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R: A Language and Environment for Statistical Computing
... All input variables were scaled, centered, and log-transformed. Analyses were carried out using the R/prcomp function and the biplots were created with custom ggplot2 scripts [39]. Likewise, k-means clustering was carried out using R/cluster library [39]. ...
... Analyses were carried out using the R/prcomp function and the biplots were created with custom ggplot2 scripts [39]. Likewise, k-means clustering was carried out using R/cluster library [39]. A significant number of clusters was determined using the "elbow" heuristic method (not shown) which converged at 2 clusters. ...
... A significant number of clusters was determined using the "elbow" heuristic method (not shown) which converged at 2 clusters. Clusters were plotted using a R/ggplot2 library [39]. ...
Carotenoids are an abundant group of lipid-soluble antioxidants in maize kernels. Maize is a key target crop for carotenoid biofortification focused on using conventional plant breeding in native germplasm of temperate areas traced back partially to traditional cultivars (landraces). In this study, the objectives were to determine the variability of lutein (LUT), zeaxanthin (ZEA), α-cryptoxanthin (αCX), β-cryptoxanthin (βCX), α-carotene (αC), and β-carotene (βC) contents in the grain of 88 accessions of temperate maize from the Croatian genebank, and to evaluate the relationships among the contents of different carotenoids as well as the relationships between kernel color and hardness and carotenoid content. Highly significant variability among the 88 accessions was detected for all carotenoids. On average, the most abundant carotenoid was LUT with 13.2 μg g−1 followed by ZEA with 6.8 μg g−1 dry matter. A Principal Component Analysis revealed a clear distinction between α- (LUT, αCX, and αC) and β-branch (ZEA; βCX, and βC) carotenoids. β-branch carotenoids were positively correlated with kernel color, and weakly positively associated with kernel hardness. Our results suggest that some genebank accessions with a certain percentage of native germplasm may be a good source of carotenoid biofortification in Southeast Europe. However, due to the lack of association between LUT and ZEA, the breeding process could be cumbersome.
... 'Low' encompassed willow, alder (Alnus glutinosa), birch, digik am.org), which enabled the presence/absence of a red squirrel to be tagged in the meta-data of each image. The metadata was then extracted for analysis in R (R Core Development Team, 2022) using the camtrapR package (Niedballa et al., 2016). Two key metrics were extracted from each camera: (1) the total number of red squirrel images over the 5-day period, which included a minimum of 10 minutes between successive sightings to ensure that the data set predominantly focussed on independent foraging events (Parsons et al., 2021;Villette et al., 2017) and (2) the time in hours taken for the first squirrel to visit the feeder. ...
... All statistical analyses were performed in R (R Core Development Team, 2022). there being three stand types -broadleaf, conifer <40 years and conifer >40 years. ...
Effective methods for monitoring animal populations are crucial for species conservation and habitat management. Motion‐activated cameras provide an affordable method for passively surveying animal presence across the landscape but have mainly been used for studying large‐bodied mammals. This paper explores the relative abundance and habitat preferences of red squirrels ( Sciurus vulgaris ) in coniferous forests using cameras and live trapping. The study was conducted in two forests (Newborough and Pentraeth) on Anglesey, North Wales, with a total of 50 sampling locations across four habitat categories. Detailed woodland structure and composition data were gathered around each sampling location. We found a strong positive correlation between the number of individual red squirrels live trapped over 10 days with the number of camera images of squirrels recorded during a previous 5‐day period. The time interval between camera deployment and the first recorded image of a red squirrel showed a significant negative correlation with the number of individuals live trapped. Red squirrel relative abundance was negatively related to forest canopy openness, while the presence of Scots pine and increased tree species diversity were positively associated with the relative abundance of squirrels. There was also a strong site difference with lower relative abundance at Newborough compared with Pentraeth, which likely reflects the heavy thinning of mature forest at Newborough reducing tree crown connectivity. The results show that remotely activated cameras are an effective method for monitoring red squirrel populations across varying animal densities. The cameras also provided crucial information on red squirrel habitat preferences that can aid in woodland management and conservation efforts. Cameras have great potential to collect data on the population status of other small mammals, but it is essential that these methods are validated on a species‐by‐species basis.
... Prevalence (percentage indicating number of infected specimens relative to total studied specimens), and its 95% confidence interval (CI) were calculated in R, v.4.0.5, an open-access environment for statistical computing [55]. To compare parasite prevalence rates, we used Chi-squared (or Fisher's exact tests). ...
... taxonomic, sex, age, season, land-use). To test the importance of certain biotic factors (host species, sex, age) and abiotic factors (land-use type, season, elevation, urbanisation gradient) on the presence versus absence of T. gondii infection, we used general linear models (GLM) under the assumption of a binomial distribution (absence/presence), with the built-in glm function [55]. To test for colinearity and combined effects of multiple predictors, we ran a logistic regression, where sampling locality was included as a random effect. ...
Background
Toxoplasma gondii is a protozoan parasite that infects a large spectrum of warm-blooded animals, including humans. Small rodents and insectivores play an important role in the epidemiology of T. gondii and may serve as a source of infection for both, domestic and wild definitive felid hosts. Factors influencing the occurrence of T. gondii in wild small mammals are unknown, despite the fact that many intermediate host species are identified. We have used small mammals (Rodentia and Lipotyphla) captured over two years in various habitats, both in urbanised and in natural landscapes. We assessed the importance of land-use, season and host ecology on T. gondii infection.
Results
We examined 471 individuals belonging to 20 small mammal species, collected at 63 locations spread over wide altitude, habitat and land-use ranges from Romania. Heart tissue samples were individually analysed by PCR targeting the 529 bp repetitive DNA fragment of T. gondii. The overall prevalence of infection was 7.3%, with nine species of rodents and two species of shrews being found to carry T. gondii DNA. Five species showed high frequency of infection, with the highest prevalence found in Myodes glareolus (35.5%), followed by Spermophilus citellus (33.3%), Sorex minutus (23.1%), S. araneus (21.7%) and Micromys minutus (11.1%). Adults seemed more often infected than young, however when controlling for season, the difference was not significant, as in spring both adults and young showed higher infection rates, but more adults were sampled. Contrary to our expectations, urban/rural areas (with their implicit high density of domestic feline presence) had no effect on infection prevalence. In addition, neither habitat, nor land-use at sampling sites was important as only geographical location and host species were contributing factors to the infection risk.
Conclusions
High prevalence of T. gondii infection showed a highly localised, patchy occurrence, with long living and higher mobility host species being the most common carriers, especially during autumn.
... We used R (Version 4.3.1, [35]; RStudio version 2023.06.1.) to conduct to parallelized computations [36] at a high performance cluster computer of the University of Greifswald [37]. ...
... to conduct to parallelized computations [36] at a high performance cluster computer of the University of Greifswald [37]. Covariance structures were simulated using the R-package MASS [38], RCS are implemented in base R [35], and graphical illustration is done using ggplot2 and ggsci [39,40]. Figure 2 shows the median and interquartile range of the MSE. ...
Objective
Studies of intersectionality are increasing to examine health inequalities. Different proposals for examining intersections have recently been published. One approach (1) considers models specified with 1st and all 2nd -order effects and another (2) the stratification based on multiple covariates; both categorize continuous covariates. A simulation study was conducted in order to review both methods with regard to correct identification of intersections, rate of false positive results, and generalizability to independent data compared to an established approach (3) of backward variable elimination according to Bayesian information criterium (BE-BIC).
Study design and setting
Two basically different settings were simulated with 1000 replications: (1) comprised the covariates age, sex, body mass index, education, and diabetes in which no association was present between covariates and a continuous response and (2), comprising the same covariates, and a non-linear interaction term of age and sex, i.e., a non-linear increase in females above middle age formed the intersection of interest. The sample size (N = 200 to N = 3000) and signal to noise ratios (SNR, 0.5 to 4) were varied. In each simulated dataset bootstrap with replacement was used to fit the model to internal learning data and to predict outcomes using the fitted models in these data as well as the internal validation data. In both, the mean squared error (MSE) was calculated.
Results
In simulation setting 1, approaches 1/2 generated spurious effects in more than 90% of simulations across all sample sizes. In smaller sample size, approach 3 (BE-BIC) selected 36.5% the correct model, in larger sample size in 89.8% and always had a lower number of spurious effects. MSE in independent data was generally higher for approaches 1/2 when compared to 3. In simulation setting 2, approach 1 selected most frequently the correct interaction but frequently showed spurious effects (> 75%). Across all sample sizes and SNR, approach 3 generated least often spurious results and had lowest MSE in independent data.
Conclusion
Categorization of continuous covariates is detrimental to studies on intersectionality. Due to high model complexity such approaches are prone to spurious effects and often lack interpretability. Approach 3 (BE-BIC) is considerably more robust against spurious findings, showed better generalizability to independent data, and can be used with most statistical software. For intersectionality research we consider it more important to describe relevant intersections rather than all possible intersections.
... All the analyses were conducted in R version 4.1 [45], using the package ape, to construct PGLS models [46]. All the PGLS models were performed with data score as a weight variable through the summary tree to account for phylogenetic relationship. ...
The variation in egg and clutch mass in sympatric species at high altitudes is poorly understood, and the potential causes of variation are rarely investigated. This study aimed to describe the interspecific variation in avian egg and clutch mass among 22 sympatric bird species at an altitude of 3430 m. Our objective was to reduce potential confounding effects of biotic/abiotic factors and investigated hypotheses concerning allometry, clutch size, parental care, nest predation, and lifespan as possible correlates and explanations for the observed variation. Our findings indicated that both egg and clutch mass evolve with body mass across species. We found that egg mass variation was not explained by clutch size when controlling for allometric effects, which contrasts the “egg mass vs. clutch size trade-off” hypothesis. Additionally, we found that clutch mass was positively associated with parental care (reflected by development period) but negatively associated with predation rate. By substituting egg mass and clutch size into the models, we found that clutch size was significantly correlated with parental care, predation rate, and lifespan, while egg mass was only significantly associated with development period. Overall, these findings support life-history theories suggesting that reduced clutch size or mass is associated with a higher risk of predation, reduced parental care, but longer adult lifespan. Interestingly, our results indicate that clutch size has a greater influence on these factors compared to egg mass. This could be attributed to the fact that smaller clutch sizes result in a more notable decrease in energetic allocation, as they require a reduced effort in terms of offspring production, incubation, and feeding, as opposed to solely reducing egg size. These findings contribute to the growing evidence that life-history and ecological traits correlate with egg and clutch mass variation in sympatric species. However, further research is needed to explore the potential evolutionary causes underlying these patterns.
... and alakazam v1.2.1.999 21,17,15 . ...
Antibodies are vital to human immune responses and are composed of genetically variable heavy and light chains. These structures are initially expressed as B cell receptors (BCRs). BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated heavy and light chains, but advancements in single cell sequencing now pair heavy and light chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired heavy and light chain sequences to build phylogenetic trees. We found incorporating light chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree building methods and persisted even when mixing bulk and single cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some light chains were missing, such as when mixing single cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for heavy and light chain gene partitions. Thus, we recommend using maximum likelihood methods with separate heavy and light chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.
... We conducted analyses using the statistical software R, version 4.1.2 [10]. For each dataset, we filtered out chemicals which were not detected in any wristbands; this resulted in 53, 44, and 69 chemicals in the NY Pilot, NY, and OR datasets, respectively. ...
Wearable silicone wristbands are a rapidly growing exposure assessment technology that offer researchers the ability to study previously inaccessible cohorts and have the potential to provide a more comprehensive picture of chemical exposure within diverse communities. However, there are no established best practices for analyzing the data within a study or across multiple studies, thereby limiting impact and access of these data for larger meta-analyses. We utilize data from three studies, from over 600 wristbands worn by participants in New York City and Eugene, Oregon, to present a first-of-its-kind manuscript detailing wristband data properties. We further discuss and provide concrete examples of key areas and considerations in common statistical modeling methods where best practices must be established to enable meta-analyses and integration of data from multiple studies. Finally, we detail important and challenging aspects of machine learning, meta-analysis, and data integration that researchers will face in order to extend beyond the limited scope of individual studies focused on specific populations.
... The analysis was done via remote data processing. Due to the size of the data, the statistical modeling was performed using the R package "speedglm" version 0.3-2 in the statistical software R [18]. Because of the adjustment for rheumatic diseases with spinal involvement (1.2% of all patient years), the calculated effects apply to all patients with spinal diseases except these. ...
Background
A different utilization of health care services due to socioeconomic status on the same health plan contradicts the principle of equal treatment. We investigated the presence and magnitude of socioeconomic differences in utilization of diagnostic imaging and non-pharmaceutical conservative therapies for patients with spinal diseases.
Methods
The cohort study based on routine healthcare data from Germany with 11.7 million patient-years between 2012 and 2016 for patients with physician-confirmed spinal diseases (ICD-10: M40-M54), occupation and age 20 to 64 years. A Poisson model estimated the effects of the socioeconomic status (school education, professional education and occupational position) for the risk ratio of receiving diagnostic imaging (radiography, computed tomography, magnetic resonance imaging) and non-pharmaceutical conservative therapies (physical therapy including exercise therapy, manual therapy and massage, spinal manipulative therapy, acupuncture).
Results
Patients received diagnostic imaging in 26%, physical therapy in 32%, spinal manipulative therapy in 25%, and acupuncture in 4% of all patient-years. Similar to previous survey-based studies higher rates of utilization were associated with higher socioeconomic status. These differences were most pronounced for manual therapy, exercise therapy, and magnetic resonance imaging.
Conclusions
The observed differences in health care utilization were highly related to socioeconomic status. Socioeconomic differences were higher for more expensive health services. Further research is necessary to identify barriers to equitable access to health services and to take appropriate action to decrease existing social disparities.
... Unless stated otherwise, statistical analyses were performed with R software 3.6.3 (R Core Team, 2017) and graphical representations with the ggplot2 package (Wickham, 2016). ...
The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large‐scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.
... In this study, the relationships between the growth parameters (shoot and root length and fresh and dry biomass), chlorophyll content, nutrient uptake (N, P, K, Ca, Mg, and Na), antioxidant activity, proline, and 2AP level accumulation of KDML105 rice seedlings as affected by ST-PGPR inoculation were evaluated using PCA. The measured parameters were introduced as variables in the PCA using R 1.2.1335 [74]. ...
Salinity is one of the most devastating abiotic stresses hampering the growth and production of rice. Nine indole-3-acetic acid (IAA)-producing salt-tolerant plant-growth-promoting rhizobacteria (ST-PGPR) were inoculated into Thai jasmine rice (Oryza sativa L.) variety Khao Dawk Mali 105 (KDML105) seedlings grown under different concentrations of NaCl (0, 50, 100, and 150 mM). The ST-PGPR strains significantly promoted the growth parameters, chlorophyll content, nutrient uptake (N, P, K, Ca, and Mg), antioxidant activity, and proline accumulation in the seedlings under both normal and saline conditions compared to the respective controls. The K+/Na+ ratio of the inoculated seedlings was much higher than that of the controls, indicating greater salt tolerance. The most salt-tolerant and IAA-producing strain, Sinomonas sp. ORF15-23, yielded the highest values for all the parameters, particularly at 50 mM NaCl. The percentage increases in these parameters relative to the controls ranged from >90% to 306%. Therefore, Sinomonas sp. ORF15-23 was considered a promising ST-PGPR to be developed as a bioinoculant for enhancing the growth, salt tolerance, and aroma of KDML105 rice in salt-affected areas. Environmentally friendly technologies such as ST-PGPR bioinoculants could also support the sustainability of KDML105 geographical indication (GI) products. However, the efficiency of Sinomonas sp. ORF15-23 should be evaluated under field conditions for its effect on rice nutrient uptake and growth, including the 2AP level.
... For bibliometric analyses in this study, we employed the Biblioshiny algorithm (Cuccurullo et al., 2016), a tool written in the R language, known for its opensource nature. At the same time, the software used is a free web-based interface (R Team, 2014).. The R programming language is an open source programming language designed specifically for statistical calculations and provides an environment used in this field. ...
The aim of this provision is to include researchers in scientific publications revealing their research activities in the field of wearable health technologies and conducting research on this subject. In this context, bibliometric analysis of English articles in the Web of Science database between 1996 and 2023 was conducted using the R programming language. The search criteria included keywords such as "health," "technology," "physical activity," "devices," "sensors," "design," "adoption," "information technology," "user acceptance," and "acceptance." This search yielded a comprehensive collection of 5,327 studies related to wearable health technologies published between 1996 and 2023.. The data set obtained from these people was analyzed where the "biblioshiny" in the RStudio program was located. As a result of the research, the most frequently used words, the most relevant institutions in the field, and the stored regional growth amounts and citation records were obtained. This study is an important resource for researchers who want to conduct research and studies in the field of wearable health technologies. Since the calendar year 2023 has not been finalised, some graphs do not show the relevant year.
... To account for potential selection bias, we performed sensitivity analyses, reproducing the logistic regression analyses with inverse probability weighting, 32 which adds a weight to those who were under-or overrepresented in our study population using measured variables (age, sex, time since diagnosis, and education). All analyses were conducted in R (version 4.1.2). 33 ...
Background
With a growing population of cancer survivors in Denmark, the evaluation of health‐related quality of life (HRQoL) has become increasingly important. We describe variations in HRQoL between educational groups in a national population of cancer survivors.
Methods
We conducted a cross‐sectional questionnaire study among breast, prostate, lung, and colon cancer survivors diagnosed in 2010–2019 in Denmark. We used the EORTC QLQ‐C30 to assess HRQoL including physical, role, emotional, cognitive, social functioning, and symptoms (fatigue, nausea and vomiting, pain, dyspnea, insomnia, appetite loss, constipation, diarrhea, and financial difficulties). Information on educational level and clinical data were extracted from national registers and clinical databases. Levels of impaired functioning and severe symptoms were identified using newly established thresholds for clinical importance. Multivariate logistic regression was used to examine associations between education and HRQoL. All statistical tests were 2‐sided.
Results
In total, 27,857 (42%) participated in the study. Up to 72% and 75% of cancer survivors with short education (≤9 years) reported impaired functioning and severe symptoms, respectively. Cancer survivors with short compared to long education (>12 years) were more likely to report impaired functioning and severe symptoms, with for example significantly higher odds ratios (ORs) for impaired physical function (breast OR = 2.41, 99% CI = 2.01–2.89; prostate OR = 1.81, 99% CI = 1.48–2.21; lung OR = 2.97, 99% CI = 1.95–4.57; and colon cancer OR = 1.69, 99% CI = 1.28–2.24).
Conclusions
Cancer survivors with short education are at greater risk of impaired HRQoL than survivors with long education 2–12 years after diagnosis. This underscores the need for systematic screening and symptom management in cancer aftercare, in order to reach all cancer survivors, also cancer survivors with short education.
... A one-way ANOSIM test was conducted using the Bray-Curtis dissimilarity matrix to compare the differences between these cropping systems. All statistical analyses were carried out using R software (v4.1.2) [45]. ...
Background: The rhizosphere biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems and influence soil health and plant productivity. How different cropping systems manipulates soil and plant microbiomes is little understood. In this study, we investigated soil physicochemical properties, rhizosphere and maize-root microbiomes in an agroecological cereal-legume companion cropping system known as push-pull technology (PPT) which has been in use in farmer fields for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared this with the maize-monoculture (Mono) cropping system.
Results: PPT cropping system positively impacted the abundance and diversity of soil and maize-root microbial communities and influenced soil physicochemical characteristics compared to Mono. Specific genera of both bacterial and fungal communities drove the variation in diversity of the microbial communities in these cropping systems. Soil and maize-root from the PPT cropping system had enriched Trichoderma, Mortierella, and Bionectria fungal genera while Streptomyces, RB41, and Nitrospira, among other bacterial genera linked to essential ecosystem services like plant protection, decomposition, carbon utilization, production of bioinsecticides, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Bacterial from the genus Bryobacter linked to plant pathogenesis was more abundant in Mono-root. Similarly, fungal genera such as Gibberella, Neocosmospora, and Aspergillus, linked to plant pathogenesis and food contamination, were abundant in Mono. Notable differences were observed in the overall diversity of metabiome functional protein pathways, such as syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.
Conclusion: Push-pull cropping system improves soil physicochemical properties and shifts soil and maize-root microbiomes in farmer fields in favour of microbial communities involved in important ecological services. The current findings add to the diversification of ecosystem services provided by this cropping system where it is practiced and contributes to the system’s resilience and functional redundancy. Underpinning the mechanism through PPT affects the soil and maize-root microbial communities – whether it is through the influence of plant metabolites from the intercrop root exudates or is the alteration of the soil nutritional status which affects microbial enzymatic activities should be the future focus.
... We used the monotone homogeneity model (MHM) in MSA to examine the dimensionality of the SOC-13 from an IRT perspective. MSA was conducted using the package "Mokken" [48] in R [49]. The MHM model has three assumptions: unidimensionality (the items are indicators of a single latent construct), local independence (conditional on the latent trait value of a person, the responses to different items are assumed to be independent, meaning that the latent trait value is the only source of relationship between the responses) and monotonicity (the likelihood of endorsing an item increases as the latent variable increases). ...
Studies on the dimensionality and factor structure of the Sense of Coherence-13 (SOC-13) scale have produced inconsistent results, and there is a need for comprehensive psychometric testing of the scale in different populations and using diverse methodologies. SOC refers to the individual’s ability to perceive life as comprehensible, manageable, and meaningful. The current study investigated the dimensionality of the SOC-13 through the use of confirmatory factor analysis (CFA), ancillary bifactor indices and item response theory in a sample of young adults in South Africa. Participants were students (n = 322) who completed the SOC-13, the Connor–Davidson Resilience Scale, the PTSD Checklist for DSM-5 and short forms of the Center for Epidemiological Studies Depression Scale, and the trait scale of the Spielberger State-Trait Anxiety Inventory. CFA indicated the best fit for a one-factor model, but the problematic parameter estimates raise concerns about the construct validity of the scale. Non-parametric item response theory (Mokken scale analysis [MSA]) identified limitations in the original 13-item version, suggesting a more dependable seven-item version (SOC-7). This revised scale exhibited strong psychometric characteristics and was consistent with the theoretical foundations that underpin the construct. We verified the unidimensional structure of the SOC with the more stringent parametric item-response theory (Rasch analysis) which confirmed that the seven-item SOC is unidimensional. Rasch analysis confirmed the measurement invariance of the SOC-13 in terms of gender and area of residence. The study suggests that a shorter seven-item version consisting of items from the three components of sense of coherence has comparative properties to the 13-item version but the evidence does not provide support for the use of the SOC-13 as a multidimensional measure. Research in the area of sense of coherence would benefit from further validation studies of both the original SOC-13 and the revised SOC-7, especially across populations and settings.
... The results were plotted with the R project (v4.1.0) and ggplot2 package, and the data were fitted with the generalized additive model (GAM) with integrated smoothness estimation with the following formula y~s (x, k = 50) (mgcv package), with k representing the degrees of freedom [38][39][40][41]. For a visual illustration, we used Imaris software (v9.3.1, ...
(1) Background: Stereological estimations significantly contributed to our understanding of lung anatomy and physiology. Taking stereology fully 3-dimensional facilitates the estimation of novel parameters. (2) Methods: We developed a protocol for the analysis of all airspaces of an entire lung. It includes (i) high-resolution synchrotron radiation-based X-ray tomographic microscopy, (ii) image segmentation using the free machine-learning tool Ilastik and ImageJ, and (iii) calculation of the airspace diameter distribution using a diameter map function. To evaluate the new pipeline, lungs from adult mice with cystic fibrosis (CF)-like lung disease (βENaC-transgenic mice) or mice with elastase-induced emphysema were compared to healthy controls. (3) Results: We were able to show the distribution of airspace diameters throughout the entire lung, as well as separately for the conducting airways and the gas exchange area. In the pathobiological context, we observed an irregular widening of parenchymal airspaces in mice with CF-like lung disease and elastase-induced emphysema. Comparable results were obtained when analyzing lungs imaged with μCT, sugges-ting that our pipeline is applicable to different kinds of imaging modalities. (4) Conclusions: We conclude that the airspace diameter map is well suited for a detailed analysis of unevenly distri-buted structural alterations in chronic muco-obstructive lung diseases such as cystic fibrosis and COPD.
... All analyses were conducted in R (Version 4.0.0) [41]. ...
Treatment response and resistance in major depressive disorder (MDD) are suggested to be heritable. Due to significant challenges in defining treatment-related phenotypes, our understanding of their genetic bases is limited. This study aimed to derive a stringent definition of treatment resistance and to investigate the genetic overlap between treatment response and resistance in MDD. Using electronic medical records on the use of antidepressants and electroconvulsive therapy (ECT) from Swedish registers, we derived the phenotype of treatment-resistant depression (TRD) and non-TRD within ~4500 individuals with MDD in three Swedish cohorts. Considering antidepressants and lithium are first-line treatment and augmentation used for MDD, respectively, we generated polygenic risk scores (PRS) of antidepressants and lithium response for individuals with MDD and evaluated their associations with treatment resistance by comparing TRD with non-TRD. Among 1778 ECT-treated MDD cases, nearly all (94%) used antidepressants before their first ECT and the vast majority had at least one (84%) or two (61%) antidepressants of adequate duration, suggesting these MDD cases receiving ECT were resistant to antidepressants. We did not observe a significant difference in the mean PRS of antidepressant response between TRD and non-TRD; however, we found that TRD cases had a significantly higher PRS of lithium response compared to non-TRD cases (OR = 1.10–1.12 under various definitions). The results support the evidence of heritable components in treatment-related phenotypes and highlight the overall genetic profile of lithium-sensitivity in TRD. This finding further provides a genetic explanation for lithium efficacy in treating TRD.
... Composites were generated for every month within the study period between 2001-2010. Monthly mean NDVI composites were exported from GEE for further processing in the R statistical software [47] using the raster package [48]. ...
Cyclones are a key disturbance in mangrove ecosystems, but it is challenging to assess post-storm impacts over large areas, along with the recovery of these systems at broad temporal scales. Given the high frequency of these events in the Sundarbans region, prompt and consistent assessment of vegetation conditions is an important research need. Several studies have assessed the impact of an extreme cyclone event in 2007 (Sidr); however, there is little agreement between the extent and severity of the disturbance footprint of the cyclone, and very few studies attempted to assess vegetation recovery. We used a MODIS (Moderate Resolution Imaging Spectroradiometer) time series (2001-2010) to calculate monthly plant productivity anomalies in Google Earth Engine. We summarized dry season anomalies to assess post-storm vegetation change and evaluate the recovery time. Approximately 2100 km 2 , primarily on the east side, were impacted by Sidr. The number of damaged pixels was reduced by 55% the following dry season (2008) and 93% in the dry season of 2009, indicating a near-full recovery 26 months after the event. Our results provide an additional line of evidence to provide a rapid assessment of the post-storm vegetation damage. The simple framework used can provide a comprehensive view of the extent of the damage, including lag effects on vegetation, in just a matter of months after the event.
... After scaling the data to zero mean and unit variance, Spear man's rank correlation coefficients between these variables were calculated (107). Next, dimensional reduction of the variables was obtained with PCA using the stats package (108). ...
Temperature, pH, and hydrochemistry of terrestrial hot springs play a critical role in shaping thermal microbial communities. However, the interactions of biotic and abiotic factors at this terrestrial-aquatic interface are still not well understood on a global scale, and the question of how underground events influence microbial communities remains open. To answer this, 11 new samples obtained from the El Tatio geothermal field were analyzed by 16S rRNA amplicon sequencing (V4 region), along with 191 samples from previous publications obtained from the Taupo Volcanic Zone, the Yellowstone Plateau Volcanic Field, and the Eastern Tibetan Plateau, with their temperature, pH, and major ion concentration. Microbial alpha diversity was lower in acid-sulfate waters, and no significant correlations were found with temperature. However, moderate correlations were observed between chemical parameters such as pH (mostly constrained to temperatures below 70°C), SO 4 ²⁻ and abundances of members of the phyla Armatimonadota, Deinococcota, Chloroflexota, Campilobacterota, and Thermoplasmatota. pH and SO 4 ²⁻ gradients were explained by phase separation of sulfur-rich hydrothermal fluids and oxidation of reduced sulfur in the steam phase, which were identified as key processes shaping these communities. Ordination and permutational analysis of variance showed that temperature, pH, and major element hydrochemistry explain only 24% of the microbial community structure. Therefore, most of the variance remained unexplained, suggesting that other environmental or biotic factors are also involved and highlighting the environmental complexity of the ecosystem and its great potential to test niche theory ecological associated questions.
IMPORTANCE
This is the first approach to investigate whether geothermal processes could have an influence on the ecology of thermal microbial communities on a global scale. In addition to temperature and pH, microbial communities are structured by sulfate concentrations, which depends on the tectono-magmatic settings (such as the depth of magmatic chambers) and the local settings (such as the availability of a confining layer separating NaCl waters from steam after phase separation) and the possibility of mixing with more diluted fluids. Comparison of microbial communities from different geothermal areas by homogeneous sequence processing showed that no significant geographic distance decay was detected on the microbial communities according to Bray-Curtis, Jaccard, unweighted, and weighted Unifrac similarity/dissimilarity indices. Instead, an ancient potential divergence in the same taxonomic groups is suggested between globally distant thermal zones.
... Data were analysed in RStudio (R version 4.02) (RStudio Team, 2020;R Development Core Team, 2020), using the tidyverse package (Wickham et al., 2019). Most figures were generated using ggplot2 (Wickham, 2016), but genomic data were visualised using Gviz and Bioconductor (Hahne and Ivanek, 2016). ...
Plants with innate disease and pest resistance can contribute to more sustainable agriculture. Natural defence compounds produced by plants have the potential to provide a general protective effect against pathogens and pests, but they are not a primary target in resistance breeding. Here, we identified a wild relative of potato, Solanum commersonii , that provides us with unique insight in the role of glycoalkaloids in plant immunity. We cloned two atypical resistance genes that provide resistance to Alternaria solani and Colorado potato beetle through the production of tetraose steroidal glycoalkaloids (SGA). Moreover, we provide in vitro evidence to show that these compounds have potential against a range of different (potato pathogenic) fungi. This research links structural variation in SGAs to resistance against potato diseases and pests. Further research on the biosynthesis of plant defence compounds in different tissues, their toxicity, and the mechanisms for detoxification, can aid the effective use of such compounds to improve sustainability of our food production.
... Based on the indicators of the locations where the attacks occurred, grouped by neighborhood and municipality, heat graphs were generated, pointing to the regions with the highest records of violence. All the analysis were performed with the aid of the statistical environment R (R Development Core Team), version 3.5 [21], adopting a 5% level of significance (p value < 0.05). ...
The violence against women is a theme that extrapolates health issues, since after a victim seek for a health care, there is the notification of the act [1]. In Brazil, many times, these women are first assisted by mobile urgency services (SAMU/SIATE) and, as far as we have concern, there are no other studies with specific data about these assistance. The present paper aimed to analyze SAMU/SIATE assistance to abused women. Qualitative and retrospective epidemiological study of assistance to assaulted women carried out by SIATE and SAMU Maringá/Norte Novo between 2011 and 2020. Women between 20 and 39 years old, non-pregnant, were the main victims, and 19,52% of them have used some kind of drug. The (ex)partner figured as the perpetrator in 17,35%, but there were no information about this variable in 73,75% of the records. The Qui-square test shows a mortality rate superior to 70% among the severe traumatized victims. This is one of the first studies to analyze this kind of care provided by SAMU/SIATE, and reveals some gaps in its “modus-operandi” that can limitate an extrapolation of the results to bigger spheres. More researches in mobile urgency care services, in other provinces also, are needed to propose strategies to fight against this epidemic.
... A statistical analysis plan which will be developed when the extent of available data is known, will be reviewed by an external medical statistician (MS) prior to data analysis. All analyses will be conducted using R (34). ...
Background
After treatment ends, children, and young people (CYP) with medulloblastoma and ependymoma undergo surveillance imaging to check for cancer recurrence. Surveillance imaging aims to detect tumour relapse before symptoms develop, but the evidence to suggest that they improve outcomes is uncertain. Notwithstanding, scans are costly, and are an emotional burden for families.
Aims and Objectives
This mixed methods project will explore the value of surveillance imaging for children with medulloblastoma and ependymoma in three workstreams.
1) Workstream 1: Explore CYP and their parent’s experiences and expectations of surveillance imaging for detecting recurrent medulloblastoma and ependymoma.
2) Workstream 2: Using individual participant data (IPD), determine whether detecting a relapse surveillance imaging in CYP with medulloblastoma or ependymoma improves survival outcomes and treatment options.
3) Workstream 3: Determine whether surveillance imaging for CYP with medulloblastoma or ependymoma is cost-effective.
Methods
1) CYP with medulloblastoma and ependymoma who are undergoing surveillance imaging and their parents will be recruited to a qualitative study. Creative methods and semi-structured interviews will be used to understand CYP and parent’s experiences of surveillance imaging. Transcripts will be analysed using the ‘following the thread' method.
2) IPD from two UK-wide cohorts with data on CYP with relapsed ependymoma and medulloblastoma will be used to determine whether survival outcomes differ when relapse was detected symptomatically compared to asymptomatically. Multivariable survival analyses will assess the association between survival and method of relapse detection after controlling for prognostic variables (e.g., subtype, extent of surgical resection, subsequent therapies).
3) An economic model will be developed to evaluate whether surveillance imaging is value for money compared to no surveillance imaging. IPD from Workstream 2 will inform transition probabilities between health states. Costs, resource use and quality of life estimates will be obtained from systematic literature searches.
Data from each workstream will be synthesised using a convergent parallel approach following data analysis.
Discussion
This study aims to explore surveillance imaging for CYP with medulloblastoma and ependymoma in a holistic way, making it easier for decision makers to weigh up the benefits and drawbacks value of providing routine scans for this population.
... All analyses were conducted in R statistical software (version 3.6.3) [36]. HI titers were converted to log 10 values to express the kinetics throughout the 6-month study period. ...
Background: Chronic inflammation and suboptimal immune responses to vaccinations are considered to be aspects of immune dysregulation in patients that are undergoing dialysis. The present study aimed to evaluate immune responses in hemodialysis (HD) and online hemodiafiltra-tion (OL-HDF) patients to a seasonal inactivated quadrivalent influenza vaccine (IQIV). (2) Methods: We enrolled 172 chronic dialysis patients (87 on HD and 85 on OL-HDF) and 18 control subjects without chronic kidney disease in a prospective, cross-sectional cohort study. Participants were vaccinated with a seasonal IQIV, and antibody titers using the hemagglutination inhibition (HI) assay were determined before vaccination (month 0) and 1, 3, and 6 months thereafter. Demographics and inflammatory markers (CRP, IL-6, IL-1β) were recorded at month 0. The primary endpoints were the rates of seroresponse (SR), defined as a four-fold increase in the HI titer, and seroprotection (SP), defined as HI titer ≥ 1/40 throughout the study period. Statistical analyses were conducted in R (version 3.6.3) statistical software. The differences between groups were analyzed using chi-square and t-test analyses for dichotomous and continuous variables, respectively. To identify independent determinants of SR and SP, generalized linear models were built with response or protection per virus strain as the dependent variable and group, age, sex, time (month 0, 1, 3, 6), diabetes, IL-6, dialysis vintage, HD access, and HDF volume as independent explanatory variables. (3) Results: SR and SP rates were similar between control subjects, and dialysis patients were not affected by dialysis modality. SP rates were high (> 70%) at the beginning of the study and practically reached 100% after vaccination in all study groups. These results applied to all four virus strains that were included in the IQIV. IL-6 levels significantly differed between study groups, with HD patients displaying the highest values, but this did not affect SP rates. (4) Conclusions: Dialysis patients respond to influenza immunization adequately and similarly to the general population. Thus, annual vaccination policies should be encouraged in dialysis units. OL-HDF reduces chronic inflammation; however, this has no impact on SR rates.
Modelos de regressão são utilizados para analisar o comportamento de uma variável em relação às outras. Quando os dados são provenientes da reta real podem ser usados, por exemplo, modelos de regressão linear. No entanto, quando os dados são resultantes de medidas angulares, que podem surgir a partir de observações relacionadas à direção de voos de pássaros, dados meteorológicos, meses do ano, assim, a melhor alternativa é utilizar os modelos de regressão para dados circulares. Neste trabalho, os são dados provenientes do INMET e referentes à estação meteorológica situada na cidade de São João del Rei-MG, no período de 01/01/2020 a 31/12/2021. O modelo linear-circular foi selecionado, sendo a variável resposta a radiação solar, a variável explicativa, circular, os meses do ano. Para o ajuste foi utilizado o software R, o qual foi significativo e a covariável umidade foi inserida no modelo. Os parâmetros foram significativos ao nível de significância de 1%. Para validar o modelo foi utilizada a análise dos resíduos, e indicou ajuste satisfatório. Através da estatística circular foi possível verificar os períodos de picos de radiação, e em que meses do ano ocorreram altas radiações.
Pedosphere-hydrosphere interface accounts for the association between soil hydrology and landscape, represented by topographic and Remote Sensing data support and integration. This study aimed to analyze different statistical radiometric and spectral data selection methods and dimensionality reduce environment-related data to support the classification of soil physical-hydric properties, such as soil basic infiltration rate (bir) and saturated hydraulic conductivity (Ksat); as well as to act in data mining processes applied to hydropedological properties digital mapping. Accordingly, research integrated information from Visible to Infrared (VIS-IR) spectral indices and Sentinel’s 2A mission Multispectral Instrument (MSI) sensor bands, terrain numerical modeling and aerogeophysics set to model soil-water content in two soil layers (0.00-0.20 m and 0.20-0.40 m). Pre-processed data were subjected to statistical analysis (multivariate and hypothesis tests); subsequently, the methods were applied (variation inflation factor - VIF, Stepwise Akaike information criterion – Stepwise AIC, and recursive feature elimination - RFE) to mine covariates used for Random Forest modeling. Based on the results, there were distinctions and singularities in spectral and radiometric data selection for each adopted method; the importance degree, and contribution of each one to soil physical-hydric properties have varied. According to the applied statistical metrics and decision-making criteria (highest R ² and lowest RMSE / MAE), the chosen methods were RFE (0.00-0.20 m layers) and Stepwise AIC (0.20-0.40 m layers) - both concerned with the assessed variables (bir and Ksat). This approach captured the importance of environmental variables and highlighted their potential use in hydropedological digital mapping at Guapi-Macacu watershed.
Autism Spectrum Disorder (ASD or autism) is a phenotypically and etiologically heterogeneous condition. Identifying biomarkers of clinically significant metabolic subtypes of autism could improve understanding of its underlying pathophysiology and potentially lead to more targeted interventions. We hypothesized that the application of metabolite-based biomarker techniques using decision thresholds derived from quantitative measurements could identify autism-associated subpopulations. Metabolomic profiling was carried out in a case–control study of 499 autistic and 209 typically developing (TYP) children, ages 18–48 months, enrolled in the Children’s Autism Metabolome Project (CAMP; ClinicalTrials.gov Identifier: NCT02548442). Fifty-four metabolites, associated with amino acid, organic acid, acylcarnitine and purine metabolism as well as microbiome-associated metabolites, were quantified using liquid chromatography-tandem mass spectrometry. Using quantitative thresholds, the concentrations of 4 metabolites and 149 ratios of metabolites were identified as biomarkers, each identifying subpopulations of 4.5–11% of the CAMP autistic population. A subset of 42 biomarkers could identify CAMP autistic individuals with 72% sensitivity and 90% specificity. Many participants were identified by several metabolic biomarkers. Using hierarchical clustering, 30 clusters of biomarkers were created based on participants’ biomarker profiles. Metabolic changes associated with the clusters suggest that altered regulation of cellular metabolism, especially of mitochondrial bioenergetics, were common metabolic phenotypes in this cohort of autistic participants. Autism severity and cognitive and developmental impairment were associated with increased lactate, many lactate containing ratios, and the number of biomarker clusters a participant displayed. These studies provide evidence that metabolic phenotyping is feasible and that defined autistic subgroups can lead to enhanced understanding of the underlying pathophysiology and potentially suggest pathways for targeted metabolic treatments.
The social complexity hypothesis for communicative complexity posits that animal societies with more complex social systems require more complex communication systems. We tested the social complexity hypothesis on three macaque species that vary in their degree of social tolerance and complexity. We coded facial behavior in >3000 social interactions across three social contexts (aggressive, submissive, affiliative) in 389 animals, using the Facial Action Coding System for macaques (MaqFACS). We quantified communicative complexity using three measures of uncertainty: entropy, specificity, and prediction error. We found that the relative entropy of facial behavior was higher for the more tolerant crested macaques as compared to the less tolerant Barbary and rhesus macaques across all social contexts, indicating that crested macaques more frequently use a higher diversity of facial behavior. The context specificity of facial behavior was higher in rhesus as compared to Barbary and crested macaques, demonstrating that Barbary and crested macaques used facial behavior more flexibly across different social contexts. Finally, a random forest classifier predicted social context from facial behavior with highest accuracy for rhesus and lowest for crested, indicating there is higher uncertainty and complexity in the facial behavior of crested macaques. Overall, our results support the social complexity hypothesis.
Apesar de crescente número de expedições de herpetofauna realizados nos últimos anos, em África ainda prevalecem lacunas de inventários, bem como, estudos que visam analisar e aprimorar os métodos de amostragem existentes, para aumentar a eficiência dos inventários e para também interpretar os resultados das diversas expedições. Para se obter resultados satisfatórios num inventário é necessário que se faça a identificação de técnicas eficientes de amostragem. O presente estudo tem como objectivo avaliar a eficiência e abrangência de técnicas de amostragem de herpetofauna. Para tal, fez-se uma amostragem de anfíbios e répteis durante 365 dias usando quatro técnicas: busca activa, armadilhas de intercepção e queda, armadilhas de funil e placas de refúgio. Essas técnicas foram implementadas em cinco pontos de amostragem com diferentes níveis de perturbação. No total foram avistados 2081 indivíduos, correspondentes a 17 espécies de anfíbios e 42 espécies de répteis, destas 39 espécies foram registadas pela primeira vez em Lumbo. No geral os pontos com menor perturbação registaram maior riqueza de espécies. A busca activa foi a técnica mais abrangente, tendo registado 100% dos anfíbios e 79% dos répteis, ao passo que a técnica de refúgio de placas teve menor abrangência, registando 24% dos anfíbios e 15% dos répteis. Em relação à ecologia das espécies, a busca activa foi responsável pelo registo de espécies de diferentes hábitos ecológicos, incluindo terrestre, arborícola, rupícola e aquáticos, excepto espécies de hábitos fossoriais que foram melhor amostradas pela técnica de armadilha de intercepção e queda. Embora os métodos tenham registados espécies similares, apresentaram resultados complementares. Através deste trabalho pretende-se fornecer informações sobre quais combinações de técnicas devem ser feitas em inventários de herpetofauna em função do grupo de espécies que se pretende estudar.
Some nonhuman primate species, whose original habitats have been reclaimed by artificial activities, have acquired boldness toward humans which is evident based on the diminished frequency of escape behaviors. Eventually, such species have become regular users of human settlements, and are referred to as “urban primates.” Considering this, we developed a noninvasive technique based on bioacoustics to provide a transparent assessment of troop addiction levels in anthropogenic environments, which are determined by the dependence on agricultural crops and human living sphere for their diets and daily ranging, respectively. We attempted to quantify the addiction levels based on the boldness of troops when raiding settlements, characterized by a “landscape of fear” because of the presence of humans as predators. We hypothesized that the boldness of troops could be measured using two indices: the frequency of raiding events on settlements and the amount of time spent there. For hypothesis testing, we devised an efficient method to measure these two indices using sound cues (i.e., spontaneous calls) for tracing troop movements that are obtainable throughout the day from most primate species (e.g., contact calls). We conducted a feasibility study of this assessment procedure, targeting troops of Japanese macaques ( Macaca fuscata ). For this study, we collected 346 recording weeks of data using autonomous recorders from 24 troops with different addiction levels during the nonsnowy seasons. The results demonstrated that troops that reached the threshold level, at which radical interventions including mass culling of troop members is officially permitted, could be readily identified based on the following behavioral characteristics: troop members raiding settlements two or three times per week and mean time spent in settlements per raiding event exceeding 0.4 h. Thus, bioacoustic monitoring could become a valid option to ensure the objectivity of policy judgment in urban primate management.
The management of the western Baltic cod relies on a combination of regulation tools, including a seasonal spawning fishing closure. The complex population dynamics of the stock have nevertheless been posing considerable challenges to design closures, and the actual benefits of the seasonal spawning closure are still unclear. Often, only biological indicators have been used to evaluate the effectiveness of the closure, without considering socioeconomic effects on the fishery. In this study, we applied a Species Distribution Model (SDM) integrating commercial fishery and research survey data on a 15-year time series to design multiple alternative spatial closures, all based on identifying persistent essential fish habitats (i.e., nursery, spawning, and feeding grounds). We further used the spatial-explicit Management Strategy Evaluation (MSE) tool DISPLACE to contrast the outcomes of these fishing closures, and identify which provided the optimal balance between socioeconomic and biological demands and sustainability. Our results indicated that all closures benefitted the fisheries and stock. Although fishermen redirected their fishing effort to some extent to other stocks, increased profits were largely driven by increased cod catches as a consequence of reconstructed stock structure and enhanced spawning biomass. We conclude that the benefits of the closures are more linked to their size, than their actual purpose (i.e., protecting nursery, spawning, or feeding grounds).
Introduction
The COVID-19 pandemic has resulted in heightened moral distress among health care workers (HCWs) worldwide. Past research has shown that effective leadership may mitigate potential for the development of moral distress. However, no research to date has considered the mechanisms by which leadership might have an influence on moral distress. We sought to evaluate longitudinally whether Canadian HCWs’ perceptions of workplace support and ethical work environment would mediate associations between leadership and moral distress.
Methods
A total of 239 French- and English-speaking Canadian HCWs employed during the COVID-19 pandemic were recruited to participate in a longitudinal online survey. Participants completed measures of organizational and supervisory leadership at baseline and follow-up assessments of workplace support, perceptions of an ethical work environment, and moral distress.
Results
Associations between both organizational and supervisory leadership and moral distress were fully mediated by workplace supports and perceptions of an ethical work environment.
Discussion
To ensure HCW well-being and quality of care, it is important to ensure that HCWs are provided with adequate workplace supports, including manageable work hours, social support, and recognition for efforts, as well as an ethical workplace environment.
Objective
Juvenile tiger muskellunge (Northern Pike Esox lucius × Muskellunge E. masquinongy ) are cannibalistic, which can lead to a substantial reduction in yields within an intensive culture environment. Utah hatcheries have traditionally raised the female Northern Pike × male Muskellunge cross, and hatchery managers are reluctant to raise the female Muskellunge × male Northern Pike due to a perceived difference (increase) in cannibalism rates when rearing this cross.
Methods
We raised both crosses in replicated microcosms to evaluate the differential cannibalism between them. All rearing conditions were consistent among treatments and replicates. We evaluated weekly cannibalism using generalized linear regression models.
Result
After 6 weeks, we found that the female Muskellunge × male Northern Pike cross offspring were significantly more cannibalistic than juveniles from the female Northern Pike × male Muskellunge cross, with total cannibalism across the 6‐week period estimated at 27% and 5.6%, respectively.
Conclusion
We documented a previously unreported difference in tiger muskellunge cross cannibalism rates. Choosing the female Northern Pike × male Muskellunge cross could substantially increase survival of juvenile tiger muskellunge in aquaculture facilities.
In proteomics, fast, efficient, and highly reproducible sample preparation is of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open science OT‐2 liquid handling robot from Opentrons. This platform can prepare up to 96 samples at once, performing tasks like BCA protein concentration determination, sample digestion with normalization, reduction/alkylation and peptide elution into vials or loading specified peptide amounts onto Evotips in an automated and flexible manner. The performance of the developed workflows using MassSpecPreppy was compared with standard manual sample preparation workflows. The BCA assay experiments revealed an average recovery of 101.3% (SD: ± 7.82%) for the MassSpecPreppy workflow, while the manual workflow had a recovery of 96.3% (SD: ± 9.73%). The species mix used in the evaluation experiments showed that 94.5% of protein groups for OT‐2 digestion and 95% for manual digestion passed the significance thresholds with comparable peptide level coefficient of variations. These results demonstrate that MassSpecPreppy is a versatile and scalable platform for automated sample preparation, producing injection‐ready samples for proteomics research.
Predator-prey interaction constitutes important selection pressure in determining the evolutionary pathways for both involved parties. Here, we present a new dataset of gastropod drilling predation on molluscan prey from the Upper Cretaceous of the Ariyalur Sub-basin, India. While bulk sampling is the preferred protocol, this cannot be followed when the host rock is strongly lithified. A hybrid method of surface sampling, without physical breakage of the host rock, within a grid system is employed in the present study. The Coniacian Anaipadi Member (Garudamangalam Formation) yields a highly diverse fauna, including 25 species of bivalve and 16 species of gastropod. While the assemblage-level drilling intensity is 0.27 for bivalves, three common bivalve species exhibit drilling intensities ranging from 0.32 to 0.62. In the case of gastropods, a total of 27 complete drillholes have been found in four species, all belonging to the genus Turritella. As only a part of the shell was exposed, drilling intensities are not calculated for gastropods. Behavioural stereotypy of predators, in terms of prey size and drillhole location, is evident in some of the prey species, especially bivalves. A compilation of previously published literature data suggests that although drilling was an established mode of predation by the Late Cretaceous, the majority of this temporal bin is understudied. The present study provides the first report of drilling predation on molluscan prey from the Coniacian and provides the opportunity to expand our current understanding of drilling predation behaviour during the Late Cretaceous in a spatio-temporal context.
Despite lotic systems demonstrating high levels of seasonal and spatial variability, most research and biomonitoring practices do not consider seasonality when interpreting results and are typically focused at the meso‐scale (combined pool/riffle samples) rather than considering habitat patch dynamics. We therefore sought to determine if the sampling season (spring, summer and autumn) influenced observed macroinvertebrate biodiversity, structure and function at the habitat unit scale (determined by substrate composition), and if this in turn influenced the assessment of fine sediment (sand and silt) pressures. We found that biodiversity supported at the habitat level was not seasonally consistent with the contribution of nestedness and turnover in structuring communities varying seasonally. Habitat differences in community composition were evident for taxonomic communities regardless of the season but were not seasonally consistent for functional communities, and, notably, season explained a greater amount of variance in functional community composition than the habitat unit. Macroinvertebrate biodiversity supported by silt habitats demonstrated strong seasonal differences and communities were functionally comparable to sand habitats in spring and to gravel habitats in autumn. Sand communities were impoverished compared to other habitats regardless of the season. Silt habitats demonstrated a strong increase in Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa and functional richness from spring into autumn, while vegetation habitats displayed a peak in EPT abundance in summer. Only silt and sand habitats demonstrated temporal variability in functional evenness suggesting that these habitats are different in terms of their resource partitioning and productivity over time compared to other habitats. Gravel and vegetation habitats appeared to be more stable over time with functional richness and evenness remaining consistent. To accurately evaluate the influence of fine sediment on lotic ecosystems, it is imperative that routine biomonitoring and scientific research discriminate between sand and silt fractions, given they support different biodiversity, particularly during summer and autumn months.
Background
Shame is considered an important factor in the development and maintenance of many psychological disorders, e.g., social anxiety disorder, and an interesting target point for therapeutic intervention.
Method
In the present experimental study, we used an online-adopted Autobiographical Emotional Memory Task (AEMT) to induce shame and tested different micro-interventions (self-compassion, cognitive reappraisal, and a control intervention) with respect to their potential to reduce shame intensity. One-hundred-and-fifteen healthy subjects participated in the study and completed a series of self-report questionnaires on self-compassion, shame, and social anxiety.
Results
The experimental shame induction was well accepted and successful (with significantly heightened feelings of shame); there were no study drop-outs. There was a significant time*condition interaction, which was due the self-compassion-based intervention resulting in a significantly larger reduction of shame than the control condition (counting fishes). In addition, the main effect of the factor experimental condition was further moderated (enhanced) by trait social anxiety and trait self-compassion.
Conclusion
The findings demonstrate the usefulness of online-adopted AEMT for the experimental induction of shame. They suggest that especially self-compassion interventions can be beneficial in alleviating intense shame experiences, which is in accordance with self-compassion theory. Overall, the results are promising in the context of experimental shame research and its potential clinical impacts call for further replication.
Annual induced fires have caused significant changes in the composition and structure of wildlife globally. These events are particularly critical for species with limited mobility and small clutch sizes, such as certain small and medium-sized freshwater turtles in the tropics. At the same time, this topic has received limited attention and has not been documented in countries with a high diversity of freshwater turtles, such as Mexico. In this study we report the mortality of the red-cheeked mud turtle ( Kinosternon scorpioides cruentatum ) and the Pacific Coast musk turtle ( Staurotypus salvinii ) caused by a fire in the north portion of the municipality of Suchiate, Chiapas, Mexico. Specifically, our aims were to 1) register the plant species where the turtles occurred, 2) determine the population structure of each turtle species, and 3) estimate the density, size, and sex ratio of the dead turtles of each species. Additionally, we discuss the potential effects of this event on the demography of these turtles in the study site.
Long‐term species monitoring programmes have revealed catastrophic declines in insect populations and disruption of biological communities that are contributing to biodiversity loss. Such discoveries have been possible because of standardised methods, such as line transects, of counting butterflies and other insects. However, line transects are not feasible in many tropical and mountainous habitats, so alternative methods must be explored.
To tackle this issue, we devised time‐constrained (30‐min) counts and compared butterfly diversity estimated through timed counts and line transects in three tropical habitats in India (evergreen forest, dry deciduous forest and an urban woodland). We tested the relative performance of the two methods in sampling species richness and abundance, as well as numbers of rare, endemic and specialist butterflies.
We observed greater overall species richness, and more species of habitat specialists and endemics per sample in time‐constrained counts in the evergreen forest, but not in the other two habitats. Thus, time‐constrained counts were relatively more efficient in detecting species in the species‐rich evergreen habitat. Apart from this difference, the two sampling methods captured similar levels of species richness and other measures of diversity.
Our study thus shows that time‐constrained counts are a suitable if not a superior alternative to line transects to conduct butterfly diversity surveys and population monitoring in complex tropical landscapes. Due to methodological flexibility and simplicity, time‐constrained counts may be particularly useful to study the impacts of climate change, habitat fragmentation and land use practices on butterfly, Odonata and other insect populations in populous and tech‐ready tropical countries using citizen science frameworks.
Insect pollination plays a pivotal role in ensuring agricultural sustainability within tropical agrarian communities. Insect-pollinated crops significantly contribute to enhanced crop yields and improved human nutrition by providing access to essential vitamins. In the Zambian tropics, these vital contributions face threats stemming from a complex interplay of anthropogenic and non-anthropogenic factors perceived to be responsible for the decline of Insect Pollinators (IPs). We employed semi-structured questionnaires and conducted focus group discussions to investigate smallholder farmers' knowledge of IPs, their perceptions of IP diversity trends, the factors they believe affect IP diversity, and the traditional practices employed by farmers to conserve IPs. The study unveiled that farmers associated bees, wasps, butterflies, flies, and beetles with the pollination of key crops and angiosperms, such as pumpkins, sunflowers, oranges, and guavas. A majority of the farmers observed declines in both IP abundance and richness. Anthropogenic activities, such as deforestation, pollution, and fires, were perceived as significant contributors to IP decline, alongside factors like climate change and a lack of government support. Conservation Agriculture (CA), the establishment of fire guards, the cultivation of flowering plants, and bee-keeping emerged as prevalent traditional practices that support IPs. However, these IP conservation practices were not widely adopted among smallholder farmers due to financial constraints and a lack of enforcement. Consequently, there is a pressing need for increased local enforcement and financial support from various stakeholders to promote IP conservation in the study area. We recommend that agricultural extension services collaborate with local authorities to provide farmers with comprehensive information and technical assistance for the effective implementation of traditional practices associated with IP conservation.
In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.
Riparian vegetation is a keystone ecosystem element heavily impacted by livestock grazing. Historically, regeneration approaches of the riparian vegetation use either active (planting) or passive (natural regeneration) strategies. Frameworks based on an understanding of the soil seed bank are needed to help guide the approach adopted. This study compared the soil seed bank composition to the extant riparian vegetation to assess the potential for natural regeneration to supplement active plantings, following livestock exclusion on the south-coast of Australia. At each of four sites, we surveyed the extant vegetation, and collected five soil samples from each of three zones (instream, slope, bank). Our results show that the proportions of species nativeness, growth forms, and life cycle was similar for both communities. However, while there were more terrestrial species recorded in the standing vegetation, there were more wetland specialists in the soil seed bank. A persistent native seed bank, combined with other basic management strategies, could potentially compete and limit the abundance of non-native or invasive grasses. The high abundance of native grass-types (Cyperaceae, Juncaceae, Juncaginaceae, Asparagaceae, Poaceae, Typhaceae), can be relied upon to regenerate the understorey to complement active planting of the trees and shrubs. As such, resources could be prioritised to sites where native species abundance in the seed bank is low. This study recommends that land managers should investigate the composition of the soil seed bank prior to allocating resources for active planting activities to ensure the most efficient use of resources across the landscape.
The oxygen isotope composition (δ ¹⁸ O) of tree‐ring cellulose is used to evaluate tree physiological responses to climate, but their interpretation is still limited due to the complexity of the isotope fractionation pathways.
We assessed the relative contribution of seasonal needle and xylem water δ ¹⁸ O variations to the intra‐annual tree‐ring cellulose δ ¹⁸ O signature of larch trees at two sites with contrasting soil water availability in the Swiss Alps. We combined biweekly δ ¹⁸ O measurements of soil water, needle water, and twig xylem water with intra‐annual δ ¹⁸ O measurements of tree‐ring cellulose, xylogenesis analysis, and mechanistic and structural equation modeling.
Intra‐annual cellulose δ ¹⁸ O values resembled source water δ ¹⁸ O mean levels better than needle water δ ¹⁸ O. Large parts of the rings were formed under high proportional exchange with unenriched xylem water ( p ex ). Maximum p ex values were achieved in August and imprinted on sections at 50–75% of the ring. High p ex values were associated with periods of high atmospheric evaporative demand (VPD). While VPD governed needle water δ ¹⁸ O variability, we estimated a limited Péclet effect at both sites.
Due to a variable p ex , source water has a strong influence over large parts of the intra‐annual tree‐ring cellulose δ ¹⁸ O variations, potentially masking signals coming from needle‐level processes.
No-till avocado orchards in the highlands are gaining importance in eastern Antioquia, Colombia. To evaluate the influence of management, and edaphic properties on the composition of weed communities, 50 Hass avocado orchards were studied in nine municipalities of eastern Antioquia. The variables cover and presence of weeds were used to estimate relative frequency, dominance, and Importance Value (IV); weed management was characterized by a survey. The maximum moisture retention capacity and pH of the soil were also determined. The importance of species, rotation of management strategies, and herbicides were analyzed graphically. The association between weeds dominance, and factors, was evaluated by a generalized linear model. 66 dicots and 28 monocot weeds were classified. Out of the 10 most important species, three foreign species, Melinis minutiflora P. Beauv, Digitaria horizontalis Willd, and Pennisetum clandestinum Hoschst. Ex Chiov were the most representative. The municipalities are grouping the effects of similar management strategies in the territory. Chemical management favored the equilibrium of the weed composition, while mechanical management did not. Soil properties had less influence on the distribution and dominance of weeds.
Fine root biomass (FRB) is essential for the functioning of tropical forests. However, due to the degradation generated by mining, it is necessary to evaluate the influence of the soil and the successional time on the FRB, to contribute to its restoration. Forests of biogeographic Chocó have been affected by mining; for this reason, the objective of evaluating the influence of the soil and the successional time on the FRB in abandoned mines was proposed. For this, plots were established in three successional stages: two abandoned mines (12-15 and 30-35 years) and a primary forest. Subsequently, the physicochemical conditions of the soil and the FRB (<2 mm) at 20 cm depth were measured. The registered FRB was 5.73 t ha-1 in stages of 12-15 years, 2.56 t ha-1 in stages of 30- 35 years, and 5.91 t ha-1 forests; that is, it recovered quickly, but did not increase with successional time. In general, the FRB was determined by successional age, fertility, OM, and clay. In stages of 12-15 years, it was positively associated with OM and slime; and negatively with clay and sand. While, in stages of 30-35 years, it was positively related to Al, N, Ca and clay; but, with K, MO and Mg it was negative. In summary, it was determined that the soils have a different influence on the FRB in each successional stag. In addition, the limitation of belowground biomass storage due to multiple nutrients, which affect the mitigation of global climate change, was noted.
The quality and availability of resources are known to influence spatial patterns of animal density. In Yellowstone National Park, relationships between the availability of resources and the distribution of grizzly bears ( Ursus arctos ) have been explored but have yet to be examined in American black bears ( Ursus americanus ). We conducted non‐invasive genetic sampling during 2017–2018 (mid‐May to mid‐July) and applied spatially explicit capture‐recapture models to estimate density of black bears and examine associations with landscape features. In both years, density estimates were higher in forested vegetation communities, which provide food resources and thermal and security cover preferred by black bears, compared with non‐forested areas. In 2017, density also varied by sex, with female densities being higher than males. Based on our estimates, the northern range of Yellowstone National Park supports one of the highest densities of black bears (20 black bears/100 km ² ) in the northern Rocky Mountains (6–12 black bears/100 km ² in other regions). Given these high densities, black bears could influence other wildlife populations more than previously thought, such as through displacement of sympatric predators from kills. Our study provides the first spatially explicit estimates of density for black bears within an ecosystem that contains the majority of North America's large mammal species. Our density estimates provide a baseline that can be used for future research and management decisions of black bears, including efforts to reduce human–bear conflicts.
Targeted conservation and promotion of wild bees in agroecosystems requires understanding of relationships between different groups of bees and available floral resources across land-use types during the season and at the landscape scale. Here, we quantified floral resource amount and diversity across habitat types at different times during the season at the scale of entire landscapes (500 m radius) across 20 different agricultural landscapes. Moreover, we examined whether floral resource metrics obtained from these high-resolution floral resource maps are more suitable to assess and predict abundance and species richness of different bee pollinator groups, including rare species and important crop pollinators, sampled in these agricultural landscapes compared to traditional land-cover metrics. Floral resource availability shifted from flower-rich woody vegetation early in the season to herbaceous vegetation such as grasslands and crops later in the season, which was associated with a tenfold decline in overall floral resource availability. Forest edges had highest per-area floral contributions in spring, whereas floral diversity of grasslands, in particular if extensively managed, was continuously high. Total wild bee species richness, as well as rare species richness and abundance of important crop pollinators, increased with floral resource availability and/or diversity contributed by forest edges and floral diversity of permanent grasslands. Rare bee richness was also positively related to floral resource amount provided by crops. Total bee richness and important crop pollinator abundance, but not rare bee richness, were positively related to overall floral resource amount, but not floral diversity, in the landscape. Floral resource maps based on floral resource supply by major habitat types early or late in the season predicted wild bee species richness (R 2 =0.61) better than traditional descriptors of landscape composition such as proportion of semi-natural habitat. The pronounced temporal shifts in floral resource availability for pollinators from woody towards herbaceous vegetation during the season highlights the importance of taking a landscape-scale perspective on pollinator conservation. Our findings indicate that both rare bees and important crop pollinators benefit from complementary floral resources of forest edges and grasslands in agroecosystems. This reveals a potential synergy between the conservation of endangered species and the landscape scale management to promote pollination services. Our study also highlights that floral resource maps are useful tools in supporting more targeted pollinator conservation and pollination service management at the landscape level.
Tucuquere (Bubo magellanicus) is an owl inhabiting Chile, which is classified as a species of agricultural interest, but its current conservation status is not well defined. The determination of previously unknown haematological ranges via laboratory techniques for species analysis is of great importance in the search for diagnoses in clinical veterinary work. Thirty-three samples from healthy tucuquere were obtained from zoos and rehabilitation centres in central Chile and analysed using standard laboratory techniques to obtain reference values that were determined according to the standard recommendations for animal species. The mean, standard deviation, maximum, and minimum reference limits were calculated at 95% and 97.5% error. These results differ from those of other studies, especially in terms of the white blood cells because most of the values were lower than those described for the species. These results could be explained by the habitat and location from which the samples were taken, and they corroborate the need to obtain reference values for different geographical areas. This study provides useful haematological values for use in conservation medicine and zoos and highlights the importance of carrying out these studies in different geographical areas for species of ecological interest.
The fitness cost of an antibiotic resistance gene (ARG) can differ across host strains creating refuges that allow maintenance of an ARG in the absence of direct selection for its resistance phenotype. Despite the importance of such ARG-host interactions for predicting ARG dynamics, the basis of ARG fitness costs and their variability between hosts are not well understood. We determined the genetic basis of a host-dependent cost of a β-lactamase, bla TEM-116* , that conferred a significant cost in one Escherichia coli strain but was close to neutral in 11 other Escherichia spp. strains. Selection of a bla TEM-116* encoding plasmid in the strain in which it initially had a high cost resulted in rapid and parallel compensation to that cost through mutations in a P1 phage gene, relAP1 . When the wildtype relAP1 gene was added to a strain in which it was not present and in which bla TEM-116* was neutral, it caused the ARG to become costly. Thus, relAP1 is both necessary and sufficient to explain bla TEM-116* costs in at least some host backgrounds. To our knowledge, these findings represent the first demonstrated case of the cost of an ARG being influenced by a genetic interaction with a phage gene. The interaction between a phage gene and a plasmid-borne ARG highlights the complexity of selective forces determining the maintenance and spread of ARGs, and, by extension, encoding phage and plasmids, in natural bacterial communities.
Green areas in urban landscapes are under strong anthropogenic pressure, and, at the same time are fundamental to maintaining biodiversity, as they provide resources for many animal and plant species. Knowing these species is fundamental for its maintenance and conservation, and inventories are extremely important for monitoring fauna and conserving it. Therefore, the goal of this research is to inventory the butterflies species in the park of the Instituto Butantan (Ibu), located in an urban area in the city of São Paulo, southeast Brazil. The surveys of butterflies were conducted through visual censuses from August 2017 to July 2019 and recorded a total of 324 butterfly species. The most speciose family was Hesperiidae, followed by Nymphalidae, Lycaenidae, Pieridae, Riodinidae, and Papilionidae. Among the sampled species, there is Euselasia zara which is a new record for the state of São Paulo. Neither the species accumulation nor the richness estimator curves tended to reach an asymptote, suggesting that additional butterflies' species will be recorded with more sampling effort on the site. Even with a flora composed mainly of exotic and ornamental plants, the park of Instituto Butantan exhibits a very rich butterfly community. This community exhibits a pattern of seasonally variation, with the peak of species richness related to the rainy season. When compared with Cidade Universitária Armando de Salles Oliveira (USP), another nearby urban green area, which is larger, more heterogeneous and sampled over a longer period, it is possible to notice that the Ibu butterfly community is a subsample of this larger one. These results highlight the potential that urban parks have for the maintenance and conservation of butterfly species.
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