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Team RDC.R: A Language And Environment For Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria
... All figures were plotted using the ggplot package implemented in R software v 3.6.0 [30]. ...
... The spatiotemporal spread of DENV−3 in Senegal was reconstructed under a Bayesian framework implemented in BEAST. v.1.10.4 [30]. ...
... The resulting maximum clade credibility (MCC) tree was visualized and edited using Using dataset 4, the amino acid changes in contemporary Senegalese DENV−3 strains compared to the vaccine strains of the same serotype (Dengvaxia CYD-3 and Tetravax-DV-TV003) were generated using a script written in the Python language that produced a tab-separated file containing the position where the amino acid changes occurred and the For DENV−3 mAB analysis, dataset 5 was aligned to identify the amino acid changes against the known 5J7 mAb epitope; changes were called as described below. The amino acid changes were represented using R software v3.6.0 [30]. ...
Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV−2 in southeastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV−3. Following the notification by Senegal, many other West African countries reported DENV−3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV−3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV−3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV−3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV−3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.
... Stats 2023, 6, FOR PEER REVIEW 5 By combining the strengths of VOSviewer and Bibliometrix, researchers can conduct comprehensive bibliometric analyses, encompassing data preparation, advanced statistical assessments, and interactive visualization. These tools are invaluable for data-driven decision-making in academic research, funding allocation, and strategic planning in research institutions [22][23][24]. ...
... By combining the strengths of VOSviewer and Bibliometrix, researchers can conduct comprehensive bibliometric analyses, encompassing data preparation, advanced statistical assessments, and interactive visualization. These tools are invaluable for data-driven decision-making in academic research, funding allocation, and strategic planning in research institutions [22][23][24]. ...
This study aimed to perform a bibliometric analysis of terroir and explore its conceptual horizons. Advancements in terroir research until 2022 were investigated using the Scopus database, R, and VOSviewer. Out of the 907 results, the most prevalent document types were articles (771) and reviews (70). The annual growth rate of published manuscripts in this field was 7.8%. The research on terroir encompassed a wide range of disciplines, with significant contributions from Agricultural and Biological Sciences, Social Sciences, Environmental Science, Biochemistry, Genetics, and Molecular Biology. Through keyword analysis, the study identified the most frequently occurring terms in titles, abstracts, and keywords fields, including ‘terroir’, ‘wine’, ‘soil’, ‘wines’, ‘grape’, ‘analysis’, ‘vineyard’, ‘composition’, and ‘climate’. A trend topic analysis revealed that research in terroir primarily focused on the geo-ecology and physiology of grapes. Furthermore, considerable attention was given to methods and techniques related to the physicochemical, sensory, and microbial characterization of terroir and various aspects of the wine industry. Initially, the research in this domain was focused on terroir, authenticity, grapevine, soils, soil moisture, and wine quality. However, over time, the research agenda expanded to include topics such as food analysis, viticulture, wine, taste, sustainability, and climate change. New research areas emerged, including phenolic compounds, anthocyanin, phenols, sensory analysis, and precision agriculture—all of which became integral components of the scientific studies on terroir. Overall, this study provided valuable insights into the historical trends and current developments in terroir research, contributing to our understanding of the frontiers in this field.
... The sequential swap randomization algorithm with the package "EcoSimR" in R version 4.1.0 was used [56]. ...
Phosphorus (P) is an essential macronutrient crucial for both plant growth and crop production, playing a pivotal role in agriculture since the early 20th century. The symbiotic relationship between AMF and plants serves as a classic illustration. These fungi play a regulatory role in the growth and development of plants, especially in facilitating the absorption of P and carbon molecules by plants. While there has been a growing body of research on the community assembly of arbuscular mycorrhizal fungi (AMF) in recent decades, our knowledge of the processes governing the coexistence of these AMF communities influenced by P in agroecosystems remains limited. To investigate the impact of various P fertilizers on AMF communities in temperate agroecosystems, this study was conducted using soils sourced from wheat–maize rotation farmland at Henan Agricultural University Yuanyang Base. With the Illumina MiSeq high-throughput sequencing technique, we systematically examined the taxonomic composition of soil AMF at the Yuanyang Base of Henan Agricultural University in a wheat–maize rotation agricultural field. Our primary objective was to unravel the mechanisms behind AMF community assembly and stability under varying P gradient fertilization conditions. Nonmetric Multidimensional Scaling (NMDS) analysis revealed significant differences among AMF communities in field soil subjected to various treatments (p < 0.05). A torus translations test demonstrated positive associations with the three treatments in 36 out of the 51 examined AMF operational taxonomic units (OTUs), making up 70.59% (p < 0.05) of the results. Furthermore, 37.84% (14/37) of the OTUs displayed preferences for the low P concentration treatment, while 34.29% (12/35) and 32.26% (10/31) favored medium and high P concentrations, respectively. An analysis of the Normalized Stochasticity Ratio (NST) and Checkerboard Score (C-score) indicated that in temperate agroecosystems, deterministic processes predominantly governed AMF in all treatment groups, with high P conditions exerting a stronger influence than low or medium P conditions. This study underscores the profound impact of long-term P fertilizer application on AMF community structures within temperate agricultural systems employing wheat–maize rotation. Additionally, it highlights the dominant role played by deterministic processes in shaping the assembly of AMF communities in these temperate agricultural systems that use P fertilizers. These findings emphasize the need for balanced nutrient management, particularly concerning P, to ensure the stability of AMF communities.
... Sequence divergence among individual sequences was calculated using the K2P model, which is a standard model used in barcoding studies. The function dist.dna in the R package "ape" was used for examination in the distance-based approach [29][30][31][32]. To identify whether sequences with the shortest divergences were the same, the function "nearNeighbor" in the R package "spider" was used to perform the nearest neighbor test [31]. ...
DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylo-genetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest in-traspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcod-ing. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intra-specific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.
... In the training set, error statistics are calculated using fivefold cross validation, while test set error statistics are simply calculated using the full test set. Data analysis was conducted in R version 4.2.1 using the tidyverse suite of packages for data processing and cleaning and the simple features package for handling geographic data [21][22][23]. The caret package was used for model fitting and evaluation [24]. ...
Background
Childrens’ outdoor active play is an important part of their development. Play behaviour can be predicted by a variety of physical and social environmental features. Some of these features are difficult to measure with traditional data sources.
Methods
This study investigated the viability of a machine learning method using Google Street View images for measurement of these environmental features. Models to measure natural features, pedestrian traffic, vehicle traffic, bicycle traffic, traffic signals, and sidewalks were developed in one city and tested in another.
Results
The models performed well for features that are time invariant, but poorly for features that change over time, especially when tested outside of the context where they were initially trained.
Conclusion
This method provides a potential automated data source for the development of prediction models for a variety of physical and social environment features using publicly accessible street view images.
... We fitted the models using the nonlinear generalized least squares method utilizing the "gnls" function from the "nlme" package in R ® Studio software, 4.3.1. version [40]. To assess any potential autocorrelation, we included a continuous first-order autoregressive error structure in the error term, which enabled the application of the models to longitudinal and unbalanced datasets [41]. ...
Stem profile modeling is crucial in the forestry sector, particularly for commercially valuable species like teak (Tectona grandis Linn F.), whose value depends on its stem dimensions, heartwood proportion, and age. We proposed a nonlinear mixed-effect model to describe the evolution of the stem and heartwood profiles of clonal teak trees with ages between 4 and 12 years in the Brazilian Amazon. Tapering models were used to estimate the bark, bark-free, and heartwood diameters. Dummy variables were included in each tapering model to estimate each type of diameter and enable compatibility. We used mixed models with age as a random effect in order to improve the accuracy. The Demaerschalk model provided the most accurate and compatible estimates for all three types of stem diameter. Also, age as a random effect significantly improved the model's accuracy by 7.2%. We observed a progressive increase in the heartwood proportion (14% to 34%) with advancing age, while the proportions of bark (23% to 20%) and sapwood (63% to 45%) showed inverse behavior. The growth rate of the heartwood differed from that of the bark volume, emphasizing the importance of considering the age of heartwood maximization when determining the cutting cycle of the species.
... We acquired the data of 2000 Summer Olympics from 'Assessing Judging Bias: An Example From the 2000 Olympic Games' [7], and the data of 2021 Summer Olympics from https://olympics.com/en/o lympic-games/tokyo-2020 [10]. All analyses were performed using R Statistical Software (v4.2.0; R Core Team 2022) [11]. ...
The Olympics is the most well-known sports event in the world. With the aim to ensure fairness, the Olympics has some of the strictest scoring methods in the world. However, unlike track and field where the timing and length can be precisely measured, diving has a more subjective judging procedure. Each judge gives their scores based on their own evaluation of the specific dive. Under such scoring methods, it is reasonable to suspect that the scores are influenced by the judges personal bias. For example, judges may favor their own countrymen or score the competitors lower. In order to reduce the negative effects of such bias, different scoring systems are used in diving in multiple Olympics. Using Sydney 2000 Summer Olympics' and Tokyo 2020 Summer Olympics' data sets, we investigate the phenomenon of nationalistic judging bias and compare different scoring methods' abilities in handling bias. Using three different tests, we discovered that the Mean method is the worst in resisting judging bias. The other three trimming methods were found to withstand the effect of bias successfully in different circumstances, and none of them stands up against judging bias well at all times. Further research with more abundant data is needed before we could obtain a solid conclusion about the most effective scoring system to be used in diving competitions.
... ; https://doi.org/10. 1101/2023 Increased population density provides protection against high levels of external H2O2 stress 401 (40,45,46). However, the concentrations of 100µM-1mM applied in such studies is far beyond the 402 range of known environmental concentrations, which is typically up to only 4μM (47). ...
Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining the variation available in a population. One such environmental dependency is the inverse relationship between mutation rates and population density in many microbial species. Here we determine the mechanism responsible for this mutation rate plasticity. Using dynamical computational modelling and in vivo mutation rate estimation we show that the negative relationship between mutation rate and population density arises from the collective ability of microbial populations to control concentrations of hydrogen peroxide. We demonstrate a loss of this density-associated mutation rate plasticity when Escherichia coli populations are deficient in the degradation of hydrogen peroxide. We further show that the reduction in mutation rate in denser populations is restored in peroxide degradation-deficient cells by the presence of wild-type cells in a mixed population. Together, these model-guided experiments provide a mechanistic explanation for density-associated mutation rate plasticity, applicable across all domains of life, and frames mutation rate as a dynamic trait shaped by microbial community composition.
... Follow-up analyses were conducted using three-way ANOVAs on each dependent variable. The models are fit in R [38], and the mixed effects models are fit using the lmerTest package [27] for R. Best-subset model selection according to the Bayesian information criterion (BIC) [47] was completed via complete enumeration [35] for each model. BIC penalizes false positives more than false negatives when there are eight or more observations. ...
Aging and cancer seem to be closely associated, such that cancer is generally considered a disease of the elderly in both humans and dogs. Additionally, cancer is a metabolic shift in itself towards
aerobic glycolysis. Larger dog breeds with shorter lifespans, and increased glycolytic cellular metabolic rates, die of cancer more often than smaller breeds. The tumor suppressor p53 factor is a key suppressor oncogene, and the p53 pathway arrests cellular proliferation and prevents DNA mutations from accumulating
during cellular stress. The p53 pathway is also associated with the control of cellular metabolism to prevent cellular metabolic shifts common to cancerous phenotypes. SIRT1 deacetylates the p53 tumor suppressor protein, downregulating p53 via effects
on stability and activity during stress. Here, we used primary fibroblast cells from small and large puppies and old dogs. Using UV radiation to upregulate the p53 system (100 J/m 2), control cells and UV-treated cells were used to measure aerobic and glycolytic metabolic rates using a Seahorse XFe96 oxygen flux analyzer. We also quantified p53 expression and SIRT1 concentration in canine primary fibroblasts before and after UV treatment. We demonstrate that, due to a higher p53 nuclear to cytoplasmic ratio in large breed dogs after UV treatment, p53 could have a more regulatory effect on large breed dogs' metabolism compared with smaller breeds. Thus, there may be a link between p53 upregulation and inhibition of glycolysis in large breed dogs during times of cellular stress compared with small breed dogs. However, SIRT1 concentrations decrease with age in domestic dogs of both size classes, suggesting a possible release of inhibition of p53 through the SIRT1 pathway with age. This may lead to increased incidences of cancer, especially due to the more pronounced upregulation of p53 with cellular stress.
... All statistical analyses were carried out using the R program on the R studio interface RStudio (version 3.6.1) [37]. For each sex hormone, the most suitable EIA was identified based on the individual and collective increases in androgen and progestogen metabolite concentrations following the administration of GnRH. ...
The naked mole-rat (Heterocephalus glaber) occurs in colonies with a distinct dominance hierarchy, including one dominant, breeding female (the queen), 1-3 breeding males, and non-reproductive subordinates of both sexes that are reproductively suppressed while in the colony. To non-invasively evaluate reproductive capacity in the species, we first had to examine the suitability of enzyme immunoassays (EIAs) for determining progestogen and androgen metabolite concentrations in the naked mole-rat, using urine and faeces. A saline control and gonadotrophin-releasing hormone (GnRH) were administered to twelve (six males and six females) naked mole-rats which were previously identified as dispersers and housed singly. The results revealed that urine is possibly not an ideal matrix for progestogen and androgen metabolite quantification in naked mole-rats as no signal was detected in the matrix post GnRH administration. A 5α-Progesterone EIA and an Epiandrosterone EIA were identified as suitable for quantifying faecal progesterone metabolites (fPMs) and faecal androgen metabolites (fAMs) in males and females, respectively. The results suggest that there are individual variations in baseline fPM and fAM concentrations, and only two out of six females and no males exhibited an increase in fPM concentrations greater than 100% (−20% SD) post GnRH administration. Conversely, only four out of six females and three out of six males had an increase in fAM concentrations greater than 100% (−20% SD) following GnRH administration. These results imply that some naked mole-rat individuals have a reduced reproductive capacity even when they are separated from the queen.
... Statistical analyses were performed using the R programming language [78] to compute Spearman's/Pearson's correlation, test the level of significance for Welch's t-test or Student's t-test, and generate plots with a cutoff of FDR and/or log 2 fold change values using edgeR (V3.18.1) [77]. ...
Background
Super-enhancers (SEs), which activate genes involved in cell-type specificity, have mainly been defined as genomic regions with top-ranked enrichment(s) of histone H3 with acetylated K27 (H3K27ac) and/or transcription coactivator(s) including a bromodomain and extra-terminal domain (BET) family protein, BRD4. However, BRD4 preferentially binds to multi-acetylated histone H4, typically with acetylated K5 and K8 (H4K5acK8ac), leading us to hypothesize that SEs should be defined by high H4K5acK8ac enrichment at least as well as by that of H3K27ac.
Results
Here, we conducted genome-wide profiling of H4K5acK8ac and H3K27ac, BRD4 binding, and the transcriptome by using a BET inhibitor, JQ1, in three human glial cell lines. When SEs were defined as having the top ranks for H4K5acK8ac or H3K27ac signal, 43% of H4K5acK8ac-ranked SEs were distinct from H3K27ac-ranked SEs in a glioblastoma stem-like cell (GSC) line. CRISPR-Cas9–mediated deletion of the H4K5acK8ac-preferred SEs associated with MYCN and NFIC decreased the stem-like properties in GSCs.
Conclusions
Collectively, our data highlights H4K5acK8ac’s utility for identifying genes regulating cell-type specificity.
... Total DNA was extracted from soil samples using the FastDNA™ SPIN Kit for soil (MPBiomedicals LLC, Irvine, CA, USA) according to the manufacturer's specification, and the V3-V4 region of the 16S rRNA gene was sequenced using 341F and 785R primers [68] in 2 bp × 300 bp paired-end technology using the Illumina MiSeq system (Illumina Inc., San Diego, CA, USA). Demultiplexed fastq files were processed using the DADA2 (1.12) package [69] in R software (3.4.3) [70]. Forward and reverse reads were trimmed according to the results obtained from the quality analysis, and primer sequences were removed from all reads. ...
Recycling of solid biowaste and manure would reduce the dependence of agriculture on synthetic products. Most of the available studies on the effects of exogenous organic matter (EOM) application to soil were focused on nutrients and crop yield, with much less attention to microbiological processes in soil, especially using modern molecular methods. The aim of this study was to evaluate the effects of various types of manure, sewage sludge and bottom sediment on the biochemical activity and biodiversity of soil and plant yield in a pot experiment. The soil was treated with a range of EOM types: six types of manure (cattle, pig, goat, poultry, rabbit and horse manure; two bottom sediments (from urban and rural systems); and two types of municipal sewage sludge. All EOMs stimulated dehydrogenases activity at a rate of 20 t ha−1. Alkaline phosphatase was mostly stimulated by poultry manure and one of the sludges. In general, the two-fold greater rate of EOMs did not further accelerate the soil enzymes. The functional diversity of the soil microbiome was stimulated the most by cattle and goat manure. EOMs produce a shift in distribution of the most abundant bacterial phyla and additionally introduce exogenous bacterial genera to soil. Poultry and horse manure introduced the greatest number of new genera that were able to survive the strong competition in soil. EOMs differentiated plant growth in our study, which was correlated to the rate of nitrate release to soil. The detailed impacts of particular amendments were EOM-specific, but in general, no harm for microbial parameters was observed for manure and sludge application, regardless of their type. There was also no proof that the PAH and pesticide contents measured in manure or sludge had any effect on microbial activity and diversity.
... All analyses were completed using R (Version 4.2.1; [40]). Model estimated marginal means (EMMs) and 95% confidence intervals (CI) were determined for each condition and back-transformed to proportions. ...
The cryopreservation and storage of gametes (biobanking) can provide a long-term, low-cost option for the preservation of population genetic diversity and is particularly impactful when applied to manage selective breeding within conservation breeding programs (CBPs). This study aimed to develop a sperm cryopreservation protocol for the critically endangered Booroolong frog (Litoria booroolongensis) to capture founder genetics within the recently established (est. 2019) CBP for this species. Hormone-induced sperm release was achieved using established protocols, and spermic urine samples were collected over a 6-h period. Pooled spermic urine samples (n = 3 males) were divided equally between two cryoprotectant (CPA) treatments and diluted by 1:5 (sperm:CPA) with either 15% (v/v) dimethyl sulfoxide + 1% (w/v) sucrose in simplified amphibian Ringer’s (SAR; CPAA) or 10% (v/v) dimethylformamide + 10% (w/v) trehalose dihydrate in SAR (CPAB). The samples were cryopreserved in 0.25 mL straws using either a programmable freezer (FrA) or an adapted dry shipper method (FrB). The thawed samples were activated via dilution in water and assessed for viability and motility using both manual assessment and computer-assisted sperm analysis (CASA; 0 h, 0.5 h post-thaw). Upon activation, the survival and recovery of motility (total motility, forward progression and velocity) of cryopreserved sperm suspensions were higher for sperm preserved using FrB than FrA, regardless of CPA composition. This work supports our long-term goal to pioneer the integration of biobanked cryopreserved sperm with population genetic management to maximize restoration program outcomes for Australian amphibian species.
... To account for differences in sequencing depth among samples, we rarefied OTU tables produced in QIIME2 to 1,300 sequences or 1,328 sequences for the bacterial and fungal communities, respectively, with 300 resamplings using the EcolUtilis package in R version 4.0.3 (76,77). Community composition was compared between samples using Bray-Cur tis dissimilarity matrices generated from square root transformed rarefied OTU tables. ...
Given increased wildfire activity, there is growing interest in understanding the drivers of microbial succession after fire. Dispersal may be especially important to post-fire succession as biotic communities can be more susceptible to invasion following a disturbance. Here, we experimentally manipulated dispersal into disturbed leaf litter communities collected following a wildfire and tracked bacterial and fungal dispersal assemblages over time. We show that the identity and source of microbes immigrating into the soil surface post-fire change across time with seasonal shifts and the reemergence of aboveground vegetation. Further, dispersal significantly contributed to the reassembly of leaf litter microbial communities after the fire, producing an increasingly distinct assembly trajectory. The effect of dispersal on α-diversity and β-diversity was ecosystem dependent but, unexpectedly, influenced bacterial and fungal communities in a similar manner within ecosystems. Collectively, these results demonstrate that dispersal explicitly alters the course of microbial community succession following a wildfire and may impact bacteria and fungi in parallel ways, despite differing in traits expected to alter dispersal patterns.
IMPORTANCE
Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.
... All statistical analyses were performed with R version 4.0.3 [66]. ...
Background
Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and flexibility of Symbiodiniaceae is presumably responsible for variations in coral response to physical stressors such as elevated temperature, there is little data directly comparing physiological performance that accounts for symbiont identity associated with the same coral host species. Here, using Pocillopora damicornis harboring genotypically distinct Symbiodiniaceae strains, we examined the physiological responses of the coral holobiont and the dynamics of symbiont community change under thermal stress in a laboratory-controlled experiment.
Results
We found that P. damicornis dominated with symbionts of metahaplotype D1-D4-D6 in the genus Durusdinium (i.e., PdD holobiont) was more robust to thermal stress than its counterpart with symbionts of metahaplotype C42-C1-C1b-C1c in the genus Cladocopium (i.e., PdC holobiont). Under ambient temperature, however, the thermally sensitive Cladocopium spp. exhibited higher photosynthetic efficiency and translocated more fixed carbon to the host, likely facilitating faster coral growth and calcification. Moreover, we observed a thermally induced increase in Durusdinium proportion in the PdC holobiont; however, this “symbiont shuffling” in the background was overwhelmed by the overall Cladocopium dominance, which coincided with faster coral bleaching and reduced calcification.
Conclusions
These findings support that lineage-specific symbiont dominance is a driver of distinct coral responses to thermal stress. In addition, we found that “symbiont shuffling” may begin with stress-forced, subtle changes in the rare biosphere to eventually trade off growth for increased resilience. Furthermore, the flexibility in corals’ association with thermally tolerant symbiont lineages to adapt or acclimatize to future warming oceans should be viewed with conservative optimism as the current rate of environmental changes may outpace the evolutionary capabilities of corals.
BV1Kh9uQ_-YRrbNwasQg31Video Abstract
It is now largely recognized that pollinators are threatened in agricultural habitats. Cities are thus seen as potential refuges for pollinators, if suitable green spaces are available, because they present favorable abiotic conditions for many pollinator species. However, data on resources used by bees in urban habitats are scarce. Moreover, promoting indigenous meadows in urban green spaces could help pollinator’s survival. In this study, Apis mellifera was taken as a model to investigate potential difference in plant diversity used in agricultural and urban habitat. Pollen loads were sampled in 15 hives in both habitat types, using pollen traps. Then, the attractiveness of a melliferous meadow on wild bees was tested. To that end, a new seed mix (BF) including 35 indigenous plants producing nectar and/or pollen harvested by bees was developed and its attractiveness was compared to a seed mix widely used in Geneva (PFG). For most of the season, quantity and diversity of the pollen sampled was not significantly different between agricultural and urban habitats. Nevertheless, honey bees used different species in both habitats, probably because different plant communities are present. Sixty-one wild bee species were observed foraging in the new BF seed mix compared to only 47 species in the PFG. Likewise, more plants species were used in the BF seed mix than in the PFG. These results show that urban zones can be interesting for pollinators because they display diverse and abundant plant communities. Additionally, it shows that urban parks are species rich habitats, and that pollinator communities respond immediately to additional resources when available.
Hemipteran insects are well-known for their ancient associations with beneficial bacterial endosymbionts, particularly nutritional symbionts that provide the host with essential nutrients such as amino acids or vitamins lacking in the host’s diet. Therefore, these primary endosymbionts enable the exploitation of nutrient-poor food sources such as plant sap or vertebrate blood. In turn, the strictly host-associated lifestyle strongly impacts the genome evolution of the endosymbionts, resulting in small and degraded genomes. Over time, even the essential nutritional functions can be compromised, leading to the complementation or replacement of an ancient endosymbiont by another, more functionally versatile bacterium. Herein, we provide evidence for a dual primary endosymbiosis in several psyllid species. Using metagenome sequencing, we produced the complete genome sequences of both the primary endosymbiont “ Candidatus Carsonella ruddii” and an as yet uncharacterized Enterobacteriaceae bacterium from four species of the genus Cacopsylla . The latter represents a new psyllid-associated endosymbiont clade for which we propose the name “ Candidatus Psyllophila symbiotica.” Fluorescent in situ hybridization confirmed the co-localization of both endosymbionts in the bacteriome. The metabolic repertoire of Psyllophila is highly conserved across host species and complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella . Unlike co-primary endosymbionts in other insects, the genome of Psyllophila is almost as small as the one of Carsonella , indicating an ancient co-obligate endosymbiosis rather than a recent association to rescue a degrading primary endosymbiont.
IMPORTANCE
Heritable beneficial bacterial endosymbionts have been crucial for the evolutionary success of numerous insects by enabling the exploitation of nutritionally limited food sources. Herein, we describe a previously unknown dual endosymbiosis in the psyllid genus Cacopsylla , consisting of the primary endosymbiont “ Candidatus Carsonella ruddii” and a co-occurring Enterobacteriaceae bacterium for which we propose the name “ Candidatus Psyllophila symbiotica.” Its localization within the bacteriome and its small genome size confirm that Psyllophila is a co-primary endosymbiont widespread within the genus Cacopsylla . Despite its highly eroded genome, Psyllophila perfectly complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella . Moreover, the genome of Psyllophila is almost as small as Carsonella ’s, suggesting an ancient dual endosymbiosis that has now reached a precarious stage where any additional gene loss would make the system collapse. Hence, our results shed light on the dynamic interactions of psyllids and their endosymbionts over evolutionary time.
In recent years, the use of pesticides has intensified worldwide, and many countries have tended to neglect the potential toxic effects associated with the indiscriminate use of these substances. Many diseases, such as Hodgkin’s lymphoma, lung and prostate cancer, and autoimmune disorders, have been linked to the use of pesticides. The present study compared the DNA damage observed in rural workers from five different areas of the central Brazilian state of Goiás. We attempted to identify the factors that influence the patterns of genotoxicity found in 367 rural workers from the municipalities of Goiânia, Rio Verde, Montividiu, Jatai, and Silvânia. The DNA damage was assessed using comet assays, and the results were compared with the data on epidemiological variables, behavioral parameters, and the types of pesticide used. Significant variation was found in the level of DNA damage in rural workers from different municipalities, although no clear differences were observed in demographic or behavioral parameters. All the different classes of pesticides were related to similar levels of DNA damage, which indicates that other factors may be influencing the differences observed among the populations. A positive correlation was found between the level of DNA damage and the number of pesticides used per individual, which suggests potential synergistic effects of pesticide mixtures, which may enhance the risk of DNA damage. Rural workers from Goiânia and Silvania presented the highest levels of DNA damage. In addition to the quantity of pesticides and the synergistic effects of mixtures, the results of the present study would appear to point to genetic polymorphisms in detoxification genes (e.g., OGG1 and XRCC), which may determine variation in the general susceptibility of the different populations to DNA damage. This emphasizes the need for further research on the possible variation in genetic factors in the different groups of rural workers.
Background
RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering has been widely used to classify DEGs with similar expression patterns, but rarely used to identify DEGs themselves. We recently reported that the clustering-based method (called MBCdeg) for identifying DEGs has great potential. However, a thorough investigation of its feasibility is still needed.
Results
We compared a total of six competing methods: three conventional R packages (edgeR, DESeq2, and TCC) and three versions of MBCdeg (denoted as MBCdeg1, 2, and 3) corresponding to three different normalization algorithms. Different scenarios of simulated data generated from three R packages (TCC, compcodeR, and PROPER) were mainly evaluated based on the area under the receiver operating characteristic curve (AUC) as a measure for both sensitivity and specificity. We found that the modified version of MBCdeg2 performed well for many scenarios on simulated data. However, MBCdeg showed very unstable results between trials for identical real data.
Conclusions
The current MBCdeg2 shows excellent performance in simulation analysis, but not at a practical level for real data. Since further improvements are needed for MBCdeg to reach a practical level, we cannot recommend the use of the current MBCdeg. Our report suggests not only the need for method developers to carefully describe their shortcomings, but also the need for the reader to critically decipher the conclusions reached under what conditions.
The long‐term effects of intensive forest harvest on sensitive demographic stages of the American black bear ( Ursus americanus ) have been often overlooked. Much of Maine, USA, is covered in forests that are hospitable to bears and commercial timber harvest. To investigate the potential effects of differing intensities of disturbance on black bears, and on females with cubs particularly, we designed a large‐scale natural experiment with 197 motion‐sensitive camera sites dispersed over representative forest stands in northern and central Maine. Using multi‐state occupancy models, we distinguished the overall trends in space use by females with young versus adult bears without young. Forest disturbance at large spatial scales was positively associated with the probability of use for both demographic groups and the availability of hardwood trees was an additional important factor for habitat use by females with young. Our study illustrates the use of motion‐sensitive cameras to monitor and understand habitat use by distinct life‐history stages of animals living in human‐modified landscapes, and results indicate that managers can maintain black bear habitat in areas of active forest harvest by ensuring the availability of hardwood species.
Declines and extirpations of American pika ( Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19 th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948–1949, 1988–1991, 2013–2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988–1991 and 2013–2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.
Objectives
To investigate the association between body mass and hypotension during general anaesthesia in dogs undergoing surgical and diagnostic procedures within a referral hospital.
Materials and Methods
Retrospective evaluation of the anaesthetic records of 1789 dogs was performed. Data on signalment, anaesthetic protocol and physiological variables, including mean arterial pressure, were collected. A multivariable generalised linear model was used to identify associations between explanatory variables, including body mass, and hypotension.
Results
In the population studied, increasing body mass (per 10 kg) was significantly associated with decreasing odds of hypotension (odds ratio 0.68; 95% confidence interval: 0.60 to 0.77). Additional variables associated with a decreased odds of hypotension were pre‐anaesthetic medication with alpha‐2 agonists (odds ratio 0.63; 95% confidence interval 0.48 to 0.82) and increased body temperature (per 1°C) during general anaesthesia (odds ratio 0.77; 95% confidence interval 0.67 to 0.88). Brachycephaly (odds ratio 1.72; 95% confidence interval 1.25 to 2.38), ASA physical status classification >3 (odds ratio 2.03; 95% confidence interval 1.16 to 3.56), undergoing a surgical procedure ( versus diagnostic) (odds ratio 1.57; 95% confidence interval 1.10 to 2.23) and bradycardia (odds ratio 1.37; 95% confidence interval 1.05 to 1.80) were independently associated with increased odds of hypotension.
Clinical significance
Dogs of lower body mass and brachycephalic breeds may be at higher risk of hypotension during general anaesthesia or alternatively represent subpopulations in which accurate blood pressure measurement presents a greater challenge. Monitoring blood pressure accurately in these groups requires particular attention and provisions for treating hypotension should be readily accessible.
At the end of their operational life time offshore wind farms need to be decommissioned. How and to what extent the removal of the underwater structures impairs the ecosystem that developed during the operational phase of the wind farm is not known. So, decision makers face a knowledge gap, making the consideration of such ecological impacts challenging when planning decommissioning. This study evaluates how complete or partial decommissioning of foundation structure and scour protection layer impacts local epibenthic macrofauna biodiversity. We assessed three decommissioning alternatives (one for complete and two for partial removal) regarding their impact on epibenthic macrofauna species richness. The results imply that leaving the scour protection layer in situ will preserve a considerable number of species while cutting of the foundation structure above seabed will be beneficial for the fauna of such foundation structures where no scour protection is installed. These results should be taken with a grain of salt, as the current data base is rather limited. Data need to be improved substantially to allow for reliable statements and sound advice regarding the ecological impact of offshore wind farm decommissioning.
Background
Recent data indicate a decline in overall longevity in the United States. Even prior to the COVID‐19 pandemic, an increase in midlife mortality rates had been reported. Life expectancy disparities have persisted in the United States for racial and ethnic groups and for individuals living at low socioeconomic status. These continued trends in mortality indicate the importance of examining biomarkers of mortality at midlife in at‐risk populations. Circulating levels of cytokines and inflammatory markers reflect systemic chronic inflammation, which is a well‐known driver of many age‐related diseases.
Methods
In this study, we examined the relationship of nine different inflammatory proteins with mortality in a middle‐aged socioeconomically diverse cohort of African–American and White men and women (n = 1122; mean age = 47.8 years).
Results
We found significant differences in inflammatory‐related protein serum levels between African–American and White middle‐aged adults. E‐selectin and fibrinogen were significantly higher in African–American adults. IFN‐γ, TNF‐α trimer, monocyte chemoattractant protein‐1 (MCP‐1), soluble receptor for advanced glycation end‐products (sRAGE) and P‐selectin were significantly higher in White participants compared to African–American participants. Higher levels of E‐selectin, MCP‐1 and P‐selectin were associated with a higher mortality risk. Furthermore, there was a significant interaction between sex and IL‐6 with mortality. IL‐6 levels were associated with an increased risk of mortality, an association that was significantly greater in women than men. In addition, White participants with high levels of sRAGE had significantly higher survival probability than White participants with low levels of sRAGE, while African–American participants had similar survival probabilities across sRAGE levels.
Conclusions
These results suggest that circulating inflammatory markers can be utilized as indicators of midlife mortality risk in a socioeconomically diverse cohort of African–American and White individuals.
O objetivo do trabalho foi estudar e avaliar a curva de crescimento de pêssegos “Aurora 1”, com base em dados de altura e diâmetro do fruto, avaliados ao longo do tempo por modelos não lineares duplo sigmoidais Brody, Gompertz e Logístico generalizados. Os dados utilizados no estudo foram extraídos de um experimento conduzido em 2005, no município de Vista Alegre do Alto, Estado de São Paulo, Brasil. Os parâmetros dos modelos foram estimados pelo método de mínimos quadrados, com base no algoritmo de Gauss-Newton executado por meio do software R. As pressuposições de normalidade, independência e homogeneidade dos resíduos foram averiguadas pelos testes de Shapiro-Wilk, Durbin-Watson e Breusch-Pagan, respectivamente. O ajuste dos modelos aos dados foi comparado considerando os valores obtidos para o critério de informação de Akaike corrigido (AICc), o desvio padrão residual (DPR), o índice de ajuste da assíntota (IA) e por medidas de não linearidade. Todos os modelos atenderam aos pressupostos de normalidade, independência e homogeneidade de variâncias e apresentaram ajuste adequado aos dados de altura e diâmetro do fruto, tendo em vista os valores do IA que foram próximos de um, bem como os baixos valores do DPR e das medidas de não linearidade.
Background: The coexistence of stunting and wasting in a child increases the risk of mortality and requires more intensive treatment and care. However, there is limited research on the burden of concurrent stunting and wasting among children and the socioeconomic factors that are correlated with having both conditions. Aim: To understand the prevalence and sociodemographic correlates of stunting, wasting, and concurrent stunting and wasting among a sample of children ages 6–144 months experiencing poverty in the Philippines. Methods: Cross-sectional data were drawn from nutrition screening and sociodemographic surveys conducted by International Care Ministries in 2018-2019. Descriptive statistics were calculated to determine the prevalence of stunting, wasting, and concurrent stunting and wasting. Multilevel logistic regression modelling was conducted to understand the sociodemographic factors that were associated with stunting and wasting. Results: Among the 3005 children in this sample, the prevalence of stunting, wasting, and concurrent stunting and wasting was 49.9%, 9.3%, and 4.6%, respectively. Children experiencing concurrent stunting and wasting lived in households in lower wealth index quintiles, had a household head with fewer years of education, and were more likely to experience food insecurity compared to children who were not stunted or wasted. The education of the household head, the number of household members, and the wealth of the household were correlated with stunting across age groups, while food insecurity was correlated with wasting among younger children. Conclusion: The presence of concurrent stunting and wasting among children provides the impetus to integrate both conditions into nutrition monitoring, prevention, and treatment interventions.
Background
Predicting patterns of fire behavior and effects in frequent fire forests relies on an understanding of fine-scale spatial patterns of available fuels. Leaf litter is a significant canopy-derived fine fuel in fire-maintained forests. Litter dispersal is dependent on foliage production, stand structure, and wind direction, but the relative importance of these factors is unknown.
Results
Using a 10-year litterfall dataset collected within eighteen 4-ha longleaf pine ( Pinus palustris Mill.) plots varying in canopy spatial pattern, we compared four spatially explicit models of annual needle litter dispersal: a model based only on basal area, an overstory abundance index (OAI) model, both isotropic and anisotropic litter kernel models, and a null model that assumed no spatial relationship. The best model was the anisotropic model (R 2 = 0.656) that incorporated tree size, location, and prevailing wind direction, followed by the isotropic model (R ² = 0.612), basal area model (R ² = 0.488), OAI model (R ² = 0.416), and the null model (R ² = 0.08).
Conclusions
As with previous studies, the predictive capability of the litter models was robust when internally validated with a subset of the original dataset (R ² = 0.196–0.549); however, the models were less robust when challenged with an independent dataset (R ² = 0.122–0.319) from novel forest stands. Our model validation underscores the need for rigorous tests with independent, external datasets to confirm the validity of litter dispersal models. These models can be used in the application of prescribed fire to estimate fuel distribution and loading, as well as aid in the fine tuning of fire behavior models to better understand fire outcomes across a range of forest canopy structures.
Mountain glaciers are retreating rapidly due to climate change, leading to the formation of downstream lakes. However, little is known about the physical and biogeochemical conditions in these lakes across a range of glacial influence. We surveyed alpine lakes fed by both glacial and snowpack meltwaters and those fed by snowpack alone to compare nutrient concentrations, stoichiometry, water clarity, chlorophyll, and zooplankton communities. Total phosphorus (TP) and soluble reactive phosphorus were two times higher in glacial lakes than in non‐glacial lakes, while nitrate concentrations were three times higher. However, organic carbon concentrations in glacial lakes were two times lower than in non‐glacial lakes. The carbon‐to‐phosphorus ratio and the nitrogen‐to‐phosphorus ratio of lake seston increased with water clarity in glacial lakes, suggesting that turbidity from glacial flour increases light limitation and increases stoichiometric food quality for zooplankton in newly formed lakes. However, chlorophyll a concentrations did not differ between lake types. Through structural equation modeling, we found that glaciers exhibit a bidirectional association with nitrate and TP concentrations, perhaps mediated through landscape vegetation and lake clarity. Zooplankton communities in high‐turbidity glacial lakes were largely composed of cyclopoid copepods and rotifers (i.e., non‐filter feeders), while non‐glacial lakes tended to be dominated by calanoid copepods and cladocerans (i.e., filter feeders). Our results show that glacier‐influenced lakes have biogeochemical and ecological characteristics distinct from snow‐fed mountain lakes. Sustained studies are needed to assess the dynamics of these unique features as the influence of the alpine cryosphere fades under ongoing climate change.
Premise
Dominant in many ecosystems around the world, clonal plants can reach considerable ages and sizes. Due to their modular growth patterns, individual clonal plants (genets) can consist of many subunits (ramets). Since single ramets do not reflect the actual age of genets, the ratio between genet size (radius) and longitudinal annual growth rate (LAGR) of living ramets is often used to approximate the age of clonal plants. However, information on how the LAGR changes along ramets and how LAGR variability may affect age estimates of genets is still limited.
Methods
We assessed the variability of LAGR based on wood‐section position along the ramets and on the duration of the growing season on three genetically distinct genets of Salix herbacea growing in the Northern Apennines (Italy). We compared genet ages estimated by dividing genet radius by the LAGRs of its ramets.
Results
LAGR increased significantly from the stem apex to the root collar; indicating that ramet growth rate decreased with time. Furthermore, a difference of ca. 2 weeks in the onset of the growing period did not impact LAGR. Considering the high LAGR variability, we estimated that the three genets started to grow between ~2100 and ~7000 years ago, which makes them the oldest known clones of S. herbacea even considering the most conservative age estimate.
Conclusions
Our findings indicate that analyzing ramets at the root collar provides an integrative measurement of their overall LAGR, which is crucial for estimating the age of genets.
Kernel density estimations of circular data are an effective type of nonparametric estimation. The performance of these estimations depends significantly on a smoothing parameter referred to as bandwidth. Selecting suitable bandwidths for these types of estimation pose fundamental challenges, therefore fixed bandwidth selectors are often the initial choice. The study investigates common bandwidth selection methods and proposes novel methods which adopt the idea from the linear case. The attention is also paid to variable bandwidth selection. Using simulations which incorporate a range of circular distributions that exhibit multimodality, peakedness and skewness, the proposed methods were evaluated and then compared with other bandwidth selectors to determine their potential advantages. Two real datasets, one containing animal movements and the other wind direction data, were applied to illustrate the utility of the proposed methods.
Background and aims
Hakea prostrata (Proteaceae) is a highly phosphorus-use-efficient plant native to southwest Australia. It maintains a high photosynthetic rate at low leaf phosphorus (P) and exhibits delayed leaf greening, a convergent adaptation that increases nutrient-use efficiency. This study aimed to provide broad physiological and gene expression profiles across leaf development, uncovering pathways leading from young leaves as nutrient sinks to mature leaves as low-nutrient, energy-transducing sources.
Methods
To explore gene expression underlying delayed greening, we analysed a de novo transcriptome for H. prostrata across five stages of leaf development. Photosynthesis and respiration rates, and foliar pigment, P and nitrogen (N) concentrations were determined, including the division of P into five biochemical fractions.
Key results
Transcripts encoding functions associated with leaf structure generally decreased in abundance across leaf development, concomitant with decreases in foliar concentrations of 85% for anthocyanins, 90% for P and 70% for N. The expression of genes associated with photosynthetic function increased during or after leaf expansion, in parallel with increases in photosynthetic pigments and activity, much later in leaf development than in species that do not have delayed greening. As leaves developed, transcript abundance for cytosolic and mitochondrial ribosomal proteins generally declined, whilst transcripts for chloroplast ribosomal proteins increased.
Conclusions
There was a much longer temporal separation of leaf cell growth from chloroplast development in H. prostrata than is found in species that lack delayed greening. Transcriptome-guided analysis of leaf development in H. prostrata provided insight into delayed greening as a nutrient-saving strategy in severely phosphorus-impoverished landscapes.
Here, a new study of Sauleh distribution termed as length biased Sauleh distribution has been established. The mathematical and statistical properties of the proposed distribution have been discussed and the model parameters are estimated by using the technique of maximum likelihood estimation. Finally, the distribution has been analysed and investigated with two real life data sets to demonstrate its goodness of fit. A numerical study is carried out in the agricultural production of India. The vulnerable factors of food security and climate change are also discussed. In probability distribution theory, researchers have shown that the classical distributions may not provide the best fit to lifetime data. In such cases, a need arise to add an extra parameter to the existing classical distribution. This extra parameter can be added through various techniques. One of such technique is the weighted technique. The theory of weighted distributions was introduced by Fisher (1934) to model the ascertainment bias, which was later modified by Rao (1965) in a unifying theory for the problems where the observations fall in non-experimental, non-replicated and non-random categories. In weighted distributions, the addition of extra parameter makes the distribution more flexible and reliable, while comparing with other distributions. The weighted distributions arise when the observations are generated from a stochastic process are not given equal chances of being recorded, instead they are recorded according to some weight function. The weighted distributions provide a unifying approach to deal with model specification and data interpretation. The weighted distributions are applied in various research areas related to reliability, biomedicine, ecology, Meta analysis, analysis of family data, analysis of intervention data and other areas for the proper development of statistical models. The weighted distributions provide a technique for fitting a model to the unknown weight function when the samples can be taken both from original and developed distribution. The weighted distribution reduces to length biased when the weight function considers only the length of the units of interest. The statistical interpretation of length biased sampling was originally introduced by Cox (1962) in the context of renewal theory. The concept of length biased sampling was introduced by Cox (1969) and Zelen (1974). Length biased sampling situation may occur in clinical trials, reliability theory and population studies were a proper sampling frame is absent. Many researchers have developed and studied the various length biased probability models along with their illustrations and applications in different fields. Modi and Gill (2015) discussed on the length-biased weighted Maxwell distribution. Mudasir and Ahmad (2018) proposed characterization and estimation of length biased Nakagami distribution. Haq et al. (2019) proposed the Marshall-Olkin length-biased exponential distribution and its applications. Al-Omari et al. (2019) studies power length-biased Suja distribution with properties and application. Mathew (2020) introduced on some length-biased distributions with an overview. Atikankul et al. (2020) studies the length biased weighted Lindley distribution with applications. Abd-Elfattah et al. (2021) studied the length biased Burr-XII distribution with properties and application. Ganaie and Rajagopalan (2021) introduced the length biased power quasi Lindley distribution with properties and applications. Ghorbal (2022) discussed on properties of length-biased exponential model. Chaito et al. (2022) presented the length-biased Gamma-Rayleigh distribution with applications. Recently, Mustafa and Khan (2022) introduced the length-biased powered inverse Rayleigh distribution with applications. Sauleh distribution is a one parametric lifetime model proposed by Aijaz et al. (2020). The mathematical and statistical properties including the shapes of pdf and cdf, Moments, Moment generating function, mean deviations, order statistics, reliability analysis, bonferroni and Lorenz curves of the proposed distribution have
The grasses are one of the most diverse plant families on Earth. However, their classification and evolutionary history are obscured by their pollen stenopalynous (similar) morphology. A combination of high‐resolution imaging of pollen surface ornamentation and computational analysis has previously been proposed as a promising tool to classify grass taxonomic boundaries. In this study, we test this hypothesis by studying Poaceae pollen across the phylogeny from plants collected in northern South America and also from published literature across the globe. We assessed if morphotypes that we establish using descriptive terminology are supported by computational analysis, if they vary along six (a)biotic variables and vary across the phylogeny. Based on this analysis, we constructed a reference framework for pollen surface ornamentation morphotypes. Our results showed that there is a wide variation of grass pollen surface ornamentation. We identified nine new and confirmed six known morphotypes, establishing a data set for 223 species (243 individual plant specimens) that represent 11 subfamilies. Computational analysis showed that our morphotypes are well‐supported by two quantitative features of pollen sculptural elements (size and density). The specific data set and mapping of the phylogeny confirmed that pollen morphological sculpture is unrelated to (a)biotic variables and is diverse across the phylogeny.
Backround
Dysfunctional interpersonal beliefs (DIBs) are a key symptom domain in numerous mental disorders. Because DIBs exert a strong influence on social experience and behavior, they play an important role in a mental disorder's development and progression. To date, only the Interpersonal Cognitive Distortions Scale (ICDS) captures DIBs independently of specific disorders, populations, or contexts. The present study's aim was to psychometrically evaluate and validate a German translation of the ICDS.
Methods
The ICDS was administered along with indicators of convergent (rejection sensitivity, depressive expectations, interpersonal trust, interpersonal problems, perceived social support), discriminant (self-efficacy, perseverative negative thinking, optimism), and clinical validity (psychopathology, perceived stress, well-being) to a pooled sample incorporating non-clinical (N = 114) and clinical (N = 94) participants.
Results
An exploratory factor analysis (EFA) suggested a five-factor solution (factor loadings: .44 to .85). Correlational analyses demonstrated acceptable convergent (ρ = -.29 to -.35, ρ = .27 to .59), suboptimal discriminant (ρ = -.27 to -.38, ρ = .52), and acceptable clinical validity (ρ = -.21, ρ = .36 to .44) at the total-scale level. However, results at the subscale level were mixed and required nuanced interpretation. Likewise, internal consistency was acceptable at the total-scale level (α = .76), but ranged from good to poor at the subscale level (α = .61 to .80). DIBs mediated the negative relationship between mental disorder onset and psychopathology levels.
Discussion
Our results imply DIBs' relevance to mental health and related outcomes. When working with the ICDS’s German version, we recommend employing only the “insecurity” subscale, as this was the only scale revealing acceptable psychometric properties. Future studies should improve the construct validity of the ICDS (and its subscales), e.g., by adding more items to the respective subscales and further classes of DIBs.
The estimation of the reference evapotranspiration is fundamental in defining irrigation projects. However, an estimation using the standard equation requires climate variables that are difficult to measure and are not very accessible. Thus, the objective of this study was to calibrate and validate alternative methods to estimate evapotranspiration that use simple variables and to compare performance with the standard Penman-Monteith method for the municipality of Nova Venécia, Espírito Santo, Brazil. For this, a 12-year time series (2008-2019) of meteorological data from the Instituto Nacional de Meteorología was used. The standard FAO-56 Penman–Monteith method was used to evaluate alternative methods: Hargreaves and Samani, Benevides and Lopes, Linacre, Hamon and Camargo. Method performance was analyzed by correlation coefficient, Willmott index, root mean square of normalized error, and performance index. Calibration improved the statistical indices, increasing the performance of the Hargreaves and Samani, Benevides and Lopes, and Linacre methods to “very good” in the rainy season and to “intermediate” in the dry season. They were superior to the Hamon and Camargo methods, which continued to show “tolerable” to “very poor” performance in both periods.
Immersive virtual reality (VR) provides a versatile method for investigating human time perception, because it allows the manipulation and control of relevant variables (e.g., the speed of environmental changes) that cannot be modified in the real world. However, an important premise for interpreting the results of VR studies, namely that the method itself does not affect time perception, has received little attention. Here we tested this assumption by comparing timing performance in a real environment and a VR scenario. Participants performed two timing tasks, requiring the production of intervals defined either by numerical values ("eight seconds") or by a physical process (“the time it takes for a bottle to run out when turned over"). We found that the experience of immersive VR exclusively altered judgments about the duration of physical processes, whereas judgments about the duration of abstract time units were unaffected. These results demonstrate that effects of VR on timing performance are not driven by changes in time perception itself, but rather by altered expectations regarding the duration of physical processes. The present study validates the use of VR in time perception research and strengthens the interpretation of changed timing behaviour induced by manipulations within VR.
Herbicides used in agriculture and their metabolites are frequently detected in surface water bodies, where they can persist and cause adverse effects on aquatic organisms. The aim of this study was to evaluate the acute toxicity and genotoxic effects of the S-metolachlor (SM)-based herbicide Dual Gold® (DG®), on Leptodactylus luctator tadpoles (Anura: Leptodactylidae). To assess the toxicity of the herbicide, including the median lethal concentration (LC50) at 24h, the no-observed-effect concentration (NOEC), and the lowest-observed-effect concentration (LOEC), tadpoles were exposed to five nominal concentrations of DG® (5.0, 6.2, 7.8, 9.8, and 12.2 mg/L), and to dechlorinated water as a negative control (NC). The LC5024h of DG® was 7.0 mg/L, the NOEC was 5.0 mg/L and the LOEC=6.2 mg/L. L. luctator tadpoles were sensitive to the herbicide, reaching 100% mortality after 24 h of exposure to the highest concentration tested (12.2 mg/L). To evaluate the potential genotoxicity of the herbicide, the frequencies of micronuclei (MN) and other erythrocyte nuclear abnormalities (ENA) were determined in larvae exposed to three nominal concentrations of DG® (1.0, 5.0, and 6.2 mg/L) for 48 and 96 h. The frequencies of MN and ENA were compared with a positive control (40 mg/L of Cyclophosphamide) and a negative control. The frequencies of MN and ENA in the erythrocytes of tadpoles exposed to the test concentrations of DG® and Cyclophosphamide were significantly higher than in the negative control group at both 48 and 96 h (with the only exception of MN at 1.0 mg/L at 48 h). Our results confirm the genotoxic and cytotoxic effects of this widely used herbicide in agriculture, a fact that represents a potential risk to amphibians that develop in ponds associated with or immersed in agroecosystems.
This study evaluated the sensitivity of male and female of guppies (Poecilia reticulata) to ammonia. LC50-96h for males, females and combined sexes of P. reticulata was 37.33, 48.34, and 42.45 mg/L of total ammonia or 1.03, 1.34, and 1.17 mg/L of un-ionized ammonia. The mortality at the concentration of 40 mg/L of total ammonia differed between the sexes with higher mortality in males. These results have implications for production systems, since recommendations of ammonia toxicity reference values that do not consider the difference between the sexes, can lead to the mortality of males, and cause economic losses because males have higher commercial value in the ornamental market.
Background and Objectives: Simulation-based learning within neurosurgery provides valuable and realistic educational experiences in a safe environment, enhancing the current teaching model. Mixed reality (MR) simulation can deliver a highly immersive experience through head-mounted displays and has become one of the most promising teaching tools in medical education. We aimed to identify whether an MR neurosurgical simulation module within the setting of an undergraduate neurosurgical hands-on course could improve the satisfaction of medical students. Materials and Methods: The quasi-experimental study with 223 medical students [120 in the conventional group (CG) and 103 in the MR-group (MRG)] was conducted at the University Hospital Münster, Münster, Germany. An MR simulation module was presented to the intervention group during an undergraduate neurosurgical hands-on course. Images of a skull fracture were reconstructed into 3D formats compatible with the MR-Viewer (Brainlab, Munich, Germany). Participants could interact virtually with the model and plan a surgical strategy using Magic Leap goggles. The experience was assessed by rating the course on a visual analog scale ranging from 1 (very poor) to 100 (very good) and an additional Likert-scale questionnaire. Results: The satisfaction score for CG and MRG were 89.3 ± 13.3 and 94.2 ± 7.5, respectively. The Wilcoxon rank-sum test showed that MR users (Mdn = 97.0, IQR = 4, n = 103) were significantly more satisfied than CG users (Mdn = 93.0, IQR = 10, n = 120; ln(W) = 8.99, p < 0.001) with moderate effect size (r^biserial = 0.30, CI95 [0.15, 0.43]), thus indicating that the utilization of MR-simulation is associated with greater satisfaction. Conclusions: This study reports a positive response from medical students towards MR as an educational tool. Feedback from the medical students encourages the adoption of disruptive technologies into medical school curricula.
Only a small amount of the light absorbed by the photosynthetic pigments including chlorophylls and carotenoids is de-excited via emission as heat or red and far-red chlorophyll fluorescence under normal physiological conditions. Most of the energy is utilized for photosynthetic quantum conversion. In contrast, photosynthetic performance decreases under numerous stress effects, which is accompanied by a rise in the steady-state levels of chlorophyll fluorescence. Field crops in Hungary are increasingly exposed to extreme weather conditions. Therefore, the main objective of our field study in wheat and sunflower crops was to investigate the effects of heat and drought stress and heterogeneous nutrient availability on the vegetation by quantifying the spatial and temporal variability of photosynthetic efficiency and fluorescence. In a parallel laboratory experiment we attempted to create a pool of plants developing under controlled environment, to meet similar appearance as under field conditions.
We found that simultaneous observation of multiple spectral domains and an approach based on field and laboratory measurements were adequate to assess stress and its severity for individual plants and for vegetation canopy. Vegetation indices were good tools to separate the healthy state from the stressed state, and, further combined with fluorescence parameters, we could even draw some conclusion about stress severity. Indices linked to anthocyanin and carotenoid were found to be higher in the already damaged plants, while steady-state fluorescence was higher for leaves with still functioning tissues. Above all, individual species differences were much larger than expected.
Background
Australia provides a valuable international case study of life expectancy during the pandemic. In contrast to many other countries, it experienced relatively stringent restrictions and low COVID-19 mortality during 2020–21, followed by relaxation of these restrictions when high vaccination rates were achieved. This study measures Australia’s life expectancy trends and the contributions of age group and causes of death, during the pandemic.
Methods
Trends in life expectancy at birth in Australia and its states and territories were measured from 2020 to 2022. The contributions of age group and cause of death to these trends were measured using decomposition methods. Life expectancy was compared with other high-income countries.
Results
Australia’s life expectancy fell by more than half a year in 2022, following a sharp increase in 2020 and moderate decline in 2021. For the 3 years 2020 to 2022, life expectancy was 0.13 years (95% confidence interval 0.07-0.19) higher for males and 0.09 years (0.03-0.14) higher for females versus 2017–19. Australia’s life expectancy increase in 2020 was larger than that in the vast majority of other high-income countries, but its decline in 2022 was greater than in other countries whose life expectancy rose in the first year of the pandemic. The small negative contribution of COVID-19 deaths to life expectancy in Australia was more than offset by lower non-communicable disease mortality. There were only small differences in life expectancy change between the states with the most stringent restrictions (Victoria and New South Wales) and the rest of Australia.
Conclusions
Australia’s life expectancy trends during 2020–22 were relatively favourable compared with other high-income countries, with the exception of its sharp decline in 2022 once restrictions were loosened.
Climate literacy (CL) comprises knowledge, skills, and attitudes that enable individuals to counteract the global threat of anthropogenic climate change. Teachers’ knowledge and pedagogy are main predictors of students’ learning outcomes, but teachers are insufficiently prepared in the interdisciplinary field of CL. In a multilevel interrogation of experts in the fields of climate science, education research, and school, we derived 13 delineated themes describing necessary knowledge concerning the scientific background of climate change as well as pedagogy and teaching strategies. These themes indicate that teachers need a broad basis of understanding the climate system, climate science, causes of, impacts of, and dealing with climate change as well as the ability to convey this interdisciplinary content into teaching, by making the topic personally relevant and strengthening students’ role as change agents. The findings underline the need to promote interdisciplinary ways of teaching towards CL and provide a baseline for the development of future teacher preparation.
Esta pesquisa teve como objetivo avaliar o comportamento dos consumidores em relação aos produtos diet e light. Foi realizado por meio de uma pesquisa de mercado com aplicação de um questionário estruturado na cidade Barbacena-MG no primeiro semestre de 2019, constituída por 385 indivíduos. Seguido de uma avaliação da aceitação com escala hedônica de 9 pontos com iogurte nas versões tradicionais, light e zero, ocorreram em duas situações às cegas e com informação das versões. Por fim, aplicação das sessões de grupo focal. Dentre os participantes do teste, a maioria era do gênero feminino, sendo a minoria os que afirmam consumir produtos diet e light, apontaram a dieta como principal motivo para o consumo. Os alimentos mais consumidos, destaca-se o iogurte, seguido do refrigerante. Em relação à influência da informação na avaliação dos produtos, observou-se que a informação sobre a versão do iogurte (light, zero ou tradicional) não afetou a aceitação dos produtos. Os resultados sugerem que o nível de conhecimento dos consumidores sobre alimentos diet e light é baixo e muitas vezes fazem confusão com estes dois produtos.
Clostridioides difficile is a Gram-positive bacterium that can cause mild to severe diarrhea, inflammation, and colonic tissue damage in animal hosts. Symptoms of the disease can be attributed to the activity of toxin B (TcdB) secreted by C. difficile during infection. TcdB can engage multiple host cell surface receptors in vitro ; however, little is known about where these receptors localize on colonic tissue and how these interactions promote disease. Here, we used immunofluorescence microscopy to first visualize TcdB interactions with two of the reported receptors, CSPG4 and Nectin-3, on cells in vitro . In cells expressing both receptors, we found that TcdB preferentially interacts with CSPG4. In moving to host colonic tissue, we observed novel localization of Nectin-3 within the brush border of epithelial cells and CSPG4 localization at epithelial cell junctions. The unexpected junctional CSPG4 signal led us to the hypothesis that the signal could represent a soluble form of the CSPG4 extracellular domain (ECD) being shed from fibroblasts in the underlying stromal layer of the tissue. To test, we set up a co-culture of epithelial cells and fibroblasts separated by transwell inserts. We observed CSPG4-ECD shed into the media of cultured fibroblasts and an accumulation in epithelial cells following co-culture. We also found that soluble CSPG4-ECD present in the conditioned media from fibroblasts can potentiate TcdB-mediated cytopathic responses in epithelial cells lacking CSPG4 expression. Based on these observations, we propose that Nectin-3 can facilitate the binding of TcdB at the epithelial surface and that a soluble form of CSPG4 derived from stromal cells can contribute to TcdB intoxication of epithelial cells in vivo .
IMPORTANCE
Toxin B (TcdB) is a major virulence factor of Clostridioides difficile , a Gram-positive pathogen that is a leading cause of hospital-acquired diarrhea. While previous studies have established that TcdB can engage multiple cell surface receptors in vitro , little is known about how these interactions promote disease and where these receptors localize on colonic tissue. Here, we used immunofluorescence microscopy to visualize Nectin-3 and CSPG4 on tissue, revealing unexpected localization of both receptors on colonic epithelial cells. We show that Nectin-3, which was previously characterized as an adherens junction protein, is also localized to the brush border of colonocytes. Staining for CSPG4 revealed that it is present along epithelial cell junctions, suggesting that it is shed by fibroblasts along the crypt-surface axis. Collectively, our study provides new insights into how TcdB can gain access to the receptors Nectin-3 and CSPG4 to intoxicate colonic epithelial cells.
Microbes can have profound effects on host fitness and health and the appearance of late‐onset diseases. Host–microbe interactions thus represent a major environmental context for healthy aging of the host and might also mediate trade‐offs between life‐history traits in the evolution of host senescence. Here, we have used the nematode Caenorhabditis elegans to study how host–microbe interactions may modulate the evolution of life histories and aging. We first characterized the effects of two non‐pathogenic and one pathogenic Escherichia coli strains, together with the pathogenic Serratia marcescens DB11 strain, on population growth rates and survival of C . elegans from five different genetic backgrounds. We then focused on an outbred C . elegans population, to understand if microbe‐specific effects on the reproductive schedule and in traits such as developmental rate and survival were also expressed in the presence of males and standing genetic variation, which could be relevant for the evolution of C . elegans and other nematode species in nature. Our results show that host–microbe interactions have a substantial host‐genotype‐dependent impact on the reproductive aging and survival of the nematode host. Although both pathogenic bacteria reduced host survival in comparison with benign strains, they differed in how they affected other host traits. Host fertility and population growth rate were affected by S . marcescens DB11 only during early adulthood, whereas this occurred at later ages with the pathogenic E . coli IAI1. In both cases, these effects were largely dependent on the host genotypes. Given such microbe‐specific genotypic differences in host life history, we predict that the evolution of reproductive schedules and senescence might be critically contingent on host–microbe interactions in nature.
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