Article

lme4: Linear mixed-effects models using Eigen and S4

Authors:
To read the full-text of this research, you can request a copy directly from the authors.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... Analysis of the transcription results (i.e., correct or incorrect transcription of the non-word sequence) was performed with a mixed effects logistic regression model using R and the lme4 package (Bates et al., 2014). For all trials, a model was constructed with Participant Group (i.e., native Mandarin listeners, beginning Dutch learners and advanced Dutch learners), Tone Pair (i.e., six tone pairs and one segmental control condition) and their interaction as fixed effects (fixed effects are indicated with capital initial letters). ...
... Analyses of A scores were performed with a linear mixedeffects model using R and the lme4 package (Bates et al., 2014). A model was constructed with Participant Group (i.e., native Mandarin listeners, beginning Dutch learners, and advanced Dutch learners), Word Pairs (i.e., twelve tone pairs and four segmental conditions) and their interaction as fixed effects. ...
... The raw reaction times for correct responses was converted to logarithmic RT to achieve better normalcy. The analysis of log RT was also performed with a linear mixed effect model using R and the lme4 package (Bates et al., 2014). A model was constructed with Participant Group, Tone Pairs, and their interaction as fixed effects (fixed factors are indicated with capital initial letters). ...
Article
Full-text available
This study explores the difficulties in distinguishing different lexical tone contrasts at both sub-lexical and lexical levels for beginning and advanced Dutch learners of Mandarin, using a sequence-recall task and an auditory lexical decision task. In both tasks, the Tone 2-Tone 3 contrast is most prone to errors for both groups of learners. A significant improvement in the advanced group was found for this tone contrast in the sub-lexical sequence recall task, but not in the lexical decision task. This is taken as evidence that utilizing tones in on-line spoken word recognition is more complex and demanding for L2 learners than in a memory-based task. The results of the lexical decision task also revealed that advanced learners have developed a stronger sensitivity to Tone 1 compared to the other three tones, with Tone 4 showing the least sensitivity. These findings suggest different levels of robustness and distinctiveness for the representation of different lexical tones in L2 learners’ lexicon and consequently different levels of proficiency in integrating tones for lexical processing. The observed patterns of difficulty are potentially related to the acoustic characteristics of different lexical tone contrasts as well as to the interference of the suprasegmental features of learner’s native language (i.e., the tonal contrasts of Dutch intonation) on the acquisition of the Mandarin lexical tone contrasts.
... Analysis used R with the package ggplot2 [56] to plot density distributions of mal and female wing lengths by sample location. Wing length was analysed with linear mixed effects models using R packages lme4 [57] and lmerTest [58]. Wing length was log-trans formed to remove positive skew and heteroscedasticity in residuals. ...
... Sex Analysis used R with the package ggplot2 [56] to plot density distributions of male and female wing lengths by sample location. Wing length was analysed with linear mixed effects models using R packages lme4 [57] and lmerTest [58]. Wing length was log-transformed to remove positive skew and heteroscedasticity in residuals. ...
Article
Full-text available
OPEN ACCESS https://doi.org/10.3390/insects13070567 The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.
... The log-transformed RTs (3626 data points) were analyzed using mixed-effects modeling in R (Version 3.1.0; R Core Team, 2014) using the 'lme4' package (Bates et al., 2014). The model was built with one fixed factor (i.e., block condition [two levels: orthographically homogeneous and heterogeneous]), two random intercepts (i.e., participants and target pictures), and one control variable (i.e., presentation cycle [from 1 to 4 within a block]). ...
... The log-transformed RTs (3701 data points) were analyzed using mixed-effects modeling in R (Version 3.1.0; R Core Team, 2014) using the 'lme4' package (Bates et al., 2014). The model was first built and analyzed in the same way as in Experiment 1. ...
Article
Does the way a word is written influence its spoken production? Previous studies suggest that orthography is involved only when the orthographic representation is highly relevant during speaking (e.g., in reading-aloud tasks). To address this issue, we carried out two experiments using the blocked cyclic picture-naming paradigm. In both experiments, participants were asked to name pictures repeatedly in orthographically homogeneous or heterogeneous blocks. In the naming task, the written form was not shown; however, the radical of the first character overlapped between the four pictures in this block type. A facilitative orthographic effect was found when picture names shared part of their written forms, compared with the heterogeneous condition. This facilitative effect was independent of the position of orthographic overlap (i.e., the left, the lower, or the outer part of the character). These findings strongly suggest that orthography can influence speaking even when it is not highly relevant (i.e., during picture naming) and the orthographic effect is less likely to be attributed to strategic preparation.
... We constructed a negative binomial model with a 'log' link implemented with the function 'glmer.nb' from the R-package"lme4" (Bates et al. 2015) in which the number of observations of the Lined Seedeater per grid cell per month was the response variable, and percentage of precipitation occurring in the last quarter per grid cell was the main fixed effect. We also included the total number of records of all species per grid cell, as a proxy for sampling effort to account for differences in sampling effort between grid cells (adapted from Fletcher et al. 2005). ...
... The 95% confidence intervals were calculated using the function "confint.merMod from the 'lme4' R-package (Bates et al. 2015) with the 'Wald' method. To evaluate the model, we calculated marginal and conditional pseudo-R 2 adapted for generalised mixed effect models (Nakagawa, and Schielzeth 2013;Johnson 2014;Nakagawa et al. 2017), implemented with the function 'r.squaredGLMM' from the 'MuMIn' R-package (MuMIn 2020). ...
... Binary data (0s and 1s) were used in the statistical analyses for survival. Individual larva survived was recorded as 1 and individual death larva was recorded as 0. The effect of the treatments (control, PLA and PS) on the survival for Day 10 and Day 28 were analyzed with generalized linear fixed model fit by a maximum likelihood using a binominal distribution with the lme4 package in R-Statistical Software and the function glmer (Bates et al. 2014). Treatment was the factor, survival the response variable and individual was treated as a random factor nested within glass jar (replicate). ...
... Treatment was the factor, survival the response variable and individual was treated as a random factor nested within glass jar (replicate). The effect of treatment on development time was tested with a linear mixed model fitted by REML assuming a normal distribution using the lmer function in the lmer package in R (Bates et al., 2014). All the graphs were plotted with Statistica 10. ...
Thesis
Full-text available
Biodegradable plant-based plastics are made and used as a substitute for plastics made from petrochemicals. However, the negative impacts of plant-based plastics are not well studied. This study addressed the question as to whether or not corn-based microplastic beads affect the lifehistory traits of the harlequin fly Chironomus riparius, a species of non-biting midge. The effects of microplastic beads made from corn (polylactic acid: PLA) on the life history traits of chironomid larvae were compared against the effects of microplastic beads made from petrochemical (polystyrene: PS) and a control (without microplastic beads), by exposing them to artificial sediment spiked with PLA and PS for 10 days and 28 days exposures. The endpoints used in this research to determine performances of chironomid larvae were survival and development time. Results showed that there were no differences in survival between treatments after 10 days of exposure. However after 28 days of exposure chironomid larvae exposed to PS and PLA showed a trend for a significantly lower survival compared to the control without microplastics(P = 0.059). Development time of Day 28 exposure did not differ between any of the treatments: PS, PLA and control. Female chironomid larvae did however show a significantly longer development time but this was not affected by treatment. In summary, there were no differences between polylactic acid (PLA) and polystyrene (PS) based microplastics in terms of survival and development time.
... Variables with the best explanatory power were selected by stepAIC function in the R package MASS [48]. Linear regression models were performed by lmer and glmer functions in R package lme4 [49]. We used multi-model inference with the information criterion, corrected for small sample size (AICc) and predictor relative importance to rank our subset models in the package MuMIn (model.avg ...
Article
Full-text available
The European roller (Coracias garrulus) is an endangered species whose breeding in Serbia depends almost entirely on nest boxes. The aim of the present study was to assess the influence of prey availability and foraging habitat characteristics on nest-box occupancy and breeding parameters. Data from 20 roller foraging sites over 5 breeding seasons were used in a set of linear regression models to evaluate which factors affect the diversity and biomass of roller prey, as well as nest-box occupancy and breeding parameters. Our analyses revealed that prey availability parameters were significantly affected by the grazing regime and biophysical parameters. An area under grassland negatively affected nest-box occupancy, clutch size and fledging success. In contrast, grazing intensity showed positive effects. Although grazing negatively affected prey diversity and quantity, it potentially increased the likelihood of a successful hunt by forming short vegetation. These results indicate that the habitat characteristics linked to the ability of the species to hunt successfully should be considered when installing nest boxes as a part of the broader management of roller breeding sites. Furthermore, nest-box installation in open agricultural habitats other than grasslands should be considered in the conservation strategy for the species in Serbia.
... We explored the relationship between biomass, carbon sequestration rate and the patch attributes by performing GLMMs (R package lme4; Bates et al. 2014), using either biomass or carbon sequestration as dependent variables (square root-transformed to achieve normality), and the patch attributes as independent variables. The vegetation type was set as random factor. ...
Article
Full-text available
Coastal dune vegetation has been proved to contribute to several crucial ecosystem services, as coastal protection, water purification, recreation; conversely, its capacity to regulate the concentration of greenhouse gases received less attention. To fill this gap, the present work focalized on the assessment of the contribution of coastal dune herbaceous vegetation to carbon storage and carbon sequestration rate, also in relation to possible effects of disturbance. To this aim, we measured the dry biomass and carbon sequestration rate in three different vegetation types (foredune, dry grasslands, humid grasslands), and habitat patch attributes as proxies of the disturbance regime. Relationships between disturbance, and carbon storage and sequestration rate have been analysed by GLMMs. The target vegetation types did not equally contribute to the medium-long term sequestration of carbon with a gradient that increased from the seashore inlands and related to both the growth form and the strategy of resource acquisition of dominant species, and plant community attributes. Disturbance in the form of trampling negatively affected carbon sequestration rate. Results suggest that, when different plant communities are spatially interconnected, the landscape scale results in a better understanding of ecosystem dynamics, functioning and resistance to perturbations and allows to plan coherent management strategies.
... The effect of year was considered by using 'glm.er' function (Bates et al., 2021) in RStudio. ...
Article
Full-text available
Marine ecosystems are experiencing rapid shifts under climate change scenarios and baleen whales are vulnerable to environmental change, although not all impacts are yet clear. We identify how the migration behaviour of the Chagos whale, likely a pygmy blue whale (Balaenoptera musculus brevicauda), has changed in association with shifts in environmental factors. We used up to 18 years of continuous underwater acoustic recordings to analyse the relationships between whale acoustic presence and sea surface temperature (SST), chlorophyll-a concentration, El-Niño Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD). We compared these relationships between two independent sites Diego Garcia southeast (DGS) and Diego Garcia northwest (DGN) where Chagos whales are detected and are suspected to move interannually across the Chagos-Laccadive ridge. We showed that the number of whale songs detected increased on average by 7.7% and 12.6% annually at DGS and DGN respectively. At the DGS site, Chagos whales shifted their arrival time earlier by 4.2 ± 2.0 days/year ± SE and were detected for a longer period by 7.3 ± 1.2 days/year ± SE across 18 years. A larger number of songs were detected during periods of higher chlorophyll-a concentration, and with positive IOD phases. At the DGN site, we did not see an earlier shift in arrival and songs were not detected for a longer period across the 13 years. Whale presence at DGN had a weaker but opposite relationship with chlorophyll-a and IOD. The oceanic conditions in the Indian Ocean are predicted to change under future climate scenarios and this will likely influence Chagos whale migratory behaviour. Understanding how environmental factors influence whale movement patterns can help predict how whales may respond to future environmental change. We demonstrate the value of long-term acoustic monitoring of marine fauna to determine how they may be affected by changing environmental conditions.
... Vection onset and vection duration times were recorded by button press. Statistical analysis was conducted using R 1.2.5019 (R Core Team, 2019) using the 'lmer' function of the lme4 package (Bates et al., 2014) to perform linear mixed-effects analyses. EEG signal was recorded using a 64-channel Biosemi Active-Two system (BIOSEMI, https://www.biosemi.com/). ...
Conference Paper
Full-text available
The Effect of Cognitive Load on Vection and Cybersickness in VR and the neuronal correlates of Vection
... All analysis was performed in R (version 3.6.1) [27], using 'epitools' [28], 'binom' [29], 'wBoot' [30], and 'lme4' [31]. ...
Article
Full-text available
Purpose Cancer-related cognitive impairment (CRCI) is a recognised adverse consequence of cancer and its treatment. This study assessed the feasibility of collecting longitudinal data on cognition in patients with newly diagnosed, aggressive lymphoma undergoing standard therapy with curative intent via self-report, neuropsychological assessment, peripheral markers of inflammation, and neuroimaging. An exploration and description of patterns of cancer-related cognitive impairment over the course of treatment and recovery was also undertaken and will be reported separately. Methods Eligible participants completed repeated measures of cognition including self-report and neuropsychological assessment, and correlates of cognition including blood cell–based inflammatory markers, and neuroimaging at three pre-specified timepoints, time 1 (T1) — pre-treatment (treatment naïve), time 2 (T2) — mid-treatment, and time 3 (T3) — 6 to 8 weeks post-completion of treatment. Results 30/33 eligible patients (91%, 95% CI: 76%, 97%) were recruited over 10 months. The recruitment rate was 3 patients/month (95% CI: 2.0, 4.3 patients/month). Reasons for declining included feeling overwhelmed and rapid treatment commencement. Mean age was 57 years (SD = 17 years) and 16/30 (53%) were male. Most patients (20/30, 67%) had diffuse large B cell lymphoma or Hodgkin lymphoma (4/30, 13%). The neuroimaging sub-study was optional, 11/30 participants (37%) were eligible to take part, and all agreed. The remaining 19 participants were ineligible as their diagnostic PET/CT scan was completed prior. Retention and compliance with all assessments were 89 to 100% at all timepoints. Only one participant was withdrawn due to disease progression. Conclusions Findings from this study including excellent recruitment, retention, and compliance rates demonstrate it is feasible to longitudinally assess cognition in people with newly diagnosed aggressive lymphoma during their initial treatment and recovery to inform the development of future research to improve patient experiences and cognitive outcomes. Trial registration. Australian New Zealand Clinical Trials Registry ACTRN12619001649101.
... In this experiment, as well as the next, I used logistic mixed effects models with the maximal converging by-subject and by-item random effects structure (Barr et al., 2013), as implemented in the lme4 package (Bates et al., 2020). Models with a maximal random slope structure often failed to converge, in which case the slopes or slope interactions accounting for the least amount of variance were removed, until the model converged. ...
... To determine differences in activity frequency among species and hibernation stage, we used linear mixed-effects models using the lme4 package (Bates et al., 2017) in R 3.6.2 (R Development Core ...
Article
Full-text available
Prior to the introduction of white‐nose syndrome (WNS) to North America, temperate bats were thought to remain within hibernacula throughout most of the winter. However, recent research has shown that bats in the southeastern United States emerge regularly from hibernation and are active on the landscape, regardless of their WNS status. The relationship between winter activity and susceptibility to WNS has yet to be explored but warrants attention, as it may enable managers to implement targeted management for WNS‐affected species. We investigated this relationship by implanting 1346 passive integrated transponder (PIT) tags in four species that vary in their susceptibility to WNS. Based on PIT‐tag detections, three species entered hibernation from late October to early November. Bats were active at hibernacula entrances on days when midpoint temperatures ranged from −1.94 to 22.78°C (mean midpoint temperature = 8.70 ± 0.33°C). Eastern small‐footed bats (Myotis leibii), a species with low susceptibility to WNS, were active throughout winter, with a significant decrease in activity in mid‐hibernation (December 16 to February 15). Tricolored bats (Perimyotis subflavus), a species that is highly susceptible to WNS, exhibited an increase in activity beginning in mid‐hibernation and extending through late hibernation (February 16 to March 31). Indiana bats (M. sodalis), a species determined to have a medium–high susceptibility to WNS, remained on the landscape into early hibernation (November 1 to December 15), after which we did not record any again until the latter portion of mid‐hibernation. Finally, gray bats (M. grisescens), another species with low susceptibility to WNS, maintained low but regular levels of activity throughout winter. Given these results, we determined that emergence activity from hibernacula during winter is highly variable among bat species and our data will assist wildlife managers to make informed decisions regarding the timing of implementation of species‐specific conservation actions. Hibernating bats in eastern North America vary in their susceptibility to white‐nose syndrome, but mechanisms causing this variation are unclear. We investigated the relationship between activity during hibernation and susceptibility to white‐nose syndrome among four species of bats that vary in their susceptibility. We found that species with low susceptibility maintained regular activity levels throughout winter, albeit to different degrees. In comparison, medium‐high susceptibility species had pronounced activity levels during early and late hibernation.
... titre � time þ ð1jidÞ þ ε We implemented this model in R using the lme4 package [44]. Three serovars were identified by the MAT in the Lupidi et al. [25] point source outbreak, however, it was not clear which was the infecting serovar (likely due to cross-reactivity of the MAT). ...
Article
Background Leptospirosis is a zoonotic disease prevalent throughout the world, but with particularly high burden in Oceania (including the Pacific Island Countries and Territories). Leptospirosis is endemic in Fiji, with outbreaks often occurring following heavy rainfall and flooding. As a result of non-specific clinical manifestation and diagnostic challenges, cases are often misdiagnosed or under-ascertained. Furthermore, little is known about the duration of persistence of antibodies to leptospirosis, which has important clinical and epidemiological implications. Methodology and principal findings Using the results from a serosurvey conducted in Fiji in 2013, we fitted serocatalytic models to estimate the duration of antibody positivity and the force of infection (FOI, the rate at which susceptible individuals acquire infection or seroconversion), whilst accounting for seroreversion. Additionally, we estimated the most likely timing of infection. Using the reverse catalytic model, we estimated the duration of antibody persistence to be 8.33 years (4.76–12.50; assuming constant FOI) and 7.25 years (3.36–11.36; assuming time-varying FOI), which is longer than previous estimates. Using population age-structured seroprevalence data alone, we were not able to distinguish between these two models. However, by bringing in additional longitudinal data on antibody kinetics we were able to estimate the most likely time of infection, lending support to the time-varying FOI model. We found that most individuals who were antibody-positive in the 2013 serosurvey were likely to have been infected within the previous two years, and this finding is consistent with surveillance data showing high numbers of cases reported in 2012 and 2013. Conclusions This is the first study to use serocatalytic models to estimate the FOI and seroreversion rate for Leptospira infection. As well as providing an estimate for the duration of antibody positivity, we also present a novel method to estimate the most likely time of infection from seroprevalence data. These approaches can allow for richer, longitudinal information to be inferred from cross-sectional studies, and could be applied to other endemic diseases where antibody waning occurs.
... Since species' counts showed a negative binomial distribution, and to account for groups of sessions from the same 2-day visits of each month, general linear mixed-effects models using a log link negative binomial error distribution were used with the month as the random variable, using the "glmer.nb" function from "lme4" package 43,44 . Variable selection within the multivariate analysis was based on automated selection based on AIC using the function "dredge" from package "MuMIn" 45 , starting from a full model with all interactions between explanatory variables. ...
Article
Full-text available
The role of commensal birds in the epidemiology of pathogens in poultry farms remains unclear. Our study aimed to identify potential key species for interactions with domestic ducks on one free-range duck farm in southwest France. Methods combined direct individual observations on duck outdoor foraging areas, network analysis, and general linear mixed models of abundances. Results showed a wide diversity of wild bird species visiting foraging areas, heavily dominated in frequency by White wagtails (Motacilla alba) and Sparrows (Passer domesticus and Passer montanus). These also were the only species seen entering duck premises or perching on drinkers in the presence of ducks. Moreover, White wagtails were the species most frequently observed on the ground and in close proximity to ducks. Network analysis suggested the role of White wagtails and Sparrows in linking ducks to other wild birds on the farm. The abundance of White wagtails was positively associated with open vegetation, with the presence of ducks and particularly in the afternoon, while the abundance of Sparrows was positively associated only with the fall-winter season. By precisely characterising interactions, the study was able to identify few wild bird species which should be prioritized in infectious investigations at the interface with poultry.
... Both behavioral data and picture-locked ERP data from the two language switching tasks were analyzed with mixed-effects models in R using the lme4 package (Bates et al., 2014) and the lmerTest package (Kuznetsova et al., 2014). For each model, the fixed effects included task (mandatory, voluntary), language (L1, L2), type (repeat, switch) and their interactions. ...
Article
Full-text available
The present study measured event-related potentials (ERP) and behavioral performance to examine whether inhibitory control is involved in voluntary language switching, and if so, to explore the differences in inhibitory control between voluntary and mandatory language switching. Unbalanced Chinese-English bilinguals completed two picture naming tasks: one involving mandatory language switches and one in which participants could voluntarily switch between the two languages. Behavioral data showed significant switch costs and a reversed language dominance effect in both switching tasks. Critically, both effects were larger in mandatory compared to voluntary switching. ERP results revealed that neural switch costs during mandatory switching was significantly different than voluntary switching in both N2 and LPC amplitudes. In contrast, a significant difference in the reversed language dominance effect between both tasks was only observed in LPC amplitude. Together, these findings suggest the involvement of inhibitory control in both mandatory and voluntary language switching, but the degree of inhibition and the time-course of control processes between both tasks appear to be distinct.
... Spatial independence of all datasets was examined using the Mantel test of the ade4 package (Dray and Dufour, 2007). To test the effects, generalized linear mixed models (GLMMs), generalized linear models (GLMs), linear mixed models (LMMs) or linear models (LMs) or using the lme4 package (Bates et al., 2014) (Table 1) were performed depending on model distributions tested in the car package (Fox and Weisberg, 2017) (Table 1) and where applicable, plantation estate was included as random parameter (Fig. 1). Post hoc tests were conducted using the multcomp package (Bretz et al., 2008). ...
Article
Humanity relies on soil fauna for important ecosystem services, as such our soils need sustainable management to ensure long-term biotic viability. However, environmental factors influencing the distribution and diversity of soil fauna are poorly understood, which limits effective conservation management. To address this issue, we assessed the influence of variables at different spatial scales (site, soil, and landscape) in different biotopes (natural forest patches and grasslands) in two contrasting geographical regions (inland Midlands and coastal Zululand, South Africa) on ant and springtail diversity in large-scale conservation corridors among commercial plantations. Midlands sites, with complex topography and nutrient-rich and deep soils, had higher soil arthropod diversity than sandy, shallow Zululand soils. Indigenous forest and grassland supported complementary arthropod assemblages. The responses of arthropod diversity and assemblage composition to local environmental variables varied greatly among biotopes, taxa, and regions, but responses were more pronounced in the Midlands than in Zululand, and arthropods were more responsive to site- and soil-related variables than to landscape variables. Lower soil biodiversity in Zululand compared to the Midlands emphasizes that management efforts to limit further homogenization from inappropriate management is particularly important in this sandy region. Lack of common drivers of soil arthropod diversity suggests that conservation strategies need to be tailored to different locations. Nonetheless, the conservation of both indigenous forest and grassland, together with promotion of small-scale spatial heterogeneity, will maximally benefit the widest range of soil-inhabiting organisms.
... Generalized multilevel linear models also provide maximum flexibility (i.e., they allow for inclusion of continuous/categorical and time-varying/invariant predictors, complex interaction terms, nonlinear distribution of outcome variables, and controls for nonindependent data) and robustness (i.e., they provide unbiased estimates of parameters under a variety of conditions) when analyzing multilevel experimental data (Gelman & Hill, 2006;Hoffman & Rovine, 2007). Individual multilevel models were estimated for each outcome measure using the Lme4 package in R (Bates et al., 2014). Preliminary analysis of fluency data indicated that a nonzero inflated negative binomial distribution (i.e., a statistical distribution for count data with high variance or spread) best fit both SLD and non-SLD rate counts. ...
Article
Purpose Contemporary motor theories indicate that well-practiced movements are best performed automatically, without conscious attention or monitoring. We applied this perspective to speech production in school-age children and examined how dual-task conditions that engaged sustained attention affected speech fluency, speech rate, and language productivity in children with and without stuttering disorders. Method Participants included 47 children (19 children who stutter, 28 children who do not stutter) from 7 to 12 years of age. Children produced speech in two baseline conditions with no concurrent task and under a dual-task condition requiring sustained attention to on-screen stimuli. Measures of speech fluency, speech rate, and language productivity were obtained for each trial and compared across conditions and groups. Results Dual-task conditions resulted in a reduction in stutter-like disfluencies relative to the initial baseline speaking condition. Effects were similar for both groups of children and could not be attributed to decreases in language productivity or a simple order effect. Conclusions Findings suggest that diverting attention during the process of speech production enhances speech fluency in children, possibly by increasing the automaticity of motor speech sequences. Further research is needed to clarify neurophysiological mechanisms underlying these changes and to evaluate potential clinical applications of such effects. Supplemental Material https://doi.org/10.23641/asha.19945838
... 1.1-27.1, [69]) and 'glmmTMB' (v. 1.1.2.3, [70]) to run generalized linear mixed models (GLMMs) and generalized linear models (GLMs). ...
Article
Male–male relationships are mostly characterized by competition. However, males also cooperate with one another if socio-ecological conditions are suitable. Due to their male philopatry, the need for cooperation in home range defence and high degree of fission–fusion dynamics, spider monkeys provide an opportunity to investigate how male–male interactions are associated with socio-ecological factors, such as the presence of potentially receptive females, the degree of food availability and the likelihood of home range defence. We tested predictions about changes in social interactions between wild spider monkey males in relation to these factors. First, males did not change their interaction patterns when potentially receptive females were in the subgroup compared to when they were absent. Second, males tended to be less tolerant of one another when feeding, but spent more time grooming, in contact and proximity with one another when food availability was lower than when it was higher. Third, males exchanged fewer embraces, spent less time grooming, in proximity and in contact with one another, and spent more time vigilant at the home range boundary area than at other locations. Our findings contribute to the understanding of social flexibility and the importance of considering males in socio-ecological models of any group-living species.
... To obtain the decomposition of the variability according to the indicated model (Eq 3), the aov and lmer functions of the basic and lme4 libraries [21] were used. aov and lmer functions fit an ANOVA model using linear models for each factor involved in the experimental design, but aov uses ordinary least squares (OLS) estimation [22], and lmer uses restricted maximum likelihood REML (a version of the maximum likelihood (ML) method) [23]. ...
Article
Full-text available
Due to greater environmental awareness, domestic laundry habits are changing, and antimicrobial control by chemical methods has become an essential factor to compensate for the use of lower temperatures during washing machine cycles. Disinfectants added to laundry detergents are a preventive strategy to reduce the transmission of bacteria, fungi, and viruses in the home, correct aesthetic damage (e.g., spotting, discolouration, and staining), and control the microbial contamination that leads to malodour. In Europe, disinfectants are regulated by the EU Biocidal Products Regulation (No. 528/2012), which stipulates that antimicrobial efficacy must be evaluated according to standardized methods. Current European standards for laundry sanitization only apply to clinical settings (EN 16616: 2015) and are restricted to the main wash cycle. Therefore, there is a gap in the EU standards regarding the testing of product efficacy in household laundering. With the aim of addressing this gap, an international ring trial was organized to evaluate the robustness of a new method (prEN 17658) designed to test the efficacy of antimicrobial laundry products in a domestic setting. The seven participating laboratories were equipped with 5 different laboratory-scale devices to simulate the washing process, and they evaluated 7 microbial parameters for 2 experimental conditions and 3 levels of active substance. The analysis of data according to ISO 5725–2 and ISO 13528 demonstrated that the method was robust. All reproducibility standard deviation values were between 0.00 and 1.40 and the relative standard deviation indicates satisfactory reproducibility. Values of logarithmic reduction ranged from less than 2 log 10 for tests with water to more than 5 log 10 when disinfectants were added. The evidence generated by the ring trial was presented in a proposal for a standardized method under CEN/TC 216, in which the SOP used in the ring trial is referred to as the prEN 17658 phase 2 step 2 test method covering chemothermal textile disinfection in domestic settings.
... We used the lmer function in the R package lme4 for the following analyses (version 1.1-27.1, Bates et al., 2021). To test the predicted interaction effect of ambiguity and agreement on sentiment (Hypothesis 2), we regressed sentiment on parents' mean ambiguity and mean agreement and their interaction term, controlling for parents' mean sentiment. ...
Preprint
Full-text available
Discussions on social media have been considered a contributing factor to the increasing polarization the Western world is witnessing. In this study, we use automated and manual coding to analyze diplomatic behavior in online discussions and its consequences for polarization dynamics. We analyze Reddit forums with differing norms: reddits known for civil debate (N = 4594), reddits considered incivil discussion spaces (N = 2126), and reddits dedicated to social support (N = 1401). The automated content analysis shows diplomatic behavior in all forums, but diplomacy does not affect the subsequent discussion. The manual discourse analysis reveals why: discussions consist of disjointed statements rather than dialogic exchange, which makes diplomacy inconsequential. These results have consequences for the field. First, evidence of online polarization needs to be studied very closely, because what appears to be polarized dialogue might actually be a string of personal viewpoints broadcasted in a shared space. Second, the usefulness of automated content analysis in studying interaction dynamics is limited because of difficulties distinguishing broadcasting from dialogue.
... To test the effect of the source population and seed germination responses to the range of tested temperatures, for each species we performed GLMs with binomial error distribution and logit link function, setting temperature as numeric variable and population as factor (R Core Team, package lme4; Bates et al., 2014). For tests performed on integer seeds of C. arenaria, we included in the model also the photoperiod as factor. ...
Article
Full-text available
Within-species variation is a key component of biodiversity and linking it to climatic gradients may significantly improve our understanding of ecological processes. High variability can be expected in plant traits, but it is unclear to which extent it varies across populations under different climatic conditions. Here, we investigated seed trait variability and its environmental dependency across a latitudinal gradient of two widely distributed dune-engineering species ( Thinopyrum junceum and Calamagrostis arenaria ). Seed germination responses against temperature and seed mass were compared within and among six populations exposed to a gradient of temperature and precipitation regimes (Spiekeroog, DE; Bordeaux, FR; Valencia, ES; Cagliari, IT, Rome, IT; Venice, IT). Seed germination showed opposite trends in response to temperature experienced during emergence in both species: with some expectation, in populations exposed to severe winters, seed germination was warm-cued, whereas in populations from warm sites with dry summer, seed germination was cold-cued. In C. arenaria , variability in seed germination responses disappeared once the seed coat was incised. Seed mass from sites with low precipitation was smaller than that from sites with higher precipitation and was better explained by rainfall continentality than by aridity in summer. Within-population variability in seed germination accounted for 5 to 54%, while for seed mass it was lower than 40%. Seed trait variability can be considerable both within- and among-populations even at broad spatial scale. The variability may be hardly predictable since it only partially correlated with the analyzed climatic variables, and with expectation based on the climatic features of the seed site of origin. Considering seed traits variability in the analysis of ecological processes at both within- and among-population levels may help elucidate unclear patterns of species dynamics, thereby contributing to plan adequate measures to counteract biodiversity loss.
... For both LMMs, we used the "lme4" package (Bates et al. 2016) in R 3.3.0 software (RStudio Team 2020). ...
Article
Full-text available
Key message Leaf pigment concentration varied among populations, watersheds and between two consecutive years. The highest concentration of pigments was found in 2018, but both years showed the same trend among populations. Physiological, morphological and phenological attributes are potentially adaptive traits that determine functional responses to certain environmental conditions. They are crucial for understanding adaptations to environmental variation along a species natural range. Our goal was to evaluate the variation in pigment traits among Nothofagus alpina populations in a common garden trial to infer local adaptation. We also aimed to test variation in pigment traits between two consecutive years and to analyze the correlation between pigment and phenological traits (i.e., day of the year to bud burst and to beginning of senescence, growing degree days, growing season length). We analyzed 400 individuals (65 open-pollinated families) from eight natural populations coming from four lake watersheds comprising the species range in Argentina. Pigment traits were estimated using a spectrophotometer and analyzed with linear mixed models (LMMs). Significant differences among fixed factors (populations and watersheds) were found in chlorophyll a, chlorophyll b, total chlorophyll, carotenoids and anthocyanins concentrations. Two populations were always the most contrasting ones. These results and the influence of the family factor on the variance of the pigment traits are evidence of the genetic control as well as of the potential adaptive value of leaf pigment content in N. alpina, giving a base for adaptation to a long-lasting change in climate. The highest values for all pigments were found in 2018, but among populations they showed the same trend for both years. Significant correlations between the population means of pigment concentrations and phenological traits were found.
... The effects of school, age cohort and collection point (before and after) on children's wellbeing and resilience questionnaires were examined with generalised linear mixed models to account for influential random effects of individuals with Poisson error structure using the R package lme4 (Bates, Maechle, & Bolker, 2014). Interaction and statistical significance were gathered by removing terms sequentially and testing the significance between the models until a minimum model was achieved. ...
Article
Evidence increasingly demonstrates nature engagement benefits. However, little evidence shows nature engagement provides children with a reflective perception of biodiversity, nor whether perception influ- ences children’s wellbeing and resilience. We explored the impact of weekly nature engagement in schoolgrounds on 509 eight-to-eleven- year-olds’ biodiversity perception, wellbeing, and resilience. At the start and end of the academic year, wellbeing and resilience questionnaires were completed, and biodiversity perception was assessed by children drawing what they thought was in their schoolgrounds. Children initially perceived few organisms within easily visible taxa, and perceived more vertebrates compared to invertebrate species. After, children were more aware of taxa, resulting in a more reflective biodiversity perception. Children with initially low scores in wellbeing and resilience increased in these measures, and a positive association was found between increased invertebrates and vertebrates perception and improved resilience. Nature engagement within curriculum could reduce children’s extinction of experience and improve wellbeing and resilience.
... All diversity indices were calculated using the vegan package (Oksanen et al., 2019). GLMMs and LMMs were fitted using the lme4 package (Bates et al., 2013). ...
Article
Full-text available
There is mounting evidence that top‐down control by natural enemies helps maintain plant diversity in natural ecosystems. Previous work has concentrated on either forest trees or grassland herbs. Our knowledge of how natural enemies affect herb diversity in forests is limited. We used fungicides and insecticide to experimentally examine the effects of fungi and insects on herb abundance and diversity at the community‐wide scale, and within groups of species with certain traits. We also assessed how the effects of fungi and insects on herb assemblages were modified by neighbouring tree diversity and composition in an old‐growth temperate forest. We found that fungicides increased overall herb abundance by 7% while decreasing herb diversity by 5%. This effect of fungicides on both herb abundance and diversity weakened with the increase of neighbouring tree diversity. Insecticide did not affect either herb abundance or diversity noticeably, except in areas dominated by deciduous trees where insecticide application reduced herb diversity. Fungicides and insecticide decreased the diversity of relatively less defended species (i.e., thin‐leaved, and non‐clonal), but had no effect on the diversity of herbs with stronger defensive traits (i.e., thick‐leaved and clonal). Fungicides increased the abundance of non‐mycorrhizal (NM) species but not arbuscular‐ mycorrhizal (AM) species, although the effect of fungicides on herb diversity was unrelated to species’ mycorrhizal association. Insecticide had stronger effects on the abundance and diversity of NM species than AM species. Synthesis. We conclude that fungi and insect herbivores are critical to regulating herb abundance and diversity in this temperate forest, with their effects dependent on species’ traits and neighbouring tree diversity and composition. Our results highlight the importance of top‐down control of understory herb communities by natural enemies in temperate forests, advancing our understanding of the processes shaping plant diversity in natural ecosystems.
... Linear mixed effects models were generated using lme4, a statistical package in R (Bates et al., 2020). Each eye-movement parameter was predicted by a separate model with the three individual difference measure scores and task as fixed effects with by-participant random intercepts. ...
Article
Full-text available
When viewing scenes, observers differ in how long they linger at each fixation location and how far they move their eyes between fixations. What factors drive these differences in eye-movement behaviors? Previous work suggests individual differences in working memory capacity may influence fixation durations and saccade amplitudes. In the present study, participants (N = 98) performed two scene-viewing tasks, aesthetic judgment and memorization, while viewing 100 photographs of real-world scenes. Working memory capacity, working memory processing ability, and fluid intelligence were assessed with an operation span task, a memory updating task, and Raven’s Advanced Progressive Matrices, respectively. Across participants, we found significant effects of task on both fixation durations and saccade amplitudes. At the level of each individual participant, we also found a significant relationship between memory updating task performance and participants’ fixation duration distributions. However, we found no effect of fluid intelligence and no effect of working memory capacity on fixation duration or saccade amplitude distributions, inconsistent with previous findings. These results suggest that the ability to flexibly maintain and update working memory is strongly related to fixation duration behavior.
... (R Development Core Team 2018). We used the package 'lme4' to fit the GLMs (Bates et al. 2018) and the package 'MASS' to perform the glmer.nb function (Venables & Ripley 2002). ...
Article
Predation is one of the key factors shaping the dynamics of animal populations. In birds, nest loss due to predation can be a significant cause of low reproductive success. Ground‐nesting birds are among the bird groups most susceptible to predation, mainly because their nests are easily accessible to a broad suite of potential predators. For these birds, anthropogenic disturbances can generate changes in nest predation risk by altering their antipredator behaviour and also by altering behaviour of the predator species – i.e. the predator becoming much more aware of predation opportunities due to frequent disturbances and/or motivated to repeat predation attempts when some are successful. To date, most previous studies investigating this have focused on a single effect, either predation or disturbance, on chick survival. It remains unknown how the risk of predation with and without disturbance varies with chick age. In this study, we used behavioural observations to assess how the interaction between predators and disturbance affects predation risk in chicks and how this interacts with chick age. Specifically, we investigated the effect of disturbance caused by humans and stray dogs on the predation of Slender‐billed Gull (Chroicocephalus genei) chicks by Yellow‐legged Gulls (Larus michahellis), and whether this depended on the age of the chicks. Our results revealed that disturbance had a significant positive effect on predation measures of Slender‐billed Gull chicks by Yellow‐legged Gulls, but that this effect was mediated both by disturbance type and the age of chicks. Stray dogs entering the colony had a stronger disturbance effect on chicks than passing humans, increasing predation risk by Yellow‐legged Gulls. Our results also showed that chick age interacts with disturbance type to determine the predation risk. This is probably mediated by chicks’ capacity to escape predation by gathering in a single large crèche that runs into the water when disturbed. To preserve Slender‐billed Gull colonies in one of its few remaining breeding sites in Tunisia, and as gulls tend to react even when the disturbance occurs relatively far from the colonies, it is crucial to (1) restrict human access to dikes and islets where large colonies breed, and (2) construct artificial islets attractive to gulls and inaccessible to stray dogs.
... There were two instances in which the CI external coil was sitting directly under a source or detector optode; in these cases, those specific channels were removed from the data prior to the GLM analysis. Statistical analyses were performed on the GLM beta values using RStudio (RStudio Team, 2015) and the lme4 package (Bates et al., 2014). Linear mixedeffect modelling was performed with fixed effects of stimulus condition, region of interest, and chromophore, with a random effect of participant. ...
Article
Full-text available
Sensory deprivation causes structural and functional changes in the human brain. Cochlear implantation delivers immediate reintroduction of auditory sensory information. Previous reports have indicated that over a year is required for the brain to reestablish canonical cortical processing patterns after the reintroduction of auditory stimulation. We utilized functional near-infrared spectroscopy (fNIRS) to investigate brain activity to natural speech stimuli directly after cochlear implantation. We presented 12 cochlear implant recipients, who each had a minimum of 12 months of auditory deprivation, with unilateral auditory- and visual-speech stimuli. Regardless of the side of implantation, canonical responses were elicited primarily on the contralateral side of stimulation as early as 1 h after device activation. These data indicate that auditory pathway connections are sustained during periods of sensory deprivation in adults, and that typical cortical lateralization is observed immediately following the reintroduction of auditory sensory input.
... Linear mixed-effects regression models were fitted using the lmer function from the lme4 package (1.1-27.1) [66]. P-values were obtained using the sjPlot::tab_model function from the sjPlot package (2.8.9) [67]. ...
Article
Full-text available
Disgust is an aversive reaction protecting an organism from disease. People differ in how prone they are to experiencing it, and this fluctuates depending on how safe the environment is. Previous research has shown that the recognition and processing of disgusting words depends not on the word's disgust per se but rather on individual sensitivity to disgust. However , the influence of dynamically changing disgust on language comprehension has not yet been researched. In a series of studies, we investigated whether the media's portrayal of COVID-19 will affect subsequent language processing via changes in disgust. The participants were exposed to news headlines either depicting COVID-19 as a threat or downplay-ing it, and then rated single words for disgust and valence (Experiment 1; N = 83) or made a lexical decision (Experiment 2; N = 86). The headline type affected only word ratings and not lexical decisions, but political ideology and disgust proneness affected both. More liberal participants assigned higher disgust ratings after the headlines discounted the threat of COVID-19, whereas more conservative participants did so after the headlines emphasized it. We explain the results through the politicization and polarization of the pandemic. Further, political ideology was more predictive of reaction times in Experiment 2 than disgust prone-ness. High conservatism correlated with longer reaction times for disgusting and negative words, and the opposite was true for low conservatism. The results suggest that disgust proneness and political ideology dynamically interact with perceived environmental safety and have a measurable effect on language processing. Importantly, they also suggest that the media's stance on the pandemic and the political framing of the issue may affect the public response by increasing or decreasing our disgust.
... To determine the effects of sex, season, and the interaction of sex and season on cellular morphology and spine density, we used linear mixed models in the "lme4" (Bates et al. 2015) and "lmerTest" (Kuznetsova et al. 2017) packages in R v. 3.6.1 (R Core Team 2019) within the RStudio™ environment (RStudio Team 2019). First, we used sex, season, and the interaction effect between the two as fixed effects and animal as a random effect to account for measuring multiple neurons from each brain. ...
Article
Full-text available
Seasonally reproducing small mammals often undergo changes in brain anatomy throughout the year. Much of the research on this seasonal neuroplasticity has focused on changes in hippocampus volume and neurogenesis, with relatively little attention paid to neuronal morphology. Here, we test for sex, season and sex–season interaction effects on hippocampal neuron morphology and dendritic spine density in a seasonally reproducing rodent: Richardson’s ground squirrel (Urocitellus richardsonii). We quantified the morphology and spine densities of Golgi-stained pyramidal neurons and granule cells in the hippocampus and tested for differences between sexes and seasons with generalized linear models. Although we found no significant sex differences or sex–season interaction effects on any of our morphological measurements, there were significant differences in neuron morphology and spine density between breeding and non-breeding seasons. In the non-breeding season, ground squirrels had CA1 neurons with longer basal dendrites with more branches than in the breeding season. Non-breeding season animals also had higher apical and basal dendrite spine density in CA1 and CA3 neurons than breeding-season animals. Conversely, the spine densities of CA1 somata and granule cells were higher in breeding than in non-breeding season. These differences in neuron morphology and spine density between breeding and non-breeding seasons likely arise from a combination of activity levels, stress hormones, and photoperiod. Although the functional implications of seasonal changes in hippocampal neuron morphology and spine density are uncertain, our data suggest that ground squirrels may be a good model for understanding seasonal neuroplasticity in mammals.
Technical Report
Full-text available
En 2015, un protocole visant à montrer les bénéfices de l’implantation de bandes enherbées sur les carabidés a été mis en place par le futur Parc national de forêts, dans deux parcelles cultivées, grâce à un financement du Conseil départemental de Haute-Marne. Il avait pour objectifs de comparer les communautés de carabes selon différentes modalités de traitements appliquées au sein de ces deux parcelles, et ainsi montrer aux agriculteurs l’intérêt des infrastructures agro-écologiques comme pourvoyeur d’auxiliaires de cultures, y compris sur un territoire où les champs sont relativement proches de milieux naturels comme des forêts. Il reposait sur la pose de pièges Barber, dispositifs de capture de la faune épigée. Les résultats obtenus après quatre années successives étaient peu conclusifs sur un plan statistique. De plus la faible emprise spa-tiale du dispositif ne permettait pas la généralisation des résultats à des emprises plus vastes que les parcelles étudiées. En 2019, nous avons mis en place une étude-pilote afin de caractériser la structuration spatiale de l’activité-densité des carabidés au sein d’une des parcelles cultivées étudiées les années précé-dentes. Les relevés de pièges Barber à différents pas de temps (hebdomadaires et journaliers) nous ont alors permis d’appréhender les variations temporelles d’activité-densité. Une étude de la prédation des ravageurs venait compléter le dispositif afin de tester le lien entre activité-densité de carabidés et efficacité de la lutte contre les ravageurs des cultures. Les données collectées nous ont permis de développer des tests de puissance afin de fournir des recommandations pour le futur protocole à déployer à l’échelle du Parc national de forêts. Ce protocole visera à étudier les communautés de carabes – et les services que certains d’entre eux rendent comme auxiliaires de cultures - selon un gradient paysager prenant notamment en compte l’existence de bandes enherbées. Ce protocole privilégiera alors des dispositifs légers à l’échelle de la parcelle (nombre de pièges et temps de pose réduits) mais disposés dans de nom-breuses parcelles selon un gradient paysager intégrant certaines métriques, notamment la sur-face en éléments semi-naturels. Ce document justifie les choix méthodologiques réalisés et propose un cadre pour le recueil, le stockage et l’analyse des données. Il fixe également les moyens logistiques nécessaires à la mise en œuvre du protocole proposé. L’ensemble de ces informations garantissent la pérennité de l’étude sur le long terme.
Article
The ‘social complexity hypothesis' posits that complex social systems (which entail high uncertainty) require complex communicative systems (with high vocal flexibility). In species with fission–fusion dynamics, where the fluid composition of temporary subgroups increases the uncertainty with which group members must manage their social relationships, vocal communication must be particularly flexible. This study assessed whether contact call rates vary with caller and audience characteristics in free-living spider monkeys, as well as with fission and fusion events. Adult females and immature individuals called more when in small audience settings, while audience size did not influence adult males. Adults called more when in the presence of the opposite sex, whereas immatures vocalized more in subgroups composed only by females. Females also called more when with their mature sons. We found higher call rates in periods during which fission and fusion events took place than in periods with more stable compositions and when the composition after a fission or fusion event changed from one sex to two sexes. A flexible use of contact calls allows individuals to identify themselves when they join others, particularly if they are members of the opposite sex. This socio-spatial cohesion function reduces the uncertainty about subgroup composition. This article is part of the theme issue ‘Cognition, communication and social bonds in primates’.
Article
Full-text available
Las poblaciones de animales suelen disminuir debido a la alteración del hábitat, pero la respuesta inicial de los organismos a los cambios ambientales inducidos por el hombre suele ser de tipo comportamental. Las interacciones intra e interespecíficas pueden restringir o facilitar el acceso a los recursos, lo que provoca cambios en la adecuación (fitness) de los individuos, y también, el agotamiento de los recursos puede afectar la frecuencia y la fuerza de las interacciones. En las aves, se suele considerar que la alimentación en grupo aumenta la eficacia en la búsqueda de alimento. Hemos evaluado cómo la reducción de los recursos (semillas) provocada por el pastoreo del ganado afectó diferentes propiedades de las bandadas de aves granívoras en bosques abiertos con las mismas características estructurales, pero que difieren en la abundancia de semillas. Con una menor disponibilidad de semillas de pastos (es decir, en los bosques pastoreados) las bandadas eran más pequeñas y con menor riqueza de especies, y las aves mostraban una menor propensión a formar bandadas. Este patrón podría explicarse mediante tres hipótesis no excluyentes. La reducción de alimento causada por el pastoreo (i) disminuye la abundancia de aves que comen semillas, y genera concomitantemente bandadas más pequeñas; (ii) reduce la densidad de las especies núcleo, disminuyendo la cohesión del grupo en las bandadas grandes; (iii) hace que las bandadas grandes sean menos atractivas al aumentar la competencia individual por el alimento. Nuestros resultados proporcionan pruebas de que el pastoreo por ganado afecta las interacciones de las aves granívoras, y sugieren la importancia de comprender el comportamiento de las bandadas para llevar a cabo acciones de gestión.
Article
Full-text available
The recent invasion of the Japanese beetle Popillia japonica Newman (Coleoptera: Scarabaeidae) in northern Italy offered the opportunity to explore the entomopathogenic nematodes (EPNs) associated with the soil of hay meadows. A total of 61 sites were considered for nematode sampling, and from 17 of them (27.9%) EPNs were isolated and further characterized with molecular and morphological techniques as well as with laboratory bioassays. Two main species, Heterorhabditis bacteriophora Poinar (Rhabditida: Heterorhabditidae) and Steinernema carpocapsae Weiser (Rhabditida: Steinernematidae), were recorded with the same frequency together with a few other species (Rhabditida: Oscheius sp. and Phasmarhabditis sp.). The newly isolated EPN populations were characterized for their activity (penetration rate) and infectivity to P. japonica grubs. EPNs occurrence was related to the time of beetle invasion at each sampling site and there was evidence of a density-dependent response of the EPNs community to P. japonica density. The invasion of P. japonica apparently did not significantly affect the occurrence of native grubs, although a tendency to a decline was observed and should be further investigated.
Article
Full-text available
Improved forest management may offer climate mitigation needed to hold warming to below 2°C. However, uncertainties persist about the effects of harvesting intensity on forest carbon sequestration, especially when considering interactions with regional climate and climate change. Here, we investigated the combined effects of harvesting intensity, climatic aridity, and climate change on carbon stocks in Douglas-fir [ Pseudotsuga menziesii Mirb. (Franco)] stands. We used the Carbon Budget Model of the Canadian Forest Sector to simulate the harvest and regrowth of seven Douglas-fir stand types covering a 900 km-long climate gradient across British Columbia, Canada. In particular, we simulated stand growth under three regimes (+17%, −17% and historical growth increment) and used three temperature regimes [historical, representative concentration pathways (RCP) 2.6 and RCP 8.5]. Increasing harvesting intensity led to significant losses in total ecosystem carbon stocks 50 years post-harvest. Specifically, forests that underwent clearcutting were projected to stock about 36% less carbon by 2,069 than forests that were left untouched. Belowground carbon stocks 50 years into the future were less sensitive to harvesting intensity than aboveground carbon stocks and carbon losses were greater in arid interior Douglas-fir forests than in humid, more productive forests. In addition, growth multipliers and decay due to the RCP’s had little effect on total ecosystem carbon, but aboveground carbon declined by 7% (95% confidence interval [−10.98, −1.81]) in the high emissions (RCP8.5) scenario. We call attention to the implementation of low intensity harvesting systems to preserve aboveground forest carbon stocks until we have a more complete understanding of the impacts of climate change on British Columbia’s forests.
Article
Full-text available
After naming pictures in their second language (L2), bilinguals experience difficulty in naming pictures in their native language (L1). This phenomenon, the “L2 after-effect”, is a lingering consequence of language control mechanisms regulating the activation of L1 and L2 to facilitate L2 production. Building on the Inhibitory Control model proposed by Green (1998), we propose that how much language control is applied depends on the relative balance between the current activation of L1 and L2. In two experiments, Polish-English bilinguals immersed in their L1 performed a blocked picture-naming task. This paradigm provided a continuous measure of the relative balance between the two languages and made it possible to index engagement of control by measuring the L2 after-effect. The results indicate that the higher the activation level of L1 and the lower the activation level of L2, the bigger the L2 after-effect. The results also revealed an enduring down-regulation of L1 activation level in more language-balanced speakers.
Article
Interspecific hybridization has varied consequences for offspring fitness, with implications for the maintenance of species integrity. Hybrid vigour, when it occurs, can peak in first-generation (F1) hybrids and then decline in advanced-generation (F2+) hybrids. This hybrid breakdown, together with the processes affecting patterns of hybridization and hybrid fitness, determine the evolutionary stability of hybrid zones. An extensive hybrid zone in North America involving the cattails Typha latifolia, T. angustifolia, and their invasive hybrid T. × glauca is characterized by hybrid vigour among F1s, but the fitness of advanced-generation hybrids has not been studied. We compared seed germination and plant growth of T. latifolia (parental L), F1 T. × glauca (F1), hybrid backcrosses to T. angustifolia (bcA) and T. latifolia (bcL), and advanced-generation (F2) hybrids. Consistent with expectations under hybrid breakdown, we found reduced plant growth for F2 hybrids in comparison with F1s (plant height and above-ground biomass) and parental Ls (above-ground biomass). Backcrossed hybrids had intermediate measures of plant growth and bcLs were characterized by reduced seed germination in comparison with parental Ls. Hybrid breakdown could make the formation of F1s in North America finite because (1) hybridization among cattails is asymmetric, with T. angustifolia but not T. latifolia subject to genetic swamping, and (2) T. angustifolia is less common and subject to competitive displacement by F1s. Hybrid breakdown is therefore expected to reduce hybrid frequencies over time, contributing to the long-term maintenance of T. latifolia – the only native cattail in the study region.
Article
Full-text available
Recently, we have shown that pupil dilation during a recognition memory task can serve as an index of memory retrieval difficulties in autism. At the time of publication, we were unaware of specific data‐analysis methods that can be used to shed further light on the origins of such memory related pupil dilation. Specifically, by distinguishing “tonic” from “phasic” changes in pupil dilation and considering their temporal progression, it is possible to draw inferences about the functional integrity of a locus coeruleus—norepinephrine system (LC‐NE) that is known to play a key role in regulating memory encoding and retrieval processes. We therefore apply these analyses to our previously published eye‐tracking data of adults with ASD (N = 24) and neurotypical development (TD, N = 30) during the recognition memory task. In this re‐analysis, we related pupil dilation during encoding and retrieval to recognition accuracy in a per‐trial analysis of linear mixed models. In ASD, we replicated attenuated recognition accuracy, which was accompanied by attenuated pupil dilation during encoding and retrieval. Group differences in pupil dilation during retrieval occurred late during the trial (after 1.75 s) and indicated an altered top‐down processing like attenuated attribution of semantic salience in response to previously encoded stimuli. In addition, only in the ASD group were higher pupil dilation during encoding and lower pupil dilation during retrieval associated with decreased recognition accuracy. This supports altered modulation of memory encoding and retrieval in ASD, with LC‐NE phasic activity as promising underlying mechanism. We investigated the changes of pupil size during memory testing in autism spectrum disorder. Adults with ASD remembered fewer items correctly than neurotypical individuals (TD). This reduced memory was related to increased pupillary responses at study and decreased pupil dilation at test only for adults with ASD indicating a different modulation of memory by the locus coeruleus.
Article
Purpose: This feasibility study evaluated the intra-fractional prostate motion using an ultrasound image-guided system during step and shoot intensity-modulated radiation therapy (SS-IMRT) and volumetric modulated arc therapy (VMAT). Moreover, the internal margins (IMs) using different margin formulas were calculated. Methods: Fourteen consecutive patients with prostate cancer who underwent SS-IMRT (n = 5) or VMAT (n = 9) between March 2019 and April 2020 were considered. The intra-fractional prostate motion was observed in the superior-inferior (SI), anterior-posterior (AP), and left-right (LR) directions. The displacement of the prostate was defined as the displacement from the initial position at the scanning start time, which was evaluated using the mean ± standard deviation (SD). IMs were calculated using the van Herk and restricted maximum likelihood (REML) formulas for SS-IMRT and VMAT. Results: For SS-IMRT, the maximum displacements of the prostate motion were 0.17 ± 0.18, 0.56 ± 0.86, and 0.18 ± 0.59 mm in the SI, AP, and LR directions, respectively. For VMAT, the maximum displacements of the prostate motion were 0.19 ± 0.64, 0.22 ± 0.35, and 0.14 ± 0.37 mm in the SI, AP, and LR directions, respectively. The IMs obtained for SS-IMRT and VMAT were within 2.3 mm and 1.2 mm using the van Herk formula and within 1.2 mm and 0.8 mm using the REML formula. Conclusions: This feasibility study confirmed that intra-fractional prostate motion was observed with SS-IMRT and VMAT using different margin formulas. The IMs should be determined according to each irradiation technique using the REML margin.
Article
The efficiency of different plant defenses is expected to vary depending on the combination and abundance of herbivores. Effectiveness of ant‐mediated defenses can also depend on ant activity and local ant assemblage, which can vary due to human activities such as intensive grazing. We used the plant Crotalaria pallida (Fabaceae), its two pod‐boring herbivores and the ants that visit the extrafloral nectaries (EFNs) to understand how chemical defense and ant–plant associations affect plant damage. We hypothesized causal relationships between plant chemical defense, ant presence on plants and herbivore damage in scenarios of constitutive and induced plant defenses and tested the different possible relationships using path analysis. The constitutive model explained the data more adequately, and each plant defense had different effects on each herbivore species. First, chemical defense significantly reduced damage by the generalist pod borer Etiella zinckenella but not by the specialist Utetheisa ornatrix. Second, ant presence reduced damage by the generalist, but had no effect on damage by the specialist. Third, a larger number of pods on the plant increased ant presence, as expected since more pods results in more EFNs. Finally, we show that these density‐dependent responses by ants mediate indirect cascades on herbivory and generate context‐specific responses reducing damage by E. zinckenella in sites with cattle grazing. In synthesis, we highlight that plant defenses have distinct effects on co‐occurring herbivores and that indirect defenses can mediate ecological cascades that generate context dependency in the efficiency of different defenses. Abstract in Portuguese is available with online material. Espera‐se que a eficiência de diferentes defesas de plantas varie de acordo com a combinação e abundância de herbívoros. A efetividade de defesas mediadas por formigas pode também depender da atividade e composição local de espécies de formigas, que pode ser afetado por atividades humanas como por exemplo a pastagem intensiva. Nós usamos a planta Crotalaria pallida, seus dois herbívoros brocadores de vagens e as formigas que visitam os nectários extraflorais para entender como a defesa química e a associação formiga‐planta afetam o dano incidido sobre planta. Hipotetizamos diferentes relações causais entre defesa química, presença de formigas na planta e dano pelos herbívoros em cenários de defesas constitutivas e induzidas, e testamos as possíveis relações por meio de análise de rotas. O modelo constitutivo explicou os dados de forma mais parcimoniosa, e cada tipo de defesa da planta teve efeitos diferentes em cada herbívoro. Primeiro a defesa química diminuiu o dano pelo brocador generalista Etiella zinckenella, mas não afetou o dano pelo especialista Utetheisa ornatrix, enquanto que as formigas afetaram ambas espécies. Segundo, a presença de formigas reduziu o dano pelo generalista, mas não pelo especialista. Terceiro, o aumento no número de vagens na planta aumentou a presença de formigas. Por último, mostramos que as respostas densodependentes pelas formigas medeiam cascatas indiretas na herbivoria e geram respostas contexto‐específicas que diminuem o dano por E. zinckenella em locais onde havia pastagem por gado. Em resumo, demonstramos que defesas de plantas têm efeitos diferenciados em herbívoros coocorrentes e que defesas indiretas podem mediar cascatas ecológicas que geram dependência de contexto na eficiência de defesas. We show that different plant defences have different effects on a specialist and generalist pod boring herbivore. We also demonstrate that herbivore damage by the generalist is affected by indirectly by grazing through grazing's effects on pod number and ant presence on the plant.
Article
Full-text available
Context Many forest ecosystems around the world are facing increasing drought-induced dieback, causing mortality patches across the landscape at multiple scales. This increases the supply of biological legacies and differentially affects forest insect communities. Objectives We analysed the relative effects of local- and landscape-level dieback on local saproxylic beetle assemblages. We assessed how classical concepts in spatial ecology (e.g., habitat-amount and habitat-patch hypotheses) are involved in relationships between multi-scale spatial patterns of available resources and local communities. Methods We sampled saproxylic beetle assemblages in commercial fir forests in the French highlands. Through automatic aerial mapping, we used percentage of dead tree crown pixels to assess dieback levels at several nested spatial scales. We analysed beetle taxonomic, phylogenetic and functional diversity related to differing levels of multi-scale dieback. Results We found that taxonomic, functional, and phylogenetic diversity of saproxylic beetle assemblages significantly benefitted from forest dieback, at both local and landscape scales. We detected significant effects in the multiplicative models combining local and landscape variables only for phylogenetic diversity. Increased landscape-scale dieback also caused a functional specialisation of beetle assemblages, favouring those related to large and well-decayed deadwood. Conclusions Increasing tree mortality under benign neglect provides conservation benefits by heterogenising the forest landscape and enhancing deadwood habitats. Legacy retention practices could take advantage of unharvested, declining forest stands to promote species richness and functional diversity within conventionally managed forest landscapes.
Article
Full-text available
Adoption of practices that reduce the risk of pest outbreaks is one of the pillars of agroecology and is largely based on biological control. Multiple infield and landscape parameters affect biocontrol, but the effects of conservation soil management on biological control have been poorly investigated over crop season. By comparing winter wheat fields within the same landscape but with different soil management, the direct and indirect effects of soil management (conservation and conventional systems) on natural enemies’ communities and their biological control on aphids was studied from the tillering stage to the harvest. In addition to aphid infestation, two families of the main natural enemies’ guilds were monitored, as well as their associated services: aphid parasitoid, a specialist and flying natural enemy, with parasitism service, and carabid beetles, a generalist and ground-dwelling predator, with aphidophagy service. Soil conservation system hosted more abundant and diverse carabid beetles’ assemblages, and received higher aphidophagy service in June than conventional system. However, neither parasitoid abundance, nor parasitism rates, were affected by soil management. Aphid infestation and its associated damage did not depend on soil management either. Our results suggest that ground-dwelling natural enemies are more impacted by soil management than foliage-dwelling natural enemies, which is partly reflected in aphid biocontrol. In agricultural systems with reduced soil perturbation, direct mortality on ground-dwelling communities due to tillage may be lower than in a conventional system, but habitat heterogeneity is also greater, increasing the number of ecological niches for natural enemies. Both factors are supposed to favor an early presence of natural enemies and a tendency toward a precocious aphidophagy service is indeed observed in conservation system.
Article
Full-text available
Conflict adaptation refers to the dynamic modulation of conflict processing across successive trials and reflects improved cognitive control. Interestingly, aversive motivation can increase conflict adaptation, although it remains unclear through which process this modulation occurs because previous studies presented punishment feedback following suboptimal performance on both congruent and incongruent trials. According to integrative accounts of conflict monitoring and aversive motivation in the dorsal anterior cingulate cortex, punishment feedback following slow or erroneous performance on incongruent trials in particular should lead to improved conflict adaptation. Second, selectively increasing motivation on incongruent trials should reduce the overall congruency effect. The current study sought to test both hypotheses. Specifically, we administered the confound-minimized Stroop task to a large group of participants and manipulated the position of feedback (following either congruent or incongruent trials) and aversive motivation (tied to a monetary loss or not) across different blocks. As expected, the congruency effect was found to be smaller when punishment was coupled with incongruent versus congruent trials. However, results showed that conflict adaptation was increased when punishment feedback was selectively coupled with congruent rather than incongruent trials. Together, these results suggest that aversive motivation does not uniformly improve cognitive control but this gain appears to be context dependent.
Article
Full-text available
Spectral properties of earlier sounds (context) influence recognition of later sounds (target). Acoustic variability in context stimuli can disrupt this process. When mean fundamental frequencies (f0’s) of preceding context sentences were highly variable across trials, shifts in target vowel categorization [due to spectral contrast effects (SCEs)] were smaller than when sentence mean f0’s were less variable; when sentences were rearranged to exhibit high or low variability in mean first formant frequencies (F 1 ) in a given block, SCE magnitudes were equivalent [Assgari, Theodore, and Stilp (2019) J. Acoust. Soc. Am. 145(3), 1443–1454]. However, since sentences were originally chosen based on variability in mean f0, stimuli underrepresented the extent to which mean F 1 could vary. Here, target vowels (/ɪ/-/ɛ/) were categorized following context sentences that varied substantially in mean F 1 (experiment 1) or mean F 3 (experiment 2) with variability in mean f0 held constant. In experiment 1, SCE magnitudes were equivalent whether context sentences had high or low variability in mean F 1 ; the same pattern was observed in experiment 2 for new sentences with high or low variability in mean F 3 . Variability in some acoustic properties (mean f0) can be more perceptually consequential than others (mean F 1 , mean F 3 ), but these results may be task-dependent.
Article
Full-text available
The current research addresses dynamics of the COVID-19 pandemic's disruption to goal pursuit. Specifically, we examined the effects of disengaging from frozen goals (goals for which progress had been disrupted due to COVID-19). In May 2021, we asked participants (N = 226) what percentage of their goals were COVID-frozen goals and asked them to report their engagement in one such goal (vs. an active goal): the degree to which they think about the goal, ruminate about the goal, and are committed to the goal. Participants also reported on two facets of their recent well-being: psychological distress (stress, depressive symptoms, anxiety) and life satisfaction. As expected, percentage of COVID-frozen goals was positively associated with psychological distress (stress, depressive symptoms, and anxiety). Moreover, frozen goal rumination (but not thought frequency or commitment) was negatively associated with life satisfaction and positively associated with psychological distress (stress, depressive symptoms, and anxiety; even when controlling for active goal rumination). Furthermore, individual differences in the capacity to disengage and reengage in alternatives were negatively associated with frozen goal rumination, positively associated with life satisfaction, and negatively associated with psychological distress (stress, depressive symptoms, and anxiety). These results highlight the adaptive function of disengagement in goal pursuit. We discuss implications for the goal disengagement literature and for coping with COVID-19. Supplementary information: The online version contains supplementary material available at 10.1007/s11031-022-09959-w.
Article
Understanding the genetic basis of quality-related traits contributes to the improvement of grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) in wheat, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed on the 236 wheat accessions including 160 cultivars and 76 landraces using 55K single nucleotide polymorphism (SNP) array in multiple environments. A total of twelve stable QTL/SNPs were identified to control different quality traits in this populations at least two environments under stripe rust stress; three, seven and two QTLs associated with GPC, GSC, and WGC were characterized respectively and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D with the range of phenotypic variation explained (PVE) from 4.2 to 10.7%. Compared with the previously reported QTLs/genes, five QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. KASP markers for SNPs AX-108770574 and AX-108791420 on chromosome on 5D associated with wet gluten concentration were successfully developed. Phenotype of the cultivars containing the A-allele in AX-108770574 and T-allele in AX-108791420 were extremely significantly (P<0.01) higher than that of the landraces containing the G-allele or C-allele of wet gluten concentration in each of the environments. The developed and validated KASP markers could be utilized in molecular breeding aiming to improve the quality in wheat.
Article
With the reduced availability of effective plant protection products, alternative control measures gain importance. Insect net covers are a promising tool in this regard, because they can reduce pest damage on crop by exclusion of pests. However, as under practical conditions, most crop net covers need to be removed several times during a crop cycle to manage weeds and apply fertilizers, a complete exclusion of pests is not always feasible. In addition, net covers also have an impact on natural enemies, on microclimate, and may cause direct crop damage due to their tracking weight. Therefore, effects of net applications have to be assessed accordingly, depending on the specific crops and pests. In the current paper, effects on pests, on yield, and on the occurrence of diseases are assessed in Chinese cabbage, carrot, and leek. Whereas control of Delia radicum , Phyllotreta spp . and thrips was enhanced, aphids and mining flies showed increased population build ups and caused higher damages under net cover once they had been able to invade. Some plant diseases such as Puccinia spp . and Alternaria spp . did increase under the net covers. Pitfall trap catches in carrots and Chinese cabbage were lower in almost all natural enemy groups monitored under net covers as compared to open field plots. Yield was higher with net coverage in case of Chinese cabbage and leek, but not in carrot. Results are discussed and take into account the exclusion of natural enemies and measured changes in microclimate and photosynthetically active radiation.
Article
When inferring the meaning of unknown words in a second language, learners make use of a variety of cues including the cross-linguistic formal similarities of loanwords and cognates. However, because learners do not always recognize these cross-linguistic relationships, cognate strategy training has been recommended. The present study investigated the impact of cognate strategy training on Japanese speakers’ accuracy when guessing the meaning of unknown English words. The findings revealed that participants were significantly more accurate in responding to cognates after training than prior to it, while responses to noncognates were similar in both rounds. Moreover, participants were more accurate in identifying cognates with common grapheme–phoneme correspondences in English (e.g. fleece) after training than those that had less-common correspondences (e.g. gauge). Considering error rates, the benefit-cost ratio of applying the strategy was four correct guesses to one incorrect guess. Together with insights from a small-scale qualitative follow-up study, the results reveal that both phonological decoding of English words and conversion into katakana script in Japanese contribute to difficulties in noticing cognate relationships. The primary implication of the study is that cognate strategy training may contribute positively to language teaching pedagogy in Japan and other contexts.
Article
To obtain more accurate and robust feedback information from the students’ assessment outcomes and to communicate it to students and optimize teaching and learning strategies, educational researchers and practitioners must critically refect on whether the existing methods of data analytics are capable of retrieving the information provided in the database. This study compared and contrasted the prediction performance of an item response theory method, particularly the use of an explanatory item response model (EIRM), and six supervised machine learning (ML) methods for predicting students’ item responses in educational assessments, considering student- and item-related background information. Each of seven prediction methods was evaluated through cross-validation approaches under three prediction scenarios: (a) unrealized responses of new students to existing items, (b) unrealized responses of existing students to new items, and (c) missing responses of existing students to existing items. The results of a simulation study and two real-life assessment data examples showed that employing student- and item-related background information in addition to the item response data substantially increases the prediction accuracy for new students or items. We also found that the EIRM is as competitive as the best performing ML methods in predicting the student performance outcomes for the educational assessment datasets.
Article
Full-text available
Animals that create structures often display non-random patterns in the direction of their constructions. This tendency of oriented construction is widely presumed to be an adaptive trait of the constructor’s extended phenotype, but there is little empirical support for this hypothesis. Particularly, for cavity nesting-birds there is a lack of studies examining this issue. In this study of a primary cavity excavator, the endangered red-cockaded woodpecker ( Dryobates borealis ), we show that cavity entrances exhibited a strong westward bias in all 11 of the populations examined throughout the geographic range of the species in the southeastern United States. This species requires cavities in living pine trees for roosting and nesting that often take many years to complete, resulting in many incomplete excavations on the landscape. We used population monitoring data to show that orientation was stronger among completed cavities than incomplete cavities. There was a significant correlation between latitude and average cavity direction among populations, turning northward with increasing latitude, suggesting adaptation to local conditions. Long-term monitoring data showed that cavity orientation and breeding group size are correlated with egg hatching rates, fledging rates, and the total number of fledglings produced per nest. Our results provide empirical evidence from extensive long-term data that directional orientation in animal constructions is an important feature of the extended animal phenotype and have immediate implications for animal ecology and the conservation of endangered species.
ResearchGate has not been able to resolve any references for this publication.