Modern Applied Statistics with S
Abstract
A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods. The emphasis is on presenting practical problems and full analyses of real data sets.
Chapters (6)
Statistics is fundamentally about understanding data. We start by looking at how data are represented in S, then move on to importing, exporting and manipulating data.
In linear regression the mean surface is a plane in sample space; in non-linear regression it may be an arbitrary curved surface but in all other respects the models are the same. Fortunately the mean surface in most non-linear regression models met in practice will be approximately planar in the region of highest likelihood, allowing some good approximations based on linear regression to be used, but non-linear regression models can still present tricky computational and inferential problems.
We collect together several ways to handle linear and non-linear models with random effects, possibly as well as fixed effects.
Multivariate analysis is concerned with datasets that have more than one response variable for each observational or experimental unit. The datasets can be summarized by data matrices X with n rows and p columns, the rows representing the observations or cases, and the columns the variables. The matrix can be viewed either way, depending on whether the main interest is in the relationships between the cases or between the variables. Note that for consistency we represent the variables of a case by the row vector x.
Classification is an increasingly important application of modern methods in statistics. In the statistical literature the word is used in two distinct senses. The entry (Hartigan, 1982) in the original Encyclopedia of Statistical Sciences uses the sense of cluster analysis discussed in Section 11.2. Modern usage is leaning to the other meaning (Ripley, 1997) of allocating future cases to one of g prespecified classes. Medical diagnosis is an archetypal classification problem in the modern sense. (The older statistical literature sometimes refers to this as allocation.)
Statisticians1 often under-estimate the usefulness of general optimization methods in maximizing likelihoods and in other model-fitting problems. Not only are the general-purpose methods available in the S environments quick to use, they also often outperform the specialized methods that are available. A lot of the software we have illustrated in earlier chapters is based on the functions described in this. Code that seemed slow when the first edition was being prepared in 1993 now seems almost instant.
... For models fitted on Box-Cox transformed latency data, transformation parameters were estimated using the MASS package [60]. Marginal means for the fixed effects (context and object) were computed and back-transformed to the original scale (seconds) using the Box-Cox inverse transformation, or an inverse log transformation for eating latency, with the emmeans package [61]. ...
Neophobia, the fear or avoidance of the unfamiliar, can have significant fitness consequences. It is typically assessed by exposing individuals to unfamiliar objects when they are alone, but in social species, the presence of conspecifics can influence neophobia. However, previous research on the effect of group dynamics on neophobic responses has produced mixed results. Here, we explored the degree of neophobia of an individual in different social contexts in a highly social species, the herring gull. To this end, we exposed juvenile herring gulls (n = 54) to novel objects in both individual and group settings (4–5 individuals), replicating each condition twice. Individuals tested in groups were quicker to eat and spent more time near a novel object than individuals tested alone. The results of our study suggest that the presence of group members reduces perceived individual risk, allowing individuals to behave less cautiously. Preregistered Stage 1 protocol: https://osf.io/u4b7q (date of in-principle acceptance: 17 May 2024).
... [19] and visualized using Evolview v. 3 [19]. Besides, a well-established machine learning (ML) technique for classification, linear discriminant analysis (LDA), was utilized for predicting categories [20]. To evaluate the preliminary performance of Y-STR haplotypes in classifying diverse populations in Tibetan-Yi corridor, genotyping data from Han, Qiang, Tibetan and Yi populations were adopted in LDA (electronic supplementary material, table S1) via the R package 'lda' based on 23 single-copy Y-STR loci. ...
Known for its legendary history and peculiar culture, Chinese Qiang minority aroused interest among geneticists and anthropologists. However, the paternal genetic landscape of its sub-branches coupled with its migration history has never been uncovered. In this study, 37 Y-chromosomal short tandem repeat (Y-STR) loci of three Qiang ethnic groups (N = 564) were investigated to shed light on their paternal genetic landscape. The phylogenetic reconstruction among 29 populations was conducted based on their Y-chromosomal haplotypes. The genetic affinities of the four different Qiang subgroups exhibited obviously variant when compared with Han, Yi or Tibetan in Tibetan-Yi corridor. Based on machine learning method, the predicted Y chromosome haplogroups demonstrated the predominance of O2a1 and O2a2. The haplogroup distributions were compared among 40 contemporary ethnic groups in West China and DNA samples of 214 ancient humans from 59 archaeological sites. The results supported that Wenchuan Qiang had historical links with the ancients in West Liao River (WLR) region. Moreover, intrapopulation gene flow was analysed using Migrate-n. Bidirectional migration was proved to be the most frequent model among the Qiangic populations while the unidirectional migration was only observed from Wenchuan to Li County.
... We used linear discriminant analysis (LDA) with 95% confidence intervals to explore and identify the variables that distinguish between clades. We performed the multivariate analyses using MASS, car, and factoextra packages (Fox and Weisberg 2019;Kassambara 2020;Venables and Ripley 2002) in R. ...
The large-toothed shrew, Sorex macrodon , is distributed in the cloud forests of the southern Sierra Madre Oriental, the eastern Trans-Mexican Volcanic Belt, and the northeastern Sierra Madre del Sur. This study tested the hypothesis that the canyons of the Blanco, Santo Domingo, and Cajonos Rivers constitute geographical barriers that promote interpopulation differentiation in S. macrodon . We integrated ecological niche modeling, phylogenetic analyses, and morphometrics to assess potential intra-specific differentiation in response to climatic and topographic variations across its geographic range. The potential distribution map suggests that the Santo Domingo River canyon is unsuitable for S. macrodon . Phylogenetic analyses revealed two monophyletic groups within the species, with distinct haplotypes north and south of this canyon, and a p-distance of 3.16% between populations. However, morphometric analyses showed few significant differences between genetic groups. The Santo Domingo River canyon appears to promote differentiation and limit distribution in S. macrodon and in other vertebrate groups associated with cloud forests, and the ecosystem distribution itself. The discordance between genetic and morphometric data may result from recent intra-specific divergence (0.71 Ma), as suggested by divergence time analysis. To understand population dynamics and differentiation-promoting processes in this species, evaluating its historical distribution, including additional specimens, is necessary.
... Table 3 and Figure 3 summarize the data. The remaining 1,463 data points were analyzed using multinomial regression as implemented by the nnet package (Venables and Ripley 2002). The translated forms were predicted by the fixed effects STEREOTYPICALITY and the forms' ENDINGs (-er vs. not -er) in interaction, by participant GENDER, participant AGE, and particpants' attitudes towards the different form options, i.e., ATTGM, ATTPF, ATTNT, ATTPT, and ATTGS. ...
... Linear models were generated to assess whether a linear combination of the annual frequency in the synoptic types could explain variability in the DSS ice core annual snowfall accumulation record. The variables were selected using the stepAIC function from the Modern Applied Statistics with S (MASS; Venables and Ripley, 2002) package in R. The variables were not detrended for this analysis. Models were generated for different time periods (see above). ...
Weather systems in the southern Indian Ocean influence East Antarctic precipitation variability and surface mass balance. However, the long-term variability in synoptic-scale weather systems in this region is not well understood due to short instrumental records that are mostly limited to the satellite era (post-1979). Ice core records from coastal East Antarctica suggest significant decadal variability in snowfall accumulation, indicating that data from the satellite era alone are not enough to characterise climate variability in the high southern latitudes. It is therefore challenging to contextualise recent precipitation trends and extremes in relation to climate change in this area. We use synoptic typing of daily 500 hPa geopotential height anomalies and the Law Dome ice core (East Antarctica) annual snowfall accumulation record to investigate whether the 20th Century Reanalysis (20CR) project can represent the synoptic conditions associated with precipitation variability at Law Dome prior to the satellite era. We identify 12 synoptic types using self-organising maps (SOMs) based on their dominant pressure anomaly patterns over the southern Indian Ocean, with 4 types associated with above-average daily precipitation at Law Dome. Our results show the 20th Century Reanalysis project represents the meridional synoptic conditions associated with precipitation variability at Law Dome more reliably from 1948, aligning with the increased availability and thus assimilation of consistent surface pressure data from weather stations in the southern Indian Ocean from the late 1940s. This extends the time period available to contextualise recent trends and extremes in precipitation and synoptic weather conditions by up to 3 decades beyond the satellite era. Furthermore, we find a linear combination of the annual frequency in select synoptic types explains a significant amount of the variability in Law Dome snowfall accumulation compared to any individual synoptic type alone. These results will help future research on contextualising East Antarctic surface mass balance variability prior to the satellite era, with implications for improved understanding of the largest source of potential sea level rise, and the atmospheric conditions leading to decadal precipitation variability.
... All analyses were performed using the RStudio software (R Core Team, 2024). The poLCA package (Linzer & Lewis, 2011) was employed for LCA, while the nnet package (Venables & Ripley, 2002) was used to construct logistic models. Table 3 presents the results of the estimation of the multinomial models. ...
The over‐saturation of labour markets in some countries has led to a devaluation of university degrees and reshaped the factors determining employability for higher‐quality jobs. As a result, the social capital of graduates has emerged as an essential resource in addressing these challenges. This study examines the influence of social capital on the job quality of Chilean university graduates, distinguishing between first‐generation (FG) and continuing‐generation (CG) graduates. The level of social capital was estimated based on the frequency of contact with professionals and managers. Latent class analysis was employed to identify four distinct classes of job quality. Two multinomial regression models were then estimated, one for FG graduates and one for CG graduates, to assess the impact of social capital on the probability of belonging to each job quality class. The results show that frequent contact with other professionals enhances the likelihood of graduates securing high‐quality jobs, with the magnitude of this effect being more pronounced for CG graduates. Frequent contact with managers is relevant for FG graduates but not for CG graduates. These findings demonstrate the persistence of socioeconomic inequalities once graduates enter the labour market. However, they also highlight the role of social capital in levelling the playing field for access to good jobs.
... For visualisation, the 95% CI for group was calculated, the area of which we considered to be the occupied axial morphospace for each respective group. To quantify overlap in axial morphospace between lacustrine and riverine species, we generated 100,000 random points within the lacustrine morphospace using mvrnorm (MASS v7.3.58.2) (Venables and Ripley, 2002). Points were sampled based on the lacustrine centroid (mean PC1 and PC2 scores) and covariance matrix. ...
African cichlids comprise more than 1800 species of freshwater fishes, with remarkable adaptive radiations in Lakes Tanganyika, Malawi, and Victoria that have given rise to extraordinary morphological diversity. However, the evolution of the cichlid axial skeleton has been largely overlooked, despite its high variation and functional significance for locomotion. Here, we present the first macroevolutionary study of axial morphology in African cichlids, based on phylogenetic comparative analyses of 4861 individuals from 583 species. Adaptation to demersal, pelagic, and piscivorous niches has led to the evolution of elongate bodies with high vertebral counts in lacustrine cichlids, emphasising the role of the fusiform body shape in ecological adaptation. However, riverine species occupy a broader axial morphospace than lacustrine species, which is partly explained by a higher stochastic rate of vertebral count evolution in riverine lineages. In addition, the occupied axial morphospace broadly correlates with the estimated age of the lacustrine radiations, suggesting that exploration of axial morphospace is a function of divergence time. However, rates of vertebral count evolution are not the same across the lake radiations. Therefore, accumulated variation in vertebral counts (and more broadly axial morphospace) is not solely a function of divergence time. Finally, we show that the common ancestor of African cichlids possessed a distinctly riverine axial morphology, indicating that the exploration of axial morphospace radiated outward from this ancestral riverine form. These findings highlight the importance of a comparative approach to studying cichlid evolution and underscore the value of African cichlids as a model for investigating the evolutionary and developmental dynamics of the teleostean vertebral column.
... A Mann-Whitney U test for unpaired data examined differences in functional leaf traits between cultivated and wild forms. A linear discriminant analysis (LDA), conducted with the MASS package [76], tested for discrimination between olive forms based on functional traits. The Pearson correlation coefficient (r) assessed significant correlations between trait pairs across the entire dataset and separately for each form (W and C). ...
The domestication of crops, a transformative milestone in human history, has largely contributed to reshaping agricultural practices and plant characteristics. This study investigates the functional responses along the wild–cultivated continuum in olive trees in northern Morocco, focusing on leaf functional traits to elucidate domestication effects. We compared wild olive (Olea europaea subsp. europaea var. sylvestris) with traditional cultivated varieties (O. e. subsp. e. var. europaea). Our results reveal clear distinctions in leaf traits, including leaf area, specific leaf area and leaf dry matter content, indicating divergent resource-use strategies. Cultivated varieties displayed traits associated with thicker, denser leaves and higher stomatal density, suggesting adaptations to stress conditions such as water scarcity. Principal component analysis highlighted a leaf economic spectrum, which differentiated wild and cultivated forms and supported the functional trade-off between resource acquisition and conservation. Intraspecific trait variability was substantial, driven by both genetic factors and phenotypic plasticity in response to local environmental gradients. These findings underscore the significant impact of domestication on olive trees, providing insights into the adaptive mechanisms underlying crop resilience in traditional agroecosystems. Our research emphasizes the importance of conserving these traditional olive varieties, not only for their historical and cultural significance but also for the deep understanding they offer regarding the evolving relationship between humans and the plant world.
This article is part of the theme issue ‘Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future’.
... Single hidden layer (shallow) Neural Networks are implemented in R in the nnet [Venables and Ripley, 2002], which is shipped with base R. Deep learning flavors of Neural Networks are implemented on the deepnet [Rong and Rong, 2014], RcppDL [Kou and Sugomori, 2014], neuralnet, and h2o [Aiello et al., 2016] packages, among others. Regarding interfaces to high-level APIs, which provide a user-friendly interface to build and train Neural Networks, the most used R packages are keras [Chollet et al., 2015] and tensorflow [Abadi et al., 2015]. ...
Nowadays, Neural Networks are considered one of the most effective methods for various tasks such as anomaly detection, computer-aided disease detection, or natural language processing. However, these networks suffer from the ``black-box'' problem which makes it difficult to understand how they make decisions. In order to solve this issue, an R package called neuralGAM is introduced. This package implements a Neural Network topology based on Generalized Additive Models, allowing to fit an independent Neural Network to estimate the contribution of each feature to the output variable, yielding a highly accurate and interpretable Deep Learning model. The neuralGAM package provides a flexible framework for training Generalized Additive Neural Networks, which does not impose any restrictions on the Neural Network architecture. We illustrate the use of the neuralGAM package in both synthetic and real data examples.
... To calculate the RPM and TPM values, the whole of mapped reads was used as the denominator, i.e., including non-uniquely mapping reads and reads mapping in both orientations. The number of genes acting as a source of siRNAs in the two mosquito lines was compared through a negative binomial generalized linear model using the R package MASS v60.0.1 [87]. Antisense mapping reads for analysis of size distribution were extracted directly from the alignment files by intersecting the alignments with collapsed exons using BEDTools intersect (options "-f 0.5 -S"). ...
Background
Transposable elements (TEs) are DNA sequences that can change their position within a genome. In insects, small RNA pathways are central to the transcriptional and post-transcriptional regulation of TE expression. The Piwi-interacting RNA (piRNA) pathway is particularly important in germline tissues, where it silences TE transcripts via small RNAs of 24–30 nucleotides (nt) in length produced from genomic precursor transcripts as well as through a “ping-pong” amplification cycle. The small interfering RNA (siRNA) pathway helps restrict TE expression in somatic tissues via 21nt small RNAs produced from double-stranded RNA by the endonuclease Dicer2, which guide an RNA-induced silencing complex to degrade complementary RNAs. However, much of this knowledge comes from studies of the model insect Drosophila melanogaster. In the mosquito Aedes aegypti, a medically significant vector species, the siRNA pathway has mainly been investigated in connection with its antiviral role, leaving open whether it also regulates TE expression.
Results
We investigated the expression of TEs and small RNAs in both somatic and gonadal tissues of a Dicer2 mutant line of Ae. aegypti and its wild-type counterpart. Our results show a modified pattern of TE expression and a decrease in TE-derived 21nt RNAs in the Dicer2 mutant, but no major shift of TE transcript abundance. The lack of a functional siRNA pathway also causes perturbations in piRNA ping-pong signatures and the expression of certain piRNA-associated genes, but without clear evidence for compensation by increased piRNA pathway activity.
Conclusions
The mosquito Ae. aegypti produces siRNAs derived from TEs but these lack a critical role in the regulation of TE expression both in somatic and in gonadal tissues.
... While the original intent was to apply a GLMM to all three variables, the validation of GLMMs for hatchability across several distributions revealed poor fit. Consequently, a Generalized Linear Model (GLM; MASS package) with a quasipoisson error distribution and logarithmic link function was used instead (Venables and Ripley, 2002). In this model, the response variable was the number of larvae, while the explanatory variables included blood source, seasonality, gonotrophic cycle, and replicate as a four-way interaction. ...
Host selection by mosquitoes is a keystone in understanding viral circulation and predicting future infection outbreaks. Culex mosquitoes frequently feed on birds during spring and early summer, shifting into mammals towards late summer and autumn. This host switch may be due to changes in mosquito fitness. The aim of this study was to assess if the interaction effect of blood meal source and seasonality may influence reproductive traits of Culex quinquefasciatus mosquitoes. For this purpose, Cx. quinquefasciatus mosquitoes were reared in simulated summer and autumn conditions and fed on two different hosts, chickens and mice, in a factorial design. Fecundity, fertility, and hatchability during two consecutive gonotrophic cycles were estimated. We found greater fecundity and fertility for mosquitoes fed upon birds than mammals. Fecundity and fertility did not vary between seasons for chicken-fed mosquitoes, whereas in autumn they decreased for mouse-fed mosquitoes. These traits decreased in the second gonotrophic cycle for mouse-fed mosquitoes, whereas they did not vary between cycles for chicken-fed mosquitoes. There was no statistically significant effect of blood meal source, seasonality or their interaction on hatchability, hence this variable was similar among treatments. Overall, these results indicate a statistically significant interaction effect of blood meal source and seasonality on fecundity and fertility. However, the pattern was opposite in relation to our hypothesis, suggesting that further studies are needed to confirm and expand our knowledge about mosquito biology and its relationship with seasonal host use shifting.
Invasions by insect species that become pests are an increasing problem for agriculture. Introductions of parasitoids from the regions of pest origin and breeding plants resistant to invasive pests can reduce invasive pest abundance and impact. Whether interactions between parasitoids and plant resistance are positive or negative depends on the detailed mechanisms.
We studied the effects of susceptible versus resistant soybean and avirulent versus virulent soybean aphid on the parasitoids Aphelinus certus and Aphelinus glycinis , the first with a broad host range and the second with a narrow host range.
Both parasitoid species parasitized virulent aphids at least as much as avirulent aphids on susceptible and resistant soybean. Aphelinus certus parasitized fewer avirulent aphids than virulent aphids on resistant soybean and fewer avirulent aphids on resistant versus susceptible soybean. The numbers of aphids parasitized by A. glycinis did not vary with the treatments.
Emergence rates of parasitoid progeny were high for both parasitoids and did not vary with the treatments. Progeny sex ratios of the parasitoids did not vary with plant resistance or aphid virulence. However, for A. certus there was a small effect of the interaction between plant resistance and aphid virulence.
Body masses of female and male progeny of A. certus did not vary with the treatments. However, body masses of female progeny of A. glycinis were larger on susceptible versus resistant soybean and on virulent versus avirulent aphids. Body masses of male progeny of A. glycinis were larger on susceptible versus resistant plants.
Parasitism by A. certus is known to be density‐dependent, and given that density‐dependent parasitism has been found in several other species of Aphelinus , parasitism by A. glycines is very likely also to be density‐dependent. Given the higher densities of virulent versus avirulent aphids on resistant soybean reported in the literature, these parasitoids should parasitize more virulent than avirulent aphids on resistant soybean and would limit the abundance of virulent soybean aphid if much of the soybean acreage had resistant plants.
Little research has been published previously on the combined impacts of plant resistance and herbivore virulence on parasitoids. If our results hold true in other systems, plant resistance and biological control may be more compatible in suppressing herbivore virulence than has sometimes been proposed.
The most widely used definition of a species is that it is reproductively isolated from other populations. Yet, most species are described on the basis of morphological criteria, and reproductive isolation is seldom tested. Using the ant genus Myrmica Latreille (Hymenoptera, Formicidae) as a model, we ask whether species described as distinct based on (often subtle) morphological differences indeed form reproductively isolated lineages. We collected and morphologically identified 918 Myrmica ants from a 3212 km2 area in Switzerland. We then combined DNA barcoding (based on COI) and RAD sequencing to identify genetically isolated lineages. Out of the 14 morphological species identified, 13 formed genetically differentiated lineages, while the last one, M. lonae, was not supported by our genetic data. Overall, the morphological identification was congruent with genetic lineage delineation for 94.9% of individuals. Our dataset also allowed us to screen for cryptic lineages in the 5 most frequent species, including in M. scabrinodis where cryptic lineages were previously suggested, but we found no evidence for cryptic species. Overall, our results indicate that morphology parallels genetic isolation in the studied species. However, an integrative approach combining morphological identification with nuclear marker genotyping is necessary for confident species identification of all individuals. Finally, our results provide a library of validated COI barcodes for future Myrmica specimen identification.
Several studies have consistently demonstrated that people generally prefer curved over angular contours. However, the magnitude of the curvature effect varies across stimuli, for example, with a larger effect reported for abstract stimuli compared to interior spaces. A comparison across stimuli that share similar physical features and belong to the same categories is warranted to determine whether curvature is a basis of object preference. Another important question is whether inspection differences, based on contour and object category, affect object preference. In Experiment 1, we addressed these questions by recording eye movements as participants rated their preferences for images of two types of common-use objects: tables and chairs. In Experiment 2, we limited the stimuli presentation to 84 ms, as brief presentations are thought to enhance the curvature effect. Neither of the two experiments confirmed a clear preference for curvature in tables or chairs. Yet, curvature significantly influenced fixation durations, with curvilinear tables eliciting longer fixations than rectilinear ones, although without affecting overall preference. The findings are discussed in the context of familiarity and object functionality in shaping preference judgements.
La prédiction des entreprises qui connaîtront une croissance rapide, et les raisons pour lesquelles elles le font, fait l'objet de recherches depuis de nombreuses décennies. Les chercheurs explorent l'utilisation de techniques d'apprentissage machine supervisées (modèle de filet élastique, forêt d'arbres décisionnels et filet neuronal) pour trouver une population embryonnaire d'entreprises à forte croissance (EFC) dans les données administratives canadiennes des entreprises dérivées de dossiers fiscaux anonymisés. Le vaste ensemble de variables comprend des indicateurs de l'industrie, de la géographie et de la complexité (p. ex., de multiples activités industrielles), de même que la propriété étrangère. Même si environ une entreprise sur huit de l'ensemble de l’échantillon deviendra une EFC, la méthodologie fait ressortir un sous-échantillon d'environ 25 % à 30 % de cette dimension, c'est-à-dire qu'une sur quatre parviendra à ce statut et que trois résultats sur quatre seront faussement positifs. Les variables de l'industrie sont d'une importance manifeste sur le plan des prédictions, tout comme les variables indicatrices d'entreprises plus petites et (particulièrement) plus jeunes. Cependant, les chercheurs conseillent de ne pas interpréter l'analyse comme causale.
The growing prominence of Ulva in aquaculture is driven by its adaptability, rapid growth, nutritional advantages, and diverse biochemical composition. These green macroalgae have gained increasing attention for cultivation in lower salinity areas, expanding aquaculture beyond traditional euhaline environments. Our study investigated the distribution of economically valuable compounds in the most prominent Ulva crop species of the wider Baltic Sea region. We included 249 populations across the full Atlantic‐Baltic Sea transect (>3000 km) and took into account prevailing fluctuating abiotic factors like salinity and nutrient regimes during the vegetation peak season. We revealed an overall trend of increasing crude protein content with increasing salinity in species with occurrence along the whole Atlantic‐Baltic Sea transect ( U. intestinalis : slope = 0.29; U. linza : slope = 0.09) and those only present in higher salinity regions ( U. compressa : slope = 0.36; U. fenestrata : slope = 0.18) and confirmed an increase of pigments with increasing nitrogen tissue levels for most species ( U. compressa : r pigments = 0.43; U. fenestrata : r pigments = 0.01; U. intestinalis : r pigments = 0.13; U. linza : r pigments = 0.21). With this mapping of the resource availability of valuable compounds in natural Ulva biomass of the Baltic Sea region, we have contributed to the understanding of the potential of Ulva species as key players in sustainable aquaculture practices evolving in the Baltic Sea region. Further, we have underscored the necessity of habitat‐dependent crop selection and the importance of horticulture methodology for establishing Ulva as a viable future crop in the wider Baltic Sea.
Temporary ponds in agricultural landscapes, highly vulnerable to anthropogenic pressure and climatic variation, constitute unique habitats for microalgae and endangered filter feeders (large branchiopods). Such ponds play a crucial role in the functioning of farmland ecosystem, yet they remain largely understudied. Our study is the first to examine changes in phytoplankton communities in temporary kettle hole ponds in relation to rapid shifts in biotic (large branchiopods) and physical and chemical parameters of water. We conducted our research over a three-year cycle (in nine ponds in western Poland), with sampling starting in spring when inundation usually occurs, and continuing until the ponds dried out. Among 406 phytoplankton taxa (mainly euglenoids, but also diatoms and chlorophytes), locally rare species (e.g. Desmatractum indutum) were noted. When branchiopods occurred in the ponds, the phytoplankton communities shifted towards unicellular chlorophytes. Furthermore, nitrogen forms, temperature, conductivity, and pH were the abiotic factors altering the studied communities. Surprisingly, the diversity of phytoplankton species did not decrease with increasing temperature, which is inconsistent with the trend observed in permanent water bodies. The study identified specific drivers of phytoplankton community structure and dynamics, underscoring their ecological significance and management implications. These insights will be valuable for future conservation strategies of temporary ponds, crucial in sustaining biodiversity in farmland areas.
Interventions have been designed to close achievement gaps in Science, Technology, Engineering, and Math (STEM) disciplines and to remedy the “leaky STEM pipeline”. However, there has been little focus on designing complementary interventions that seek to broaden the youth population who “enter the STEM pipeline”. The current work aims to broaden STEM engagement in youth by developing a STEM intervention using unrecognized forms of cultural capital. These novel, basketball-based interventions were designed to engage a naturally occurring population of youth with pre-existing interest in sports but low levels of pre-existing STEM interest, ranging from the 2nd to the 12th grades. These interventions utilized sports as a venue for informal STEM learning across three variations: a single-hour event, a one-day clinic, and a multi-day camp. Participants’ interest in pursuing a STEM career significantly increased across all three variations of the STEM intervention. Notably, these effect sizes were descriptively larger for programs of longer duration and were significantly stronger for students who reported playing basketball prior to the program. The current work introduces a novel STEM education intervention that has been shown to be repeatedly successful in utilizing students’ pre-existing interest in sports as a bridge to STEM engagement.
The debate on voting age 16 is intensifying all over Europe, raising important empirical questions about the political maturity of underage citizens. Building on a survey of 4,000 young citizens aged 16 to 25 years, we shed light on the Swiss context. We find that Swiss citizens aged 16 and 17 are as politically mature as young adults aged 18 to 25. Regarding political dispositions, we find that citizens aged 16 and 17 are as politically interested as citizens aged 18 to 25 and that they display comparable levels of political efficacy and comparable attitudes towards voting as a civic duty. In addition, citizens aged 16 and 17 show stronger intentions to participate in elections and comparable intentions to participate in popular votes. Regarding political behavior, we find that citizens aged 16 and 17 consume more political information than citizens aged 18 to 25 and are exposed to political discussions with similar frequency. We conclude that citizens aged 16 and 17 are ready to vote.
Laying additional clutches of eggs, or renesting, can provide birds with more opportunities to breed each season, ultimately increasing reproductive potential. This is important for long-lived species like cranes, that produce relatively few offspring annually. The reintroduced Eastern Migratory Population (EMP) of endangered Whooping Cranes relies on releases of captive-reared juveniles for population growth. Using long-term nest monitoring data, we assessed the renesting propensity of 105 unique pairs of Whooping Cranes during 2005–2024 (n = 359). We used a two-tiered analysis of binomial generalized linear mixed-effects models to evaluate the effects of 15 individual covariates, related to parental age or experience, nest management geography, or chronology. Overall, 37.3% of pairs renested following failed first nesting attempts. We documented higher renesting rates from breeding females that were older or had more years of nesting experience (37.1% increase for each unit increase in female age), pairs outside of the regions in which captive-reared cranes were released (264.0% increase in “other” region compared to Necedah), or that had nests fail earlier in the season (10.1% decline for each day later in the season a first nest failed). Additionally, when eggs were collected from first nests as a part of nest management, pairs were more likely to renest (69.4% renested) than if their nest failed naturally (27.3% renested). Low rates of natural reproduction limit growth rates in the EMP, so understanding effects of management actions and limitations on breeding are important conservation tools which can be applied to other endangered species.
Previous research points to potential challenges autistic children face in constructing coherent narratives and establishing causal connections between events, although findings remain inconclusive. Furthermore, most studies focus on English-speaking children, leaving the narrative coherence skills of autistic children from other linguistic/cultural contexts underexplored. This study investigated the differences in narrative coherence between 42 autistic and 56 typically developing (TD) Spanish-speaking children matched on age (M = 8.51 years). Based on theories of rhetorical relations (RRs), which track relations between discourse units, we aimed to offer a new perspective on how coherence is achieved in children's narratives, with an emphasis on the causal RRs established. Causal RRs were coded for the specific type of RR, presence/absence of connectives, causality domain, and mention/omission of key events. Additional coherence measures included tallying the total number of RRs (causal and non-causal) and assessing narrative macrostructure through a rating scale, in line with more standard practices in the field. Results showed that, despite producing a comparable number of causal RRs, autistic children established significantly fewer causal RRs involving characters' intentions and key story events compared to TD children. Moreover, autistic children established fewer RRs overall and obtained lower macrostructure scores, suggesting lower narrative coherence levels.
Animal welfare is influenced by the cumulative life experiences of an individual. Among these, exposure to chronic stressors has a significant impact on both physical and mental health, contributing to premature aging—a process linked to telomere shortening. Conversely, positive experiences have been shown to mitigate, delay, and sometimes reverse telomere attrition. This suggests that telomere length could be a reliable indicator for assessing animal welfare. This study explored the association between telomere length and characteristics such as life history, environment, and health in domestic dogs. Buccal swabs collected DNA samples from 250 dogs, and telomere length was quantified via qPCR. Our findings revealed that environmental factors significantly influenced telomere length. Dogs housed in kennels or subjected to low physical activity levels exhibited shorter telomeres. Similarly, dogs living in groups of more than five dogs had shorter telomeres, and male dogs were found to have longer telomeres than females. Overall, these results highlight the importance of environmental conditions in influencing telomere length in dogs and the potential to use this biological indicator to evaluate animal welfare.
In semi-arid coastal wetlands, there is limited information on how the water table responds to the artificial, anthropogenic opening of sandbars (SB) at their mouths. We hypothesize that water restrictions, combined with a prolonged closure of the SB, degrade stream quality. Conversely, opening the barrier should lead to a flushing effect, causing streams to resemble seawater in composition. We studied the Tongoy estuary in the Coquimbo Region, Chile, where six station points were surveyed over 20 months, encompassing several SB openings and closings. Water pH, turbidity and redox potential tended to decrease following SB openings, while dissolved oxygen saturation, electrical conductivity, salinity, and density increased as seawater entered the estuary. Water temperature generally followed seasonal air temperature trends, whereas dissolved oxygen concentration showed a negative relationship with temperature. Nitrate and phosphorus levels were less influenced by SB openings. Although several variables exhibited trends consistent with SB status, in the long term, they tended to align with seawater conditions. Our results suggest that SB openings drive a flushing process and a directional shift towards marine conditions. This transition from freshwater to saline environments follows a predictable cycle, with potential implications for habitat creation and loss, as well as for biological communities. When respect to ecological management, determining an “ideal” state for the Tongoy stream is not straightforward. Establishing protocols for the opening and closing of the SB is crucial and requires studies on species composition dynamics and physicochemical variables to balance human interests, nature conservation and ecosystem function.
Evaluating restoration practices such as admixture provenancing or mixing of multiple source populations for greater intraspecific variation in plant restorations helps to understand the utility of the practice in different scenarios. We do not know whether any population mixtures in admixture provenancing will deliver positive outcomes when interacting. To understand how population and species' identity influence plant performance and trait outcomes in mixtures, we assessed trait variation among populations of two forb species native to the Western United States (Dieteria canescens and Heterotheca villosa) following pairwise competition in pots with single-population monocultures, two-population mixtures, and two-species mixtures with D. canescens as a focal plant in a greenhouse common environment. Plants were harvested after 7 weeks and height, leaf count, root length, and root mass fraction (RMF) traits were measured, as well as whole plant biomass. We found two-population mixtures and single-population monocultures to have similar biomass while some two-species mixtures differed from respective single-population monocultures. Neighbor trait differences in shoot height and root length best predicted plant growth following interactions, while increasing neighbor trait differences resulted in positive growth outcomes for all but one trait by treatment interaction (R2 = 0.17, p < 0.001). In this single case, plant growth decreased with increasing differences in RMF for the two-species mixture treatment, surprisingly. These findings show nuance in the outcomes of interactions within and between populations and species: they are highly dependent on population identity and traits measured, which are aspects that must be considered when evaluating restoration materials and strategies.
Replacing fallow periods with cover crops (CCs) is a key conservation agriculture measure to enhance soil health, yet its effectiveness depends on pedoclimatic conditions. However, the effects of CCs, such as tillage radish (TR), on soil health indicators under different environmental and management conditions remain insufficiently unexplored. This study assessed the effects of TR on soil health indicators related to carbon (C), nitrogen (N), and phosphorus (P) cycling in two locations (Signa –SN– and Cesa –CS–) under conservation agriculture with different pedoclimatic conditions. Biomass accumulation and P uptake by TR were significantly higher at SN than CS, likely due to more favourable soil and climatic conditions. The higher biomass at SN resulted in a threefold higher accumulation of soil organic carbon (SOC) in the upper 5 cm compared to CS. TR increased SOC, labile organic C, soil P test, and microbial biomass C, N, and P, although most effects varied by location. Soil P test increased with TR biomass, confirming its role in P mobilisation. At SN, TR improved nitrogen retention in the soil by about 34 mg N kg ⁻¹ compared to fallow management. These findings highlight TR's positive effects on some soil health indicators related to relevant ecosystem services, particularly C storage, microbial biomass, P mobilisation and recycling, and N balance, with site‐specific variations depending on pedoclimatic conditions. Future studies should explore the long‐term impacts of TR on soil fertility and nutrient cycling across diverse agroecosystems, involving different management practices and pedoclimatic conditions for solid practical recommendations.
Drosophila melanogaster, the common fruit fly, has been instrumental to our understanding of evolution, genetics and disease. There are benefits to studying these flies in the wild, including assessment of their naturally occurring microbiota. To facilitate efforts to catch wild D. melanogaster, we designed two fly traps and evaluated several candidate attractants. The first trap utilized a stable food substrate that can be used to catch live flies to establish new lab colonies. The second trap was designed to be reusable and easy to ship to enable the collection of flies over time from diverse locations. We evaluated several chemical attractants derived from banana and from marula fruit, which is the proposed ancestral food host of D. melanogaster. We found that wild flies were preferentially attracted to banana-based odorants over marula-derived ones. Overall, these traps and attractants represent an inexpensive and simple option for the collection of wild D. melanogaster and related species for sampling or colony establishment.
The past agrobiodiversity and evolution of barley, a staple cereal in the northwestern Mediterranean region for the last ca 8000 years, is still poorly documented. This study employed an intensive sampling strategy to analyse morphometric variation of 9817 grains (264 samples and 102 sites), dating from the Neolithic to the Late Middle Ages, from southern France and Catalonia. We utilized an archaeophenomic approach to quantify grain size and shape through elliptic Fourier transformation. We contrasted the variation of archaeological grains with that of 6397 caryopses from 105 modern Euro-Mediterranean varieties of 2-row/6-row subspecies, hulled/naked types. Past climate conditions in southern France/Catalonia were investigated to provide an environmental framework for interpreting morphometric variation. Barley grains increased in size, and changed in shape over time, likely owing to a combination of factors, including environmental adaptation and human selection, coupled with changes in agricultural practices. Naked barley was prevalent during the Neolithic, while the proportion of hulled barley increased from the Late Bronze Age onwards. In contrast, subspecies were identified in all assemblages, without clear temporal trends but with strong variation between assemblages. This study uncovers a complex interplay of environmental and human factors in cereal evolution, highlighting the evolution of agrobiodiversity that fuelled the development of modern societies.
This article is part of the theme issue ‘Unravelling domestication: multi-disciplinary perspectives on human and non-human relationships in the past, present and future’.
Pinus and Quercus species face anthropogenic disturbances that affect their structure and distribution. Understanding the distribution patterns of these species is crucial for establishing appropriate management practices to conserve their diversity and the ecosystem services they provide. The aim of this study was to analyze pine and oak species’ distribution, dominance, and diversity patterns along an altitudinal gradient in the Monarch Butterfly Biosphere Reserve. We established 6 elevation transects (2,250 - 3,300 m asl) with 32 points every 150 m. At each site, 25 pine and oak trees located between 0 and 60 m from a central coordinate, with a diameter at breast height ≥ 10 cm, were recorded. Distribution patterns, dominance, and alpha and beta diversity were analyzed. The least abundant species were the most geographically restricted. Pinus pseudostrobus and Quercus laurina were the most dominant species. Alpha diversity was not associated with elevation, nor did it show a defined distribution pattern. Beta diversity was associated with elevation at the highest and lowest elevations, forming an inverted hump. These patterns may be the result of human activities, such as logging and agriculture, which have altered natural patterns of diversity and distribution.
Imbalanced binary data may be more common than expected in medical trials. In this paper, we propose a new class of link function for binary response based on the cumulative distribution function of the scale mixture of skew-normal distributions, which can be useful for fitting imbalanced binary data. The proposed link class has as special cases several link functions proposed in the literature, such as the probit and Student’s-t link, and we present a Bayesian approach for model fitting. Further, we develop Bayesian case-deletion influence diagnostics based on the Kullback-Leibler divergence. The newly developed procedures are illustrated with one example as well as a simulation, which illustrates the potential of the proposed class of links as an alternative for binary regression models when imbalanced binary data is presented.
Importance
Food insecurity is a social risk factor that may be associated with cardiovascular health across the life course.
Objective
To evaluate the association of food insecurity in early childhood with cardiovascular health (CVH) in young adulthood and whether associations are modified by participation during childhood in the Supplemental Nutrition Assistance Program (SNAP).
Design, Setting, and Participants
The Future of Families–Cardiovascular Health Among Young Adults cohort study was conducted in 20 US cities among 1071 individuals enrolled at birth (February 1998 to September 2000), evaluated in childhood (age, 3-5 years), and followed up to young adulthood (September 2021 to September 2023; mean [SD] participant age, 22.3 [0.7] years).
Main Outcomes and Measures
Household food insecurity (assessed by the US Department of Agriculture Food Insecurity survey) and SNAP participation at ages 3 to 5 years and CVH (assessed by the American Heart Association Life’s Essential 8 [LE8] score, component LE8 scores, and clinical CVH risk factors).
Results
Of the 1071 participants, 570 were female (53%), 422 (39%) lived in households with food insecurity, and 475 (44%) participated in SNAP. Early childhood food insecurity was associated with having a lower LE8 score in young adulthood (β, −2.2 [95% CI, −4.0 to −0.4]). Among component LE8 scores and clinical CVH risk factors, food insecurity was associated with a lower LE8 score for body mass index (BMI; β, −4.9 [95% CI, −9.6 to −0.3]) and higher odds of having a BMI of 30 or more (adjusted odds ratio, 1.40 [95% CI, 1.07-1.84]). Food insecurity was more strongly associated with a lower LE8 score among those whose households did not participate in SNAP (β, −4.9 [95% CI, −7.6 to −2.3]) compared with those whose households participated in SNAP (β, 1.0 [95% CI, −1.6 to 3.7]).
Conclusions and Significance
This study suggests that early childhood food insecurity is associated with a higher BMI in young adulthood, which is associated with a worse overall LE8 score, especially among children whose families did not participate in SNAP. Policies to promote food security among children may promote healthy BMIs and better CVH across the life course.
In recent years, there has been a growing interest in research on Ceratozamia cycads, which has resulted in a significant increase in our understanding of their diversity. However, species complexes that have been tackled through integrative methodologies have shown a bias toward morphology over genealogy. Thus, there arises the necessity to re‐evaluate the Ceratozamia mexicana species complex at the inter‐population level using phylogeographic tools. For this purpose, we have employed an integrative taxonomy protocol. This protocol delineates species as testable hypotheses, incorporating lines of evidence within a reproducible and falsifiable framework. The evaluated data encompassed (i) phylogenetic analyses, (ii) multivariate morphometric analyses, and (iii) climatic niche analyses. Out of the 196 individuals from 13 studied populations, seven monophyletic groups were recovered. These groups were substantiated by multivariate morphometric analysis, revealing significant differences, and were further validated by niche divergence. These results underscore a “whole agreement” across the three disciplines, thus providing robust support for acknowledging the species as distinct lineages. The species delimited by these lineages, encompassing phylogenetic, morphological, and environmental factors, correspond to C. brevifrons , C. delucana , C. decumbens , C. mexicana , C. morettii , C. tenuis , and a novel cryptic species, sister to the latter. Finally, this genealogical characterization will offer utility in the future for uncovering the genetic identity of the holotype of the type species within the Ceratozamia genus.
This study examined the impact of media multitasking on the reading habits
and practices of 700 Moroccan English as a foreign language (EFL) teachers, utilizing a time-diary survey methodology. The findings reveal that a significant number of teachers engage in media multitasking, particularly watching television and using the Internet, while reading for both academic and recreational purposes. Ordinal logistic regression (OR) analyses showed that school type and specific multitasking activities were significant predictors of the displacement of time spent on reading. Teachers in urban/suburban schools reported higher levels of displacement compared with those in rural areas (OR = 2.23; 95% CI [1.59, 3.14]), while more-experienced teachers (6–10 years) reported less displacement (OR = 0.56; 95% CI [0.39, 0.80]). Watching television “most of the time” while reading was
associated with greater displacement for both recreational (OR = 2.61; 95% CI [1.18, 5.79]) and academic reading (OR = 2.64; 95% CI [1.16, 6.06]). Social network showed contrasting associations: significantly lower displacement for recreational reading, but no significant relationship with academic reading displacement. These results suggest that media multitasking has context-dependent effects on teachers’ reading practices, with implications for their professional development and literacy instruction. This study emphasizes the need for targeted interventions to help teachers manage digital distractions and foster focused reading habits in the digital age. Future research should explore the long-term consequences of media multitasking on teachers’ effectiveness and identify strategies to promote engaged reading across diverse educational settings.
Current climatic and environmental changes necessitate the development of reliable species distribution models to justify management decisions aimed at mitigating their impacts on biodiversity. Such models, in turn, require relevant data on the distribution of species at a local level. The extreme climatic conditions of Daurian pika habitats (hot summers and very cold winters) and its keystone role in ecosystems of North Asian steppes make Daurian pika a suitable model species for analyzing the consequences of climate warming. This paper quantifies predictors determining Daurian pika abundance on a local scale. Eight environmental variables are measured and Daurian pika burrow entrances counted on 236 sampling plots 10 × 10 m2 in size. Generalized linear models are used to identify relationships between the chosen environmental predictors and the number of burrow entrances. The best models use the following predictors: projective cover of dense tall vegetation, slope aspect, slope inclination, soil thickness, soil density, and soil stoniness. Daurian pikas are statistically significantly more abundant on plots featuring a thick soil layer covered by dense tall vegetation. The number of burrow entrances is significantly less on north- and east-facing slopes. Burrows are more abundant on gentle slopes and plains and in areas with less dense and stony soils. The models predict the number of burrow entrances on test plots reasonably well. The results demonstrate that the chosen set of abiotic factors accurately predicts the Daurian pika distribution on a local scale. Apparently, the factors that are analyzed include direct ones that potentially affect the Daurian pika distribution in a similar way in any environment. Such direct factors include soil parameters enabling Daurian pikas to make burrows and, probably, vegetation cover. Other factors determine the impact of climate on microclimate and food resources, and their effects vary depending on local environmental conditions.
In 21st-century American cities, urban crime remains a critical public safety concern influenced by complex social, political, and environmental structures. Crime is not randomly distributed and built-environment characteristics, such as street network configuration, impact criminal activity through spatial dependence effects at multiple scales. This study investigates the cross-sectional, multi-scale spatial effects of street network configuration on property crime across neighborhoods in Charlotte, North Carolina. Specifically, we examine whether the fundamental characteristics of a neighborhood’s street network contribute to variations in its property crime. Using a novel and granular spatial approach, incorporating spatial econometric models (SAR, CAR, and GWR), several street network characteristics, including density, connectivity, and centrality, within five nested buffer bands are measured to capture both local and non-local influences. The results provide strong and consistent evidence that certain characteristics of the neighborhood street network, such as connectivity and accessibility, significantly influence the occurrence of property crime. Impacts are also found to be spatially heterogenous, manifesting themselves at the mid-range scale rather than hyper-locally. The integration of comprehensive measures of street network configuration into spatially explicit models offers new opportunities for advancement in environmental criminology literature. Such spatial dynamics further contribute to urban safety policy by informing decision-makers so that they can ensure a defensively built environment design.
Rails are a fundamental part of rail transport ensuring smooth movement of rail vehicles. Rails may, however, break or buckle, which threatens the safety and continuity of rail traffic. In this study, we focused on broken and buckled rail incidents in Czechia between 2002 and 2022 in order to investigate their spatiotemporal patterns, the most hazardous locations, and the factors influencing both issues. Broken rails were often reported in the cold months (November–March; 78.3%). Buckled rails, on the contrary, occurred in the summer (June–August; 83.1%). From a logistic regression model that included factors such as daily air temperature, rail traffic intensity, railway line geometry, share of freight traffic, maximum axle load or maximum allowed train speed, a strong influence of daily air temperature on the occurrence of these problems was found. This is particularly important given the increase in air temperature due to climate change. The most hazardous locations on the Czech rail network were identified using the KDE+ method. The results provide infrastructure managers and other stakeholders with valuable insights into the occurrence of broken and buckled rails and can support mitigation efforts.
Instream earthworks occur in many streams in Australia, often following damage by flooding, to rehabilitate stream banks, remove flood-generated debris or protect against future flood damage. Earthworks may unavoidably disturb habitat, and understanding how species respond to such disturbance is critical to long-term conservation. We report the responses of platypuses to major instream works in the Blue Lake, upper Jenolan River, following severe catchment erosion and flooding in February 2020 and March 2021. Platypuses continued to use the Blue Lake during the works in 2020, but were observed or detected by remote cameras, moving into or out of the lake, less often as the works progressed, returning quickly on works completion and lake refilling. During later works in 2022, platypuses were seen in the Blue Lake or detected by remote cameras only for a few days after the start of the works, returning more slowly than in 2020, but indicating persistent long-term use of the Blue Lake despite these major instream works. Our analysis of available platypus occurrence data, and macroinvertebrate and benthic substrate data highlighted the importance of coarse benthic substrates associated with platypus occurrence in other streams in the Greater Blue Mountains World Heritage Area, suggesting potential benefits of targeted benthic substrate rehabilitation following such instream works.
In Taiwan, sexual minority men (SMM) account for a significant portion of new HIV cases, highlighting the need for effective prevention measures. However, pre-exposure prophylaxis (PrEP) use remains limited, necessitating a comprehensive examination of barriers. This study examined PrEP engagement and its predictors among 284 SMM in Taiwan. Participants were categorized into five stages, based on the Transtheoretical Model of Health Behavior Change, reflecting distinct levels of PrEP engagement. Ordinal logistic regression, informed by the Behavioral Model of Health Service Use, identified factors associated with being positioned at higher stages of the cascade. Significant predictors of PrEP engagement included predisposing (i.e., relationship status), enabling (i.e., PrEP knowledge, community connectedness), and need factors (i.e., number of sexual partners, chemsex). Findings highlight the need for further research on education, relationship dynamics, and sexual risk behaviors to inform tailored interventions that enhance PrEP engagement among SMM in Taiwan and the broader Asia region.
Counterattacks against predators are reported in several web‐nesting spider mites (Acari: Tetranychidae) that display communal sociality. For example, adults of Stigmaeopsis longus (Saito) kill phytoseiid larvae that invade their nests. We recently found similar defensive behaviours in various life stages of Schizotetranychus brevisetosus Ehara, a specialist of evergreen oak Quercus glauca Thunb. (Fagales: Fagaceae), which attack larvae of Feltiella acarisuga (Vallot) (Diptera: Cecidomyiidae) in groups outside the nest. However, due to the limited number of observations, we could not establish the factors inducing this counterattack or its efficiency against general predators. We conducted two experiments to evaluate the degree of S. brevisetosus female attacks against abiotic substances and living organisms. First, we assessed the behaviours towards predator‐mimicking glass beads (50–400 μm in diameter) randomly spread over the leaf surface. Second, we monitored the 24‐h survival of phytoseiid eggs ( Amblyseius swirskii Athias‐Henriot, Acari: Phytoseiidae) evenly placed near S. brevisetosus nests under various experimental conditions, including the presence or absence of adult mites, intact or removed webs, and the presence or absence of a phytoseiid larva to stimulate females (because phytoseiid larvae easily enter web nests, their presence may provoke counterattacks). In the first experiment, females responded immediately to the glass beads of all sizes, although their activity gradually declined over the subsequent 3‐day period. Three types of behaviours were observed: patrolling around the nest, pecking the glass beads, and grasping them. In the second experiment, approximately 20% of phytoseiid eggs died when females were present, whereas no eggs died in their absence. There was no effect of webs and phytoseiid larvae on the mortality of eggs. These results demonstrated that physical stimuli play a role in evoking counterattacks in S. brevisetosus females and thereby reduce potential predation risks.
Plain Language Summary
Understanding how much Earth's temperature may change in response to increasing atmospheric CO2 concentrations is essential for understanding outputs of earth system models. A key component of this process is equilibrium climate sensitivity (ECS), which estimates how temperature changes respond to a doubling of atmospheric CO2 levels. Recent earth system models have shown a wider range of ECS values than before, increasing uncertainty about the future. In this study, we used a simple climate model to investigate how different constraints on ECS uncertainty shapes the uncertainty in end‐of‐century temperature projections. Our findings show that excluding certain lines of evidence (process and paleoclimate evidence) results in more uncertain temperature projections. This occurs because leaving out critical lines of evidence increases the likelihood of ECS values falling at either ends of the distribution. Therefore, including this evidence is critical for constraining ECS distributions and reducing the uncertainty of temperature projections. Our results also show by how much inducing all information at our disposal to constrain ECS can narrow the uncertainty of future temperature projections. Simple climate models with a probabilistic framework offer a fast, interpretable way to test how ECS distributions impact climate projections.
Substantial in vitro experimental data have been produced about the safety, antioxidant, neuro- and hepatoprotective effects of a series of recently synthesized N-pyrrolyl hydrazide-hydrazones (compounds 5, 5a–5g). However, compound activity across multiple assays varies and it is challenging to elucidate the favorable physicochemical characteristics of the studied compounds and guide further lead optimization. The aim of the current study is to apply exploratory data analysis in order to profile the biological effects of the novel hydrazide-hydrazones, gain insights related to their mechanisms of action in the context of in silico predictions and identify key predictor–outcome relationships. We collected a dataset from available in vitro studies of compounds 5, 5a–5g. It included cytotoxicity values, protection against hydrogen peroxide-induced damage in HepG2 and SH-SY5Y cells, two radical scavenging assays and a hemolysis assay across a range of treatment concentrations. SwissADME-based predictions of chemometric and ADME parameters and pro-oxidant enzyme docking data were generated to provide context for the interpretation of in vitro outcome patterns and identify causal relationships. Multiple factor analysis (MFA), followed by hierarchical clustering on principal components (HCPC), was applied to profile compounds’ biological behavior. This revealed that differences in the number of H-bond donors, in the permeability coefficient and in the docking scores to two pro-oxidant enzymes could aid in explaining the effects of compounds with similar in vitro profiles. HCPC differentiated 5a as mostly neuroprotective, 5 and 5d as hepatoprotective radical scavengers, 5g with higher docking affinity to 5-lipoxygenase (5-LOX) and myeloperoxidase (MPO) and 5b, 5c and 5f as having less H-bond donors and variable in vitro activity. The consensus application of three variable selection approaches based on standard lasso regression, robust penalized regression and random forest confirmed the relationships between some in vitro outcomes and LogP, pan-assay interference (PAINS) alerts, 5-LOX allosteric site docking and H-bond donor numbers. The exploratory analysis of the combined in vitro and in silico dataset provides useful insights which could help explain the major drivers behind the experimental results. It can be informative in the design of new, improved members of the series of novel N-pyrrolyl hydrazide-hydrazones with better neuroprotective potential and less side effects.
Potassium chloride (KCl) is the main source of potassium (K) in Brazilian agriculture, but its high import dependency and the need for split applications increase costs and expose the system to supply and efficiency risks. Understanding the availability and release kinetics of potassium (K) from biochar-based fertilizers (K-BBFs) is crucial for optimizing their use as full or partial substitutes for KCl in Brazilian agriculture. This study evaluated biochars derived from banana peel (BP), coffee husk (CH), and chicken manure (CM), both in their pure form and co-pyrolyzed with KCl (composites) at 300 °C and 650 °C, as K sources for corn grown in two contrasting Oxisols. For pure biochars, feedstock type and pyrolysis temperature significantly influenced K content and release kinetics. Higher pyrolysis temperatures increased K content in BP and CH biochars but not in CM, while also slowing K release in CH and CM. Co-pyrolysis with KCl increased biochar yield, ash content, and K availability. Composites released more K than pure biochar but less than KCl, and at a slower rate. Notably, banana peel biochar co-pyrolyzed with KCl at 650 °C (CBP650) exhibited 36% slower K release and reduced KCl use by 82% while maintaining similar K use efficiency and corn growth. All K-BBFs matched KCl in promoting robust corn growth in clay soil, increasing biomass by 5.3 times and K uptake by 9 times compared to unfertilized (no K addition) plants. In sandy Oxisol, K-BBFs boosted biomass by up to 3.5 times compared to unfertilized plants, though some pure biochars were less effective than KCl in supporting full corn growth. Soil texture strongly influenced K availability, with sandier soils exhibiting higher K levels in solution. These findings suggest that kinetic release studies in abiotic systems, such as lysimeters with sand, are not suitable for evaluating K-BBFs as slow-release fertilizers. Due to lower K retention in sandy soil and solution K levels exceeding 1100 mg L−1, split applications of some K-BBFs are recommended to prevent corn cation uptake imbalances and soil K leaching. Additionally, granulating biochar–KCl composites may enhance K retention and regulate its release in sandy Oxisols.
Objective
The objective of the present study was to evaluate the impact of frailty on outcomes for older patients presenting with major trauma to a tertiary ED in Aotearoa New Zealand.
Methods
A retrospective observational study of patients 65 years and older who presented to Christchurch ED, New Zealand, with major trauma between 1 January and 31 December 2022. The primary outcome was a composite of in‐hospital mortality or increased care requirements on discharge from hospital. Demographic details, in‐hospital management, and outcomes were retrieved. Clinical Frailty Scale scoring had prospectively been recorded at the time of admission. Univariable analysis of discrete dependent variables was carried out. Mediation analysis was undertaken, wherein frailty was the mediator between age and the primary outcome variable.
Results
After exclusion criteria were applied, 134 patients were included for analysis. Even after controlling for age, for every additional point on the Clinical Frailty Scale, the odds of in‐hospital mortality or increased care requirements on discharge increased by 36.4% (95% confidence interval: 9.4–85). Only 33% of these major trauma patients were appropriately identified at presentation and so received a trauma team activation, with worsened activation rates with increasing frailty.
Conclusions
The presence of significant injuries in older trauma patients is under‐recognised. Frailty scoring could be used in the ED for early identification of those patients at high risk of poor outcomes, so that active management strategies can be put in place to optimise their care.
Submarine canyons are ubiquitous geomorphic features found intercepting the continental margins. As such,they provide environmental conditions suitable for many suspension feeding organisms, as they settle on steeprocky canyon walls, whilst taking advantage of increased currents that bring suspended organic matter and food.Additionally, demersal fishing grounds can be found surrounding submarine canyons where it can negativelyaffect species inhabiting these environments, including vulnerable ecosystems such as cold-water corals (CWCs).In order to understand the impacts of demersal fisheries in CWC communities, we first need to understand theirdistribution, species composition and vulnerability. Blanes Canyon is an example of a submarine canyon sur-rounded by demersal fishing grounds, where baseline knowledge on CWCs currently lacks. This study contributesto filling these knowledge gaps by using a dense grid of ROV transects along the canyon, high resolution ba-thymetry data and CTD surveys, which altogether provide a quantitative description of megabenthic assem-blages. Blanes Canyon hosts at least 12 CWC species within 450–1300 m depth range, mainly inhabiting the steepcanyon walls. Different assemblages of CWC species were found. Desmophyllum dianthus was the most abundantspecies, found throughout the entire canyon. Colonial scleractinian species (Desmophyllum pertusum andMadrepora oculata) were found in the canyon head but were lacking in the eastern canyon branch, whereoctocorals (Muriceides lepida) and black corals (Leiopathes glaberrima) were prevailing. Detailed CTD surveyindicated that nepheloid layers (bottom and intermediate) were found at the same depth range as the mega-benthic communities, since they provide suspension feeders with particulate organic matter (POM). Overall, thisstudy confirms Blanes Canyon as a CWC habitat, providing densities and spatial distribution of different meg-abenthic species, along with information of their environmental niches.
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