2021. We sampled 26 populations (14 species) across 11 states in the United States, including several imperiled species that could not have been sampled by traditional lethal methods. We examined whether life history traits of species and whether the concentration of total mercury in sediment or dragonflies could be used as indicators of MeHg bioaccumulation in amphibians. Methylmercury contamination was widespread, with a 33-fold difference in concentrations across sites. Variation among years and clustered subsites was less than variation across sites. Life history characteristics such as size, sex, and whether the amphibian was a frog, toad, newt, or other salamander were the factors most strongly associated with bioaccumulation. Total Hg in dragonflies was a reliable indicator of bioaccumulation of MeHg in amphibians (R2 ≥ 0.67), whereas total Hg in sediment was not (R2 ≤ 0.04). Our
study, the largest broad-scale assessment of MeHg bioaccumulation in amphibians, highlights methodological advances that allow for
nonlethal sampling of rare species and reveals immense variation among species, life histories, and sites. Our findings can help
identify sensitive populations and provide environmentally relevant concentrations for future studies to better quantify the potential
threats of MeHg to amphibians.
Restoration efforts often focus on changing the composition and structure of invaded plant communities, with two implicit assumptions: (1) functional interactions with species of other trophic levels, such as pollinators, will reassemble automatically when native plant diversity is restored and (2) restored communities will be more resilient to future stressors. However, the impact of restoration activities on pollinator richness, plant–pollinator interaction network structure, and network robustness is incompletely understood. Leveraging a restoration chronosequence in Pacific Northwest prairies, we examined the effects of restoration‐focused prescribed fire and native forb replanting on floral resources, pollinator visitation, and plant–pollinator network structure. We then simulated the effects of plant species loss/removal scenarios on secondary extinction cascades in the networks. Specifically, we explored three management‐relevant plant loss scenarios (removal of an abundant exotic forb, removal of an abundant forb designated a noxious weed, and loss of the rarest native forb) and compared them to control scenarios. Pyrodiversity and proportion of area recently burned increased the abundance and diversity of floral resources, with concomitant increases in pollinator visitation and diversity. Pyrodiversity also decreased network connectance and nestedness, increased modularity, and buffered networks against secondary extinction cascades. Rare forbs contributed disproportionately to network robustness in less restored prairies, while removal of typical “problem” plants like exotic and noxious species had relatively small impacts on network robustness, particularly in prairies with a long history of restoration activities. Restoration actions aimed mainly at improving the diversity and abundance of pollinator‐provisioning plants may also produce plant–pollinator networks with increased resilience to plant species losses.
Myrmecochory - seed dispersal by ants - is a mutualistic interaction in which ants attracted by seed appendices take them away from the parental plant location, where seeds usually have better development odds. Not all ant species benefit plants, and the mechanisms of those divergent outcomes are still unclear, especially from the perspective of microbial third parties. Here, we explore the effects of seed manipulation on fungi communities promoted by two ant species with contrasting effects on seed germination and antimicrobial cleaning strategies. We hypothesize that: i) fungi richness is higher in seeds manipulated by Acromyrmex subterraneus (species that negatively affect seed germination), followed by unmanipulated seeds and seeds manipulated by Atta sexdens (ant species that increase seed germination) and ii) seeds manipulated by A. sexdens, Ac. subterraneus and unmanipulated seeds present dissimilar fungi compositions. We identified fungal morphotypes in three groups of seeds: i) manipulated by A. sexdens ; ii) manipulated by Ac. subterraneus ; iii) unmanipulated. Seeds manipulated by Ac. subterraneus exhibited higher fungal richness than those manipulated by A. sexdens and unmanipulated seeds, indicating that the ant species known to impair germination increases the fungal load on seeds. Additionally, we found that A. sexdens ants were unable to reduce fungal richness compared to unmanipulated seeds. Furthermore, fungal composition differed among all three treatments. Our results underscore the significance of ant species identity in shaping the fungal communities associated with myrmecochorous seeds. Given the potential influence of microbial infection on seed fate, we suggest considering manipulation strategies when evaluating the overall quality of an ant as a seed disperser.
Habitat conversion and climate change are fundamental drivers of biodiversity loss worldwide but are often analyzed in isolation. We used a continental-scale, decades-long database of more than 150,000 bird nesting attempts to explore how extreme heat affects avian reproduction in forests, grasslands, and agricultural and developed areas across the US. We found that in forests, extreme heat increased nest success, but birds nesting in agricultural settings were much less likely to successfully fledge young when temperatures reached anomalously high levels. Species that build exposed cup nests and species of higher conservation concern were particularly vulnerable to maximum temperature anomalies in agricultural settings. Finally, future projections suggested that ongoing climate change may exacerbate the negative effects of habitat conversion on avian nesting success, thereby compromising conservation efforts in human-dominated landscapes.
Stimulation of deep brain areas can offer benefits against cognitive impairments associated with aging. So far, this was only possible via invasive methods accompanied by risks. Grossman et al. proposed a new noninvasive stimulation technique, transcranial temporal interference electric stimulation (tTIS), which can be steered to target and modulate activity of deep brain structures. Memory capacity depends on subcortical structures such as the hippocampus, hence, modulation of hippocampal activity could benefit declining cognitive functions. The current study investigates whether theta-burst patterned tTIS targeting the hippocampus influences performance of associative memory in older adults. We found that theta-burst patterned tTIS, but not the control stimulation, improved recollection time in a follow-up 24h after the stimulation, suggesting that theta-burst patterned tTIS can influence the efficiency of longer-term encoding. This outcome indicates that tTIS may provide a new noninvasive deep brain stimulation method to modulate senescent memory processes.
Soybean ( Glycine max ) productivity is significantly reduced by drought stress. Breeders are aiming to improve soybean grain yields both under well-watered (WW) and drought-stressed (DS) conditions, however, little is known about the genetic architecture of yield-related traits. Here, a panel of 188 soybean germplasm was used in a genome wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to yield-related traits including pod number per plant (PN), biomass per plant (BM) and seed weight per plant (SW). The SLAF-seq genotyping was conducted on the population and three phenotype traits were examined in WW and DS conditions in four environments. Based on best linear unbiased prediction (BLUP) data and individual environmental analyses, 39 SNPs were significantly associated with three soybean traits under two conditions, which were tagged to 26 genomic regions by linkage disequilibrium (LD) analysis. Of these, six QTLs qPN-WW19.1, qPN-DS8.8, qBM-WW1, qBM-DS17.4, qSW-WW4 and qSW-DS8 were identified controlling PN, BM and SW of soybean. There were larger proportions of favorable haplotypes for locus qPN-WW19.1 and qSW-WW4 rather than qBM-WW1, qBM-DS17.4, qPN-DS8.8 and qSW-DS8 in both landraces and improved cultivars. In addition, several putative candidate genes such as Glyma.19G211300 , Glyma.17G057100 and Glyma.04G124800 , encoding E3 ubiquitin-protein ligase BAH1, WRKY transcription factor 11 and protein zinc induced facilitator-like 1, respectively, were predicted. We propose that the further exploration of these locus will facilitate accelerating breeding for high-yield soybean cultivars.
A widespread view is that Artificial Intelligence cannot be creative. We tested this assumption by comparing human-generated ideas with those generated by six Generative Artificial Intelligence (GAI) chatbots: alpa.ai, Copy.ai, ChatGPT (versions 3 and 4), Studio.ai, and YouChat. Humans and a specifically trained AI indepen dently assessed the quality and quantity of ideas. We found no qualitative difference between AI and humangenerated creativity, although there are differences in how ideas are generated. Interestingly, 9.4 % of humans were more creative than the most creative GAI, GPT-4. Our findings suggest that GAIs are valuable assistants in the creative process. Continued research and development of GAI in creative tasks is crucial to fully understand this technology’s potential benefits and drawbacks in shaping the future of creativity. Finally, we discuss the question of whether GAIs are capable of being “truly” creative.
Background
Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season.
Methods
To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F 2:3 population.
Results
Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F 2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.
Background:
Clinical studies on medical cannabis (MC) treatment have shown sex-related differences, including higher susceptibility to adverse events among women and greater analgesia among men. Here, we used the Syqe metered-dose inhaler (MDI) and a single chemovar to analyze sex differences.
Methods:
A total of 1249 Israeli chronic pain patients were assessed for pain intensity, sleep and adverse events (AEs) over 240 days.
Results:
Following the first two weeks, no significant sex differences were found in the effectiveness or safety of MC treatment (p > 0.05). Inhaled Δ9-THC doses did not vary significantly between sexes (p > 0.05) except in the first month of treatment. Pain reduction and sleep improvement were similar for both sexes (p > 0.05). The overall rate of AEs was equal and relatively low at 10% (n = 65, 10% of women and n = 60, 10% of men; χ2 (1) = 0.05, p = 0.820). A secondary analysis of pharmacokinetic data showed no significant differences between sexes in Δ9-THC and its metabolite pharmacokinetics, cardiovascular measures, or AE severity (p > 0.05).
Conclusions:
Uniform MC treatment via the Syqe MDI showed no sex differences in short-term effectiveness, safety and pharmacokinetics, nor in long-term effects, under "real-life" conditions. These findings provide insights into MC treatment which may inform clinical practice and policy-making in the field.
The current study examines how bidialectalism influences non-native speech production. We compared monodialectal Mandarin Chinese with bidialectal Shanghai-Mandarin Chinese speakers in terms of their ability to produce easy and difficult American English vowels. The results showed a general advantage for the bidialectal group compared with the monodialectal group in the production of the vowel formants and duration of the easy English vowels [i] and [u]. However, for the English vowels [ɪ] and [ʊ] known to be difficult for Chinese learners of English, both groups experienced the same challenges in terms of accurately producing the formants of the target vowels. Nevertheless, the bidialectal Shanghai-Mandarin speakers were still better than the monodialectal Mandarin speakers in the durational aspect of the two difficult English vowels. The results are explained by the Second Language Linguistic Perception (L2LP) model and suggest that the bidialectal advantage in non-native speech acquisition is subject to the modulation of cross-linguistic difficulty of the target speech sounds.
Aphanomyces euteiches is the most damaging soilborne pea pathogen in France. Breeding of pea resistant varieties combining a diversity of quantitative trait loci (QTL) is a promising strategy considering previous research achievements in dissecting polygenic resistance to A. euteiches . The objective of this study was to provide an overview of the diversity of QTL and marker haplotypes for resistance to A. euteiches , by integrating a novel QTL mapping study in advanced backcross (AB) populations with previous QTL analyses and genome-wide association study (GWAS) using common markers. QTL analysis was performed in two AB populations derived from the cross between the susceptible spring pea variety “Eden” and the two new sources of partial resistance “E11” and “LISA”. The two AB populations were genotyped using 993 and 478 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for resistance to A. euteiches in controlled conditions and in infested fields at two locations. GWAS and QTL mapping previously reported in the pea-Aphanomyces collection and from four recombinant inbred line (RIL) populations, respectively, were updated using a total of 1,850 additional markers, including the markers used in the Eden x E11 and Eden x LISA populations analysis. A total of 29 resistance-associated SNPs and 171 resistance QTL were identified by GWAS and RIL or AB QTL analyses, respectively, which highlighted 10 consistent genetic regions confirming the previously reported QTL. No new consistent resistance QTL was detected from both Eden x E11 and Eden x LISA AB populations. However, a high diversity of resistance haplotypes was identified at 11 linkage disequilibrium (LD) blocks underlying consistent genetic regions, especially in 14 new sources of resistance from the pea-Aphanomyces collection. An accumulation of favorable haplotypes at these 11 blocks was confirmed in the most resistant pea lines of the collection. This study provides new SNP markers and rare haplotypes associated with the diversity of Aphanomyces root rot resistance QTL investigated, which will be useful for QTL pyramiding strategies to increase resistance levels in future pea varieties.
Previous research suggests that economic inequality has caused a wide range of negative societal impacts. However, little is known about how economic inequality influences prosocial behaviour as a socioecological environment determinant. In five studies ( N = 62,342), we examined whether economic inequality reduces prosocial behaviour by decreasing interpersonal trust and the moderation role of interpersonal targets. Studies 1, 2a, and 2b showed that interpersonal trust mediated the negative relationship between perceived economic inequality and prosocial behaviour. In Study 3, we used data from the World Values Survey to explore the relation between inequality and trust and found that it was moderated by the closeness of trust targets. In Study 4, we demonstrated that economic inequality only reduced trust and prosocial behaviour towards strangers, but not among friends and family. Taken together, the current research shed light on how economic inequality undermines trust and negatively impacts prosocial behaviour among different targets.
The drivers of susceptibility to damage and management effectiveness in reducing the biological-invasion costs remain poorly understood. We used InvaCost data describing the damage costs of, and management expenditure on, invasive species among 56 nations to test whether higher-income nations have more capacity to limit the damage incurred by invasive species by spending relatively more on management. We also tested whether nations with (i) weaker governance have a reduced capacity to manage invasive species, (ii) more educated citizens and/or greater technological/scientific output allow for improved incentives and ability to manage invasive species, and (iii) economies based on higher relative imports and resource dependencies are at greater risk of high costs. Applying generalised linear mixed-effects, boosted regression tree, and generalised least-squares models, we found that a country’s economic activity dictates its effectiveness of investing in the control and prevention of invasive species. Early-stage investment in management leads to a greater decline in relative future damage costs in higher-income countries. There was little evidence that relative corruption, education/technology/science, or reliance on primary production, altered a country’s capacity to limit relative damage through management, or its susceptibility to damage. Wealthier nations should therefore consider assisting countries with fewer resources to address biological invasions.
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