Book

Ggplot2: Elegant Graphics for Data Analysis

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Chapters (9)

In this chapter, you will learn to make a wide variety of plots with your first ggplot2 function, qplot(), short for quick plot. qplot makes it easy to produce complex plots, often requiring several lines of code using other plotting systems, in one line. qplot() can do this because it’s based on the grammar of graphics, which allows you to create a simple, yet expressive, description of the plot. In later chapters you’ll learn to use all of the expressive power of the grammar, but here we’ll start simple so you can work your way up. You will also start to learn some of the ggplot2 terminology that will be used throughout the book.
You can choose to use just qplot(), without any understanding of the underlying grammar, but if you do you will never be able to unlock the full power of ggplot2. By learning more about the grammar and its components, you will be able to create a wider range of plots, as well as being able to combine multiple sources of data, and customise to your heart’s content. You may want to skip this chapter in a first reading of the book, returning when you want a deeper understanding of how all the pieces fit together.
Layering is the mechanism by which additional data elements are added to a plot. Each layer can come from a different dataset and have a different aesthetic mapping, allowing us to create plots that could not be generated using qplot(), which permits only a single dataset and a single set of aesthetic mappings.
The layered structure of ggplot2 encourages you to design and construct graphics in a structured manner. You have learned what a layer is and how to add one to your graphic, but not what geoms and statistics are available to help you build revealing plots. This chapter lists some of the many geoms and stats included in ggplot2, broken down by their purpose. This chapter will provide a good overview of the available options, but it does not describe each geom and stat in detail. For more information about individual geoms, along with many more examples illustrating their use, see the online and electronic documentation. You may also want to consult the documentation to learn more about the datasets used in this chapter.
Scales control the mapping from data to aesthetics. They take your data and turn it into something that you can perceive visually: e.g., size, colour, position or shape. Scales also provide the tools you use to read the plot: the axes and legends (collectively known as guides). Formally, each scale is a function from a region in data space (the domain of the scale) to a region in aesthetic space (the range of the range). The domain of each scale corresponds to the range of the variable supplied to the scale, and can be continuous or discrete, ordered or unordered. The range consists of the concrete aesthetics that you can perceive and that R can understand: position, colour, shape, size and line type. If you blinked when you read that scales map data both to position and colour, you are not alone. The notion that the same kind of object is used to map data to positions and symbols strikes some people as unintuitive. However, you will see the logic and power of this notion as you read further in the chapter.
This chapter discusses position, particularly how facets are laid out on a page, and how coordinate systems within a panel work. There are four components that control position.
In this chapter you will learn how to prepare polished plots for publication. Most of this chapter focusses on the theming capability of ggplot2 which allows you to control many non-data aspects of plot appearance, but you will also learn how to adjust geom, stat and scale defaults, and the best way to save plots for inclusion into other software packages. Together with the next chapter, manipulating plot rendering with grid, you will learn how to control every visual aspect of the plot to get exactly the appearance that you want.
So far this book has assumed you have your data in a nicely structured data frame ready to feed to ggplot() or qplot(). If this is not the case, then you’ll need to do some transformation.
A major requirement of a good data analysis is flexibility. If the data changes, or you discover something that makes you rethink your basic assumptions, you need to be able to easily change many plots at once. The main inhibitor of flexibility is duplication. If you have the same plotting statement repeated over and over again, you have to make the same change in many different places. Often just the thought of making all those changes is exhausting!
... The optimal number of PCs was chosen according to the a.score (a statistic that measures the quality of discrimination, based on group reassignment probabilities). Clusters were visualised using scatterplots and density plots of the discriminant functions using ggplot2 package (Wickham, 2016). An admixture proportion model was run using the program Structure v. 2.3.4 (Pritchard et al., to obtain population genetic information (Korneliussen et al., 2014). ...
... The results were calculated using ADMIXTURE 1.3 (Alexander et al., 2009). The visualisation of the obtained results was carried out in the R 4.2.0 program (R Core Team, 2022) using the package ggplot2 (Wickham, 2016). ...
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Phylogeographic studies of evolutionary young species co-existing over a vast geographic area can provide insights in the process of evolutionary divergence and its cohesiveness in different parts of the species ranges. The Littorina snails of the saxatilis cryptic group diverged in near-glacial time, and tend to live in sympatry. L. saxatilis is widely distributed on both sides of the North Atlantic, while L. arcana and L. compressa are patchy distributed on the shores of Europe and Atlantic islands. The biogeographic history of the Littorina saxatilis cryptic group is still obscure, with L. saxatilis studied much better than the other two species. We evaluated the population structure of the three saxatilis species on the coasts of Wales, the Norwegian and the Barents seas using several genetic markers: the mitochondrial cytochrome b gene (cytb, partial, 26 haplotypes for 268 sequences), nuclear (5 microsatellite loci in 458 individuals) and whole-genome (2bRAD, 63 417 loci in 114 individuals) markers. Analyses based on the cytb and microsatellite markers showed a deep divergence between the British and the North European populations of all three species with a high genetic similarity between their sympatric populations from Wales. L. compressa had the highest differentiation from both L. arcana and L. saxatilis and demonstrated the clear population structure due to allele frequency. The degree of the genetic differentiation between sympatric L. arcana and L. saxatilis in some regions was lower than between the regions within a species. Moreover, analyses of all three types of used markers indicate that the continental populations of L. arcana include individuals with contrasting genomic profiles. Our results suggest that L. arcana and L. compressa separated from their common ancestor L. islandica after L. saxatilis. The three sibling species survived glaciation in a refugium (or refugia) on the British coasts, separated from the mainland refugium (or refugia). After the glaciation, L. compressa colonised the mainland, most likely from a single European refugium. Post-glacial continental repopulation by L. arcana could have occurred from at least two sources, with two differentiated lineages still recognisable. Further inclusion of the Littorina populations from South Norway and France is needed to complete the reconstruction of biogeographic history in these three evolutionary young species of Littorina snails.
... We used the survey (16) package in R (version 3.5.1) to incorporate the weightings provided by the Swiss Federal Statistical Office (17) and to generate results that are representative of the Swiss population. For each survey and outcome, we conducted a descriptive analysis of the weighted data and reported percentages (with 95% confidence intervals) for each categorical exposure variable, the median and interquartile range (IQR) for continuous variables and unadjusted odds ratios (OR, 95% CI) for associations between each outcome and exposures. ...
... 19(17,22) 21 (19, 24) 0.95 (0.80,1.13) Multivariable model includes all variables in the table and region of residence, p value from Wald test b. ...
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Background: Monitoring of HIV and sexually transmitted infection (STI) prevention is important for guiding national sexual health programmes for both the general population and key populations. The objectives of this study were to examine patterns of condom use at last intercourse and lifetime HIV testing from 2007 to 2017 in Switzerland, and to explore factors associated with these behaviours in men and women with opposite-sex partners and with same sex partners. Methods: We analysed data from the 2007, 2012 and 2017 Swiss Health Survey. At each time point, outcome and population group, we conducted a descriptive analysis of weighted data and conducted multivariable logistic regression to obtain adjusted odds ratios (aOR) with 95% confidence intervals (CI) and compared outcomes between the timepoints. Results: In total, 43,949 people were interviewed: 21,274 men and 22,675 women, who reported having sex only with partners of the opposite sex, 633 men who reported sex with a male partner and 699 women who reported sex with a female partner. Among the three surveys the prevalence of condom use varied from 24 to 26% of men and 18 to 21% in women with only opposite-sex partners (aOR men, 0.93, 95% CI 0.82, 1.06; women 0.98, 95% CI 0.86 to 1.11). In men with any same sex partner the prevalence of condom use increased from 43% in 2007 to 54% in 2017 (aOR 1.80, 95% CI 0.97, 3.34). In multivariable analysis, the factor most strongly associated with condom use was sex with an occasional partner at last intercourse. HIV testing ever increased across all three survey years in all groups: 2017 vs. 2007, aOR men with only opposite-sex partners 1.57 (95% CI 1.42, 1.74), women with only opposite-sex partners 1.54 (1.39, 1.71), men with any same sex partner 1.85 (0.96, 3.55), women with any same sex partner 1.31 (0.74, 2.30). Conclusions: Monitoring of condom use, and HIV testing should continue and contribute to the development of the national sexual health programme. Stronger promotion of condoms for people with opposite-sex partners might be needed, since overall condom use at last intercourse has not changed since 2007.
... The relative cross-reactivity was determined as IC50 (AFM1)/IC50 (other aflatoxins) × 100. Data were plotted using the R graphics package ggplot2 [41]. ...
... The optical density (O.D.) was measured after 15 min, stopping the reaction with 50 µ L/well HCl 3M, and reading at 450 nm via microtiter plate reader. Data were plotted using the R graphics package ggplot2 [41]. Calibration curves were interpolated by the four-parameter logistic Equation (4-PL) [45], as follows: y = ymin + (ymax − ymin)/1 + ([AFM1]/IC50) −Slope where ymin is the background signal estimated at infinite [AFM1], ymax is the maximum signal (which corresponds to the signal at [AFM1] = 0), IC50 is the AFM1 concentration that halves the ymax (50% inhibition of the maximum binding), and Slope is the slope of the curve in correspondence of IC50. ...
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A new green competitive ELISA for aflatoxin M1 quantification in raw milk was developed. This diagnostic tool is based on an anti AFM1 mAb produced by plant molecular farming in alternative to classical systems. Our assay, showing an IC50 below 25 ng/L, fits with the requirements of EU legislation limits for AFM1 (50 ng/L). Optimal accuracy was achieved in correspondence of the decision levels (25 and 50 ng/L), and the assay enabled AFM1 quantification in the range 5–110 ng/L, with limit of detection 3 ng/L. Moreover, to evaluate a real applicability in diagnostics, raw milk-spiked samples were analysed, achieving satisfactory recovery rates of AFM1. In conclusion, an efficient and ready-to-use diagnostic assay for the quantification of aflatoxin M1 in milk, based on a plant-produced recombinant mAb, has been successfully developed.
... For LMM analysis, the lme4 R package was applied [63]. The ggplot2 R package [64] was used to generate box plots depicting the median, the lower and upper quartile. Whiskers represent 1.5times the interquartile range. ...
... Whiskers represent 1.5times the interquartile range. The ggplot2 R package [64] was used to generate bar plots depicting the mean with error bars representing the standard deviation (SD). The p-values for significant changes are represented as follows: * p < 0.05; ** p < 0.01; *** p < 0.001. ...
Preprint
Unrestrained transcriptional activity of β-CATENIN and its binding partner TCF7L2 frequently underlies colorectal tumor initiation and is considered an obligatory oncogenic driver throughout intestinal carcinogenesis. Yet, the TCF7L2 gene carries inactivating mutations in about 10 % of colorectal tumors and is non-essential in colorectal cancer (CRC) cell lines. To determine whether CRC cells acquire TCF7L2-independence through cancer-specific compensation by other T-cell factor (TCF)/lymphoid enhancer binding factor (LEF) family members, or rather lose addiction to beta-CATENIN/TCF7L2-driven gene expression altogether, we generated multiple CRC cell lines entirely negative for TCF/LEF or beta-CATENIN expression. Viability of these cells demonstrates complete beta-CATENIN- and TCF/LEF-independence, albeit one beta-CATENIN-deficient cell line eventually became senescent. Absence of TCF/LEF proteins and beta-CATENIN consistently impaired CRC cell proliferation, reminiscent of mitogenic effects of WNT/beta-CATENIN signaling in the healthy intestine. Despite this common phenotype, beta-CATENIN-deficient cells exhibited highly cell-line-specific gene expression changes with little overlap between beta-CATENIN- and TCF7L2-dependent transcriptomes. Apparently, beta CATENIN and TCF7L2 control sizeable fractions of their target genes independently from each other. The observed divergence of beta-CATENIN and TCF7L2 transcriptional programs, and the finding that neither beta-CATENIN nor TCF/LEF activity is strictly required for CRC cell survival has important implications when evaluating these factors as potential drug targets.
... B Estimation of the pan-genome (blue) and the core genome (yellow) of twenty-eight L. parabuchneri strains by including genomes one by one. R programming language [27] and ggplot2 [28] package were used to plot the graph of GH family CAZyme encoding genes compared to the remaining strains. CBM and CE family CAZymes were carried by all strains at similar abundance. ...
... gov/ COG/. Core and Pan COGs were visualized using R [27] and ggplot2 [28]. ...
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Background Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms. Result Core genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L. parabuchneri strains screened. Conclusion The findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.
... We asked Darlington, Gateshead, South Tyneside and Blue Cabin for their actual costs to introduce the CLSW programme in its first year. We received responses from all four organisations (Table 3. 16). In theory this should have all been new activity that would not otherwise have happened, but we do not have enough information to say whether the programme may have redirected some staff time from other work. ...
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Coram and Ipsos MORI carried out an evaluation of a creative model of Life Story Work for looked after children. This was delivered in 2021-22 in Darlington, Gateshead and South Tyneside councils, funded by What Works for Children’s Social Care. We believe this was the first ever randomised controlled trial of a Life Story Work intervention in the UK. We also carried out a process evaluation to understand the experiences of those taking part through interviews and a survey, and a cost analysis.
... Gene expression differences between groups (KO-0h vs. WT-0h, WT-12 h vs. WT-0h, KO-12 h vs. KO-0h, KO-12 h vs. WT-12 h) were detected by using R package "DESeq2" (Love et al., 2014) and genes with adjusted p-value < 0.05 and absolute log2 (fold change) > 1 were considered significantly differentially expressed. R packages "ggplot2" (Wickham, 2009), "clusterProfiler" , "enrichplot", and "org.Hs.eg.db" were applied for volcano plotting, gene set enrichment analysis (GSEA), and enrichment analysis of gene ontology (GO) (Ashburner et al., 2000;Mi et al., 2019;Consortium, 2021) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (Kanehisa and Goto, 2000). A cutoff of adjusted p-value = 0.05 was set for the significance of enrichment analysis. ...
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Oxidation is an essential factor during cataract development. Autophagy, usually a cytoprotective process, is always found elevated in lens epithelial cells under oxidation, yet its roles and associated molecular mechanisms under such circumstances are rarely elucidated. Herein, we extracted and re-analyzed the RNA sequencing data of the GSE161701 dataset from the Gene Expression Omnibus database to identify the differentially expressed mRNAs and lncRNAs by using the R package “DESeq2”. Further analyses of gene ontology and KEGG enrichment were implemented via the packages “clusterProfiler” and “enrichplot”. We found that after the knockout of ATG7, differentially expressed genes were more associated with hemopoiesis, vasculature development, axonogenesis, and hypoxia regulation. When stimulated with H2O2, LECs displayed a gene expression profile correlating with apoptotic and proliferative pathways, such as the MAPK signaling pathway and FoxO signaling pathway. The differentially expressed gene profiles of the two types of LECs (wild type and ATG7 deficient) under oxidation were distinct to a large extent. Furthermore, 1,341 up-regulated and 1912 down-regulated differential mRNAs and 263 up-regulated and 336 down-regulated differential lncRNAs between these two types of LECs subjected to H2O2 were detected, among which 292 mRNAs and 24 lncRNAs possibly interacted with ten cataract-related miRNAs. A competing endogenous lncRNA-miRNA-mRNA network based on such interactions was finally constructed.
... Statistical analyses were conducted using R, version 3.6.2 (R Core Team 2021) and plots were made using ggplot2 (Wickham 2016). All models were fit accordingly using the formulas y~G 0 or y~G 0 * G 1 depending on the generation being analyzed. ...
Article
The inheritance of epigenetic marks induced by environmental variation in a previous generation is broadly accepted as a mediator of phenotypic plasticity. Transgenerational effects linking maternal experiences to changes in morphology, gene expression, and life history of successive generations are known across many taxa. While the number of studies linking epigenetic variation to ecological maternal effects is increasing rapidly, few if any attempts have been made to investigate molecular mechanisms governing epigenetic functions in the context of ecologically relevant maternal effects. Daphnia make an ideal model for investigating molecular epigenetic mechanisms and ecological maternal effects because they will reproduce asexually in the lab. Daphnia are also known to have strong maternal effects, involving a variety of traits and environmental variables. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food limitation within and across generations. We found strong evidence of genotypic variation of responses of life history and Dnmt expression to low food diets, both within and across generations. In general, effects of offspring diet were larger than either the direct maternal effect or offspring-maternal environment interactions, but the direction of the maternal effect was usually in the opposite direction of the within-generation effect. For both life history and Dnmt expression, we also found that when offspring had low food, effects of the maternal environment were stronger than when offspring had high food.
... (accessed on 4 November 2021)), 2DFFTUTILS MODULE (https://github.com/ebmonson/2DFFTUtils-Module (accessed on 4 November 2021)), DAOPHOT [82], FITDISTRPLUS [88], Fox and Weisberg [91], GALFIT [78], GGPLOT2 [166], IRAF [74,75], ELLIPSE [77], KEDD [89], the NASA/IPAC Extragalactic Database (NED), the NASA Astrophysics Data System (ADS), PEARSON_DS [83], PEARSPDF (https://www.mathworks.com/matlabcentral/fileexchange/ 26516-pearspdf (accessed on 4 November 2021)), R [167], SAOIMAGEDS9 [168], and SPIRALARM-COUNT [35,73]. ...
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We present an analysis of the pitch angle distribution function (PADF) for nearby galaxies and its resulting black hole mass function (BHMF) via the well-known relationship between pitch angle and black hole mass. Our sample consists of a subset of 74 spiral galaxies from the Carnegie-Irvine Galaxy Survey with absolute B-band magnitude MB>−19.12 mag and luminosity distance DL≤25.4 Mpc, which is an extension of a complementary set of 140 more luminous (MB≤−19.12 mag) late-type galaxies. We find the PADFs of the two samples are, somewhat surprisingly, not strongly dissimilar; a result that may hold important implications for spiral formation theories. Our data show a distinct bimodal population manifest in the pitch angles of the Sa–Sc types and separately the Scd–Sm types, with Sa–Sc types having tighter spiral arms on average. Importantly, we uncover a distinct bifurcation of the BHMF, such that the Sa–Sc galaxies typically host so-called “supermassive” black holes (M•≳106M⊙), whereas Scd–Sm galaxies accordingly harbor black holes that are “less-than-supermassive” (M•≲106M⊙). It is amongst this latter population of galaxies where we expect fruitful bounties of elusive intermediate-mass black holes (IMBHs), through which a better understanding will help form more precise benchmarks for future generations of gravitational wave detectors.
... Physiological time series data were visually inspected for quality in Biopac Student Lab (version xx) and in custom visualizations using R (v.3.6.2; R Core Team, 2016a) and ggplot2 (v.3.2.1;Wickham, 2009). Time series were classified as clean (i.e. ...
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We examined the superior colliculus (SC) with ultra-high resolution 7-Tesla fMRI during an N-back working memory task. We observed both increased BOLD signal intensity and functional connectivity that followed a layer-dependent pattern predicted from anatomical connections between SC and other brain structures important for visual processing, motor control, and executive function. Our results highlight a role for the human SC in cognitive functions that are usually associated with the cerebral cortex.
... R Core Team, 2017). Beta diversity metrics were performed on PhILR (Silverman et al., 2017) transformed data and visualized as a hierarchical cluster dendrogram using ggplot2 (Wickham, 2016) or PCA using the auto plot function in ggbio (Yin et al., 2012). To determine which taxa might account for the observed variation in our beta diversity plots using a different metric we also generated a NMDS biplot based on a Bray-Curtis dissimilarity matrix using phyloseq (McMurdie and Holmes, 2013). ...
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Background Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual’s post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Materials and methods In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Results We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa. Conclusion The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.
... /fclim. . (Wickham, 2016). Maps were produced with Generic Mapping Tools (Wessel et al., 2013). ...
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Efforts to naturally remove atmospheric CO2 demand that largely intact forests be maintained. Our inter-cultural research initiative tested the hypothesis that Indigenous custody of the land is compatible with the maintenance of intact forests. Here we combined traditional knowledge, phytolith analysis, remote sensing, and tree inventories to study old-growth forests in Panama's Darién. Phytoliths served to elucidate historical vegetation, remote sensing revealed the current and past Indigenous footprints while tree stature and identity characterised the forest. Until now there has been very little to no human impact within these forests and current Indigenous footprint is both small and stable. Large trees accounted for 13% of trees in the plots that we established. For over half of the species, the measured tree height was taller than previously published maximum heights, leading us to conclude that these forests are a truly exceptional ecological refugium. Noting that the local communities are not rewarded for their custody of these exceptional forests we call to revisit the Good Practice Guidance for Land Use Land Use Change and Forestry to include intact forest land. In the context of sub-optimal carbon finance options, we also propose matching as a methodology that could prove additionality of forest conservation initiatives in climate mitigation portfolios.
... Read coverage was visualized for select regions in the Integrative Genomics Viewer [82]. R package ggplot2 was contributed to the graphical representation [83]. The m6A enrichment levels of genes were represented as MFPKM (MFPKM = FPKM_ IP/FPKM_INPUT) averaged in the three biological replicates. ...
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Background Different types of skeletal myofibers exhibit distinct physiological and metabolic properties that are associated with meat quality traits in livestock. Alternative splicing (AS) of pre-mRNA can generate multiple transcripts from an individual gene by differential selection of splice sites. N6-methyladenosine (m6A) is the most abundant modification in mRNAs, but its regulation for AS in different muscles remains unknown. Results We characterized AS events and m6A methylation pattern in pig oxidative and glycolytic muscles. A tota1 of 1294 differential AS events were identified, and differentially spliced genes were significantly enriched in processes related to different phenotypes between oxidative and glycolytic muscles. We constructed the regulatory network between splicing factors and corresponding differential AS events and identified NOVA1 and KHDRBS2 as key splicing factors. AS event was enriched in m6A-modified genes, and the methylation level was positively correlated with the number of AS events in genes. The dynamic change in m6A enrichment was associated with 115 differentially skipping exon (SE-DAS) events within 92 genes involving in various processes, including muscle contraction and myofibril assembly. We obtained 23.4% SE-DAS events (27/115) regulated by METTL3-meditaed m6A and experimentally validated the aberrant splicing of ZNF280D, PHE4DIP, and NEB. The inhibition of m6A methyltransferase METTL3 could induce the conversion of oxidative fiber to glycolytic fiber in PSCs. Conclusion Our study suggested that m6A modification could contribute to significant difference in phenotypes between oxidative and glycolytic muscles by mediating the regulation of AS. These findings would provide novel insights into mechanisms underlying muscle fiber conversion.
... The optimal value of K is designated according to a cross-validation (CV) procedure, where the best value of K will show the lowest CV error (Alexander et al. 2009). Second, we used PLINK v.2.0 (Purcell et al. 2007) to perform a Principal Component Analysis (PCA) by extracting PC coordinates for each individual and visualized the results using the R packages ggplot2 v.3.3.2 and tidyverse v.1.3.0 (Wickham 2016;Wickham et al. 2019). We also estimated the amount of population divergence using the fixation index on Stacks (mean F st ). ...
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Historic and contemporary data can shed light on a species’ conservation status and work together to address two main goals in conservation biology: (1) identifying species under extinction risk and (2) the forces shaping this process. Museomics is the study of historical DNA acquired from museum specimens that allows researchers to answer myriad questions across many taxa. Museomics is an effective way to understand how populations have been affected by human and climate factors from a historic perspective. Here, our goal is to investigate changes in wild populations of two small carpenter bee species (Ceratina calcarata and C. dupla) across a 50-year time span. We sampled museum specimens and recent collections to determine their genetic diversity, population structure, effective population size, signatures of selection, and local adaptation. Both species displayed reduced genetic diversity and effective population size through time. We identified signatures of adaptation in both species across human-altered land use and climate change scenarios. We found signatures of selection in genes related to biochemical defense, insecticide, and thermal tolerance, which are consistent with the observed increase in agricultural land use development and rising temperatures over the past 50 years. Our findings suggest that these species are facing population inbreeding, possibly attributable to human land-use change and agrochemicals in their environment. Overall, this study highlights the use of museomics to understand species declines, threats to populations, and targets for remediation.
... (v5.9.2) 127 and ggplot2 (v3.1.0) 128 . Data for the ribbon plot for the network diagram was extracted from the Reactome Functional Interaction Database 129 . ...
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Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with Group 3 (G3) MB representing the most aggressive subgroup. MYC amplification is an independent poor prognostic factor in G3 MB, however, therapeutic targeting of the MYC pathway remains limited and alternative therapies for G3 MB are urgently needed. Here we show that the RNA-binding protein, Musashi-1 (MSI1) is an essential mediator of G3 MB in both MYC -overexpressing mouse models and patient-derived xenografts. MSI1 inhibition abrogates tumor initiation and significantly prolongs survival in both models. We identify binding targets of MSI1 in normal neural and G3 MB stem cells and then cross referenced these data with unbiased large-scale screens at the transcriptomic, translatomic and proteomic levels to systematically dissect its functional role. Comparative integrative multi-omic analyses of these large datasets reveal cancer-selective MSI1-bound targets sharing multiple MYC associated pathways, providing a valuable resource for context-specific therapeutic targeting of G3 MB.
... Differential gene expression (DEG) analysis (log 2 fold change ≥ 2, p-value < 0.05) was completed in R using DESeq2 [40,41] with the GenomicFeatures, tximport and tximportData packages. The visualization of the data was performed in R with EnhancedVolcano, ggplot2, and Venny 2.1 [42]. A list of genes known or hypothesized to play a role in virulence was generated (Table S1) and DEGs from this list were visualized as heat maps using ggplot2. ...
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Blue mold, caused by Penicillium spp., is an impactful postharvest disease resulting in significant economic losses due to reduced pome fruit quality and mycotoxin contamination. Using two Penicillium species with different levels of aggressiveness, transcriptomics were implemented in order to identify genes expressed during apple fruit decay and loci expressed in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 or P. polonicum RS1. There were 2442 differentially expressed genes (DEGs) between the R19 and RS1 in apple. Comparisons within species between apple and conidia revealed 4404 DEGs for R19 and 2935 for RS1, respectively. Gene ontology (GO) analysis revealed differential regulation in fungal transport and metabolism genes during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all DEG groups in apple verses conidia. Ungerminated conidia from both species showed DEGs encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination. This is the first study to identify pre-loaded transcripts in conidia from blue mold fungi, reveal unique genes between species expressed during apple decay, and show the expression dynamics of known fungal virulence factors. These findings will enable development of targeted approaches for blue mold abatement strategies.
... (R Core Team, 2018). Packages lme4 (Bates et al., 2015) and lmerTest (Kuznetsova et al., 2017) were used in the analyses and packages sjPlot (Lüdecke, 2017) and ggplot2 (Wickham, 2016) were used in producing the figures. ...
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Exposure to natural environments promotes positive psychological effects. Experimental studies on this issue typically have not been able to distinguish the contributions of top-down processes from stimulus-driven bottom-up processing. We tested in an online study whether mental imagery (top-down processing) of restorative natural environments would produce positive psychological effects, as compared with restorative built and non-restorative urban environments. The participants (n = 70) from two countries (Finland and Norway) imagined being present in different environments for 30 s, after which they rated their subjective experiences relating to vividness of imagery, relaxation, emotional arousal, valence (positivity vs. negativity) of emotions, and mental effort. In addition, a psychometric scale measuring vividness of imagination, a scale measuring nature connectedness, and a questionnaire measuring preference of the imagined environments were filled-in. Imagery of natural environments elicited stronger positive emotional valence and more relaxation than imagery of built and urban environments. Nature connectedness and preference moderated these effects, but they did not fully explain the affective benefits of nature. Scores in a psychometric imagery scale were associated in consistent way to the subjective ratings in the imagery task, suggesting that the participants performed attentively and honestly in reporting their subjective experiences. We conclude that top-down factors play a key role in the psychological effects of nature. A practical implication of the findings is that inclusion of natural elements in imagery-based interventions may help to increasing positive affective states.
... Artículo protegido por licencia Creative Commons 133 y producción gráfica de resultados se utiliza el lenguaje de programación R 3.6.5 (R Core Team, 2020), utilizando paquetes como ggplot2 (Wickham, 2016), emmeans (Length et al., 2019) y vtree (Barrowman et al., 2021). ...
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Debido a la Covid-19, las instituciones de educación deben migrar sus prácticas tradicionales a la modalidad virtual. Esto representa retos importantes en la planificación, mediación y evaluación de las asignaturas. Las analíticas de aprendizaje son un conjunto de herramientas innovadoras en el área pedagógica, en la que el uso de datos puede contribuir al mejoramiento de las asignaturas y políticas educativas. En este trabajo se pretende realizar una reflexión descriptiva de las analíticas de aprendizaje valorando el efecto de la pandemia en el aprovechamiento de la asignatura. Para esto, se realiza una investigación de tipo cuantitativo mediante el estudio de las calificaciones en la asignatura de Química I durante el periodo 2018-2021 en la UNED, Costa Rica. El aprovechamiento general de la asignatura experimenta un aumento en la calificación promedio durante el periodo 2020-2021; además, existen diferencias significativas entre los rendimientos de acuerdo con las regiones demográficas del país. Sin embargo, es necesario realizar esfuerzos que permitan medir la calidad del aprendizaje logrado en la asignatura y el grado de satisfacción de los estudiantes con lo alcanzado en la misma.
... Statistical analyses were performed using the R base and the R Stats packages [48]. Descriptive statistics and associated graphics were generated using ggplot2 [49]. ...
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The presence of a 13-desmethyl Spirolide C isomer (Iso-13-desm SPX C) is very common in some infaunal mollusks in Galicia contaminated with this toxin. Its possible origin by biological transformation was investigated by incubating homogenates of the soft tissues of limpets and cockles spiked with 13-desmethyl Spirolide C (13-desm SPX C). The involvement of an enzymatic process was also tested using a raw and boiled cockle matrix. The enzymatic biotransformation of the parent compound into its isomer was observed in the two species studied, but with different velocities. The structural similarity between 13-desm SPX C and its isomer suggests that epimerization is the most likely chemical process involved. Detoxification of marine toxins in mollusks usually implies the enzymatic biotransformation of original compounds, such as hydroxylation, demethylation, or esterification; however, this is the first time that this kind of transformation between spirolides in mollusks has been demonstrated.
... Packages utilized for sequencing panel identi ers include dplyr (Hadley Wickham, 2021), hash (Brown, 2019), rlist (Ren, 2021), and R.utils (Bengtsson, 2020). Figures were generated using ggplot2 (Wickham, 2016), ggExtra (Dean Attali, 2019) and ggpubr (Kassambara, 2020) R packages. Web application developed using shiny (Chang, 2021), shinydashboard (Chang and Ribeiro, 2021), shinycssloaders (Sali and Attali, 2020), dashboardthemes (Lilovski, 2021), DT (Xie, 2022), and plotly (Sievert, 2020) R packages. ...
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Mutations found in skin are acquired in specific patterns, clustering around mutation-prone genomic locations. The most mutation-prone genomic areas, mutation hotspots, first induce the growth of small cell clones in healthy skin. Mutations accumulate over time, and driver mutation clones may give rise to skin cancer. Early mutation accumulation is a crucial first step in photocarcinogenesis. Therefore, a sufficient understanding of the process may help predict disease onset and identify avenues for skin cancer prevention. Early epidermal mutation profiles are typically established using high depth targeted next-generation sequencing. However, there is currently a lack of tools for designing custom panels to capture mutation-enriched genomic regions efficiently. To address this issue, we created a computational algorithm that implements a pseudo-exhaustive approach to identify the best targeted genomic areas. We benchmarked the current algorithm in three independent mutation datasets of human epidermal samples. Compared to the sequencing panel designs originally used in these publications, the mutation capture efficacy (# of mutations/base pairs sequenced) of our designed panel improved 9.6 to 12.1-fold. Our web application hotSPOT provides a publicly available resource for researchers to design custom panels, enabling efficient detection of somatic mutations in clinically normal tissues and other similar targeted sequencing studies.
... Diversity indices, including observed species, abundance-based coverage estimators (ACE) index, Chao1 index, Shannon diversity index, Simpson index, and Pielou's evenness, were calculated for each sample and compared between WT and TAAR9-KO animals by the Wilcoxon test. Diagrams were produced with the R packages MicrobiotaProcess [44] and ggplot2 [45]. ...
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Trace amine-associated receptors (TAAR1-TAAR9) are a family of G-protein-coupled monoaminergic receptors which might have great pharmacological potential. It has now been well established that TAAR1 plays an important role in the central nervous system. Interestingly, deletion of TAAR9 in rats leads to alterations in the periphery. Previously, we found that knockout of TAAR9 in rats (TAAR9-KO rats) decreased low-density lipoprotein cholesterol levels in the blood. TAAR9 was also identified in intestinal tissues, and it is known that it responds to polyamines. To elucidate the role of TAAR9 in the intestinal epithelium, we analyzed TAAR9-co-expressed gene clusters in public data for cecum samples. As identified by gene ontology enrichment analysis, in the intestine, TAAR9 is co-expressed with genes involved in intestinal mucosa homeostasis and function, including cell organization, differentiation, and death. Additionally, TAAR9 was co-expressed with genes implicated in dopamine signaling, which may suggest a role for this receptor in the regulation of peripheral dopaminergic transmission. To further investigate how TAAR9 might be involved in colonic mucosal homeostasis, we analyzed the fecal microbiome composition in TAAR9-KO rats and their wild-type littermates. We identified a significant difference in the number of observed taxa between the microbiome of TAAR9-KO and wild-type rats. In TAAR9-KO rats, the gut microbial community became more variable compared with the wild-type rats. Furthermore, it was found that the family Saccharimonadaceae, which is one of the top 10 most abundant families in TAAR9-KO rat feces, is almost completely absent in wild-type animal fecal samples. Taken together, these data indicate a role of TAAR9 in intestinal function.
... The mean values of the percentage cover of live sessile organisms were calculated for each site and across top/bottom plate faces. All plots of ARMS data were created using either the package "ggplot2" v3.3.5 (Wickham, 2016) or basic R plotting tools (R Core Team, 2022). ...
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Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow velocity, wave heights, temperature, dissolved oxygen, and salinity, and short-term (3 weeks) profiles of light and pH. We recovered distinct environmental profiles between sampling sites and observed that ocean-facing reefs experienced frequent but short-lived cooling internal wave events and that these were key in shaping in situ temperature variability. By comparing temperature and wave height profiles recovered using in situ loggers with ex situ models, we discovered that global satellite products either failed to recover site-specific profiles or both over- and underestimated actual in situ conditions. We found that site choice and recruitment plate face (top or bottom) significantly impacted the percentage cover of bryozoans, gastropods, soft and calcified tube worms, as well as crustose coralline algae (CCA) and fleshy red, brown, and green encrusting macroalgae on ARMS. We observed significant correlations between the abundance of bryozoans, CCA, and colonial tunicates with lower mean temperature and higher mean dissolved oxygen profiles observed across sites. Red and brown encrusting macroalgae abundance correlated significantly with medium-to-high flow velocities and wave height profiles, as well as higher pH and dissolved oxygen. This study provides the first insight into cryptobenthic communities in the Chagos Archipelago marine-protected area and adds to our limited understanding of tropical reef sessile communities and their associations with environmental parameters in this region. With climate change accelerating the decline of reef ecosystems, integrating analyses of cryptobenthic organisms and in situ physicochemical factors are needed to understand how reef communities, if any, may withstand the impacts of climate change.
... The resulting clustering dendrogram and the cutoff used to delineate clusters are represented on Fig. S2. Figures were drawn in R v3.03 with package ggplot2 v1.0.1 (82). ...
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Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of "who is where" by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.
... tools, such as in species-habitat modeling [29], conservation management [30] and forest structure assessment [31]. NEAL makes use of several open-source R packages, such as [32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. The most notable are: ...
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Passive acoustic monitoring is used widely in ecology, biodiversity, and conservation studies. Data sets collected via acoustic monitoring are often extremely large and built to be processed automatically using Artificial Intelligence and Machine learning models, which aim to replicate the work of domain experts. These models, being supervised learning algorithms, need to be trained on high quality annotations produced by experts. Since the experts are often resource-limited, a cost-effective process for annotating audio is needed to get maximal use out of the data. We present an open-source interactive audio data annotation tool, NEAL (Nature+Energy Audio Labeller). Built using R and the associated Shiny framework, the tool provides a reactive environment where users can quickly annotate audio files and adjust settings that automatically change the corresponding elements of the user interface. The app has been designed with the goal of having both expert birders and citizen scientists contribute to acoustic annotation projects. The popularity and flexibility of R programming in bioacoustics means that the Shiny app can be modified for other bird labelling data sets, or even to generic audio labelling tasks. We demonstrate the app by labelling data collected from wind farm sites across Ireland.
... The difference was considered to be statistically significant if p < 0.05. The figures were drawn with R package of ggplot2 developed by Wickham [58]. ...
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Bio-enzymatic grafting phenolic acid to chitosan derivative is an efficient and environmentally friendly molecular synthesis technology. In the present study, N-carboxymethyl chitosan (CMCS) was grafted with gallic acid (GA) using recombinant bacterial laccase from Streptomyces coelicolor as a catalyst. GA and CMCS were successfully grafted as determined by measuring amino acid content, Fourier transform infrared (FTIR) spectroscopy and ultraviolet-visible (UV-Vis) spectroscopy. Then, the effect of GA-g-CMCS coating on the freshness of strawberries at 20 ± 2 °C was explored. The physiological and biochemical quality indicators of strawberries during storage were monitored. The 1.5% GA-g-CMCS coating helped to protect the antioxidant properties and nutrients of strawberries and extend the shelf life. Specifically, it reduced the weight loss of strawberries during preservation (originally 12.7%) to 8.4%, maintained titratable acidity content (TA) residuals above 60% and reduced decay rate from 36.7% to 8.9%. As a bioactive compound, GA-g-CMCS has the potential to become an emerging food packing method. These results provide a theoretical basis and reference method for the subsequent synthesis and application of CMCS derivatives.
... All statistical analyses and calculations were performed using R 4.2.1 (R Core Team, 2022). We used the following R-packages for the graphical presentation: ggplot2 (Wickham, 2009), gra fy (Shenoy, 2021), and sjPlot (Lüdecke, 2018). ...
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Movement facilitates and alters species interactions, the resulting food web structures, species distribution patterns, community structures and survival of populations and communities. In the light of global change, it is crucial to gain a general understanding of how movement depends on traits and environmental conditions. Although insects and notably Coleoptera represent the largest and a functionally important taxonomic group, we still know little about their general movement capacities and how they respond to warming. Here, we measured the exploratory speed of 125 individuals of eight carabid beetle species across different temperatures and body masses using automated image-based tracking. The resulting data revealed a power-law scaling relationship of average movement speed with body mass. By additionally fitting a thermal performance curve to the data, we accounted for the unimodal temperature response of movement speed. This allometric and thermodynamic equation to predict exploratory speed can be incorporated into modeling approaches to predict trophic interactions or spatial movement patterns. Overall, these findings will help improve our understanding of how temperature effects on movement cascade from small to large spatial scales as well as from individual to population fitness and survival across communities.
... Model coefficients were obtained from the model summary, and the explained deviance and significance of model terms were obtained from the ANOVA (Fisher test) of the model. The statistical analyses were performed with R software (R Core Team 2021) using car (Fox and Weisberg 2019), ggplot2 (Wickham 2016), and sjPlot (Lüdecke 2021) packages. We took burn severity categories as predictor variables: (1) low severity, (2) moderate severity, (3) high severity, (4) unburned in the last 10 years, and (5) unburned in the last 20 years. ...
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Background Burn severity plays an important role in shaping vegetation recovery in Mediterranean ecosystems. In the present study, we aimed to evaluate the influence of burn severity on short-term vegetation resilience in different ecosystems. We selected the Cabrera wildfire (northwest Iberian Peninsula), which affected shrubland, heathland, broomland, and oak woodland ecosystems in 2017. Immediately after the fire, we established 249 field plots within the burned area, in which burn severity was quantified by the application of the Composite Burn Index, differentiating three burn severity categories: low, moderate, and high. Moreover, we fixed 136 plots in unburned areas at two different maturity stages: young (unburned for the last 10 years) and old (unburned for the last 20 years) vegetation. Two years after the wildfire, we evaluated the total percentage cover of vegetation in four vertical strata ranging from 0 to > 4 m, as well as the cover of each woody species and total herbaceous vegetation in the lowest stratum (0–0.5 m). Resilience of the 2017 burned areas was interpreted in terms of the difference in vegetation cover and species composition in relation to the two different maturity stages. Results The results showed that the lowest stratum was the most resilient in the short term. In fact, all ecosystems presented high resilience of this stratum in low-severity areas. In shrublands and heathlands, this was mainly the consequence of the regeneration of herbaceous vegetation, as the dominant woody species did not fully recover in any of the burned situations (at least 21% and 11% less cover in shrubland and heathland burned plots compared to areas of young vegetation). Specifically, the resilience of this stratum was higher in broomlands and oak woodlands, mainly under moderate and high severities. In these ecosystems, woody dominant species recovered with respect to young vegetation at the 0–0.5-m level. Despite this, burn severity had a negative impact on the short-term resilience of the uppermost strata in broomlands and oak woodlands (cover values close to 0%). Conclusions The effects of burn severity on short-term vegetation resilience differed among type of ecosystems and vertical strata, so these results may constitute a starting point for the evaluation of the influence of burn severity and vegetation composition and structure on ecosystem resilience.
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Study region Vltava River basin, South Bohemian Region of the Czech Republic, Central Europe Study focus To understand the dynamics of nutrients (nitrogen, phosphorus, and organic carbon) in streams, we combined hydrometeorological, hydrochemical and isotopic data (stable water and nitrate isotopes) from three catchments with different predominant land-use effects (forest, agricultural and settlement). New hydrological insights for the study region Our study underlines that current climate change and associated hydrological changes, such as decrease in flow, play an important role in the transport and dynamics of nutrients in the catchment. We have found that due to the different origins and pathways, individual nutrients had diverse behaviour patterns in streams and responded differently to changing climate. Hydrological patterns in streams became clear when systematic and continuous monitoring under a changing climate was applied, highlighting the need for such data to better understand the impact of hydrological drivers, particularly for long-term dynamics. In three studied catchments, streamflow showed a decreasing trend in line with rising air temperature, declining snow cover and increasing evapotranspiration. Time series analyses of nitrate concentrations revealed decreasing trends, whereas dissolved organic carbon increased in all catchments regardless of land use. Long-term trends of total phosphorus concentrations were positive in anthropogenically impacted streams. Stable nitrate isotopes indicated distinct nitrate sources and processes, but also their seasonality in relation to hydrological patterns and land use.
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Indirect contact with contaminated surfaces is a potential transmission route for COVID-19. Therefore, it is necessary to investigate convenient and inexpensive surface sanitization methods, such as HOCl, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 surrogate, Phi6 (~ 7 log PFU/mL), was prepared in artificial saliva and tripartite matrices, spot inoculated (8–12 spots, 100 µL) on 25 cm ² coupons of either stainless steel or vinyl, and allowed to dry for 45 min. The coupons were sprayed with ~ 3 mL of either 500 ppm or 1,000 ppm HOCl. Exposure times were 0 s (control), 5 s, 30 s, or 60 s. Samples were eluted with 2 mL of Dey-Engley neutralizing broth by 5x repeated pipetting and plated via the double agar overlay assay. Statistical analysis was completed in R using a generalized linear model with Quasipoisson error approximations. Time, concentration, surface type, and inoculum matrix were all significant contributors to log reduction at P = 0.05. Significant three-way interactions were observed for 1000 ppm, vinyl, and 60 s (P = 0.03) and 1000 ppm, tripartite, and 60s (P = 0.0121). A significant two-way interaction between vinyl and 60 s was also observed (P = 0.0168). Overall, increased HOCl concentration and exposure time led to increased Phi6 reduction. Notably, the highest estimated mean log reduction was 3.31 (95% CI: 3.14, 3.49) for stainless steel at 60 s and 1,000 ppm HOCl in artificial saliva, indicating that this method of sanitization may not adequately reduce enveloped viruses to below infective thresholds.
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Nouns and verbs are known to differ in the types of grammatical information they encode. What is less well known is the relationship between verbal and nominal coding within and across languages. The equi-complexity hypothesis holds that all languages are equally complex overall, which entails trade-offs between coding in different domains. From a diachronic point of view, this hypothesis implies that the loss and gain of coding in different domains can be expected to balance each other out. In this study, we test to what extent such inverse coevolution can be observed in a sample of 244 languages, using data from a comprehensive cross-linguistic database (Grambank) and applying computational phylogenetic modelling to control for genealogical relatedness. We find evidence for coevolutionary relationships between specific features within nominal and verbal domains on a global scale, but not for overall degrees of grammatical coding between languages. Instead, these amounts of nominal and verbal coding are positively correlated in Sino-Tibetan languages and inversely correlated in Indo-European languages. Our findings indicate that accretion and loss of grammatical information in nominal words and verbs are lineage-specific.
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The use of the lambda-mu-sigma (LMS) method for estimating centiles and producing reference ranges has received much interest in clinical practice, especially for assessing growth in childhood. However, this method may not be directly applicable where measures are based on a score calculated from question response categories that is bounded within finite intervals, for example, in psychometrics. In such cases, the main assumption of normality of the conditional distribution of the transformed response measurement is violated due to the presence of ceiling (and floor) effects, leading to biased fitted centiles when derived using the common LMS method. This paper describes the methodology for constructing reference intervals when the response variable is bounded and explores different distribution families for the centile estimation, using a score derived from a parent-completed assessment of cognitive and language development in 24 month-old children. Results indicated that the z-scores, and thus the extracted centiles, improved when kurtosis was also modeled and that the ceiling effect was addressed with the use of the inflated binomial distribution. Therefore, the selection of the appropriate distribution when constructing centile curves is crucial.
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OBJECTIVE. Depression is a common co-morbidity of type 2 diabetes. However, the causality and underlying mechanisms remain unclear. RESEARCH DESIGN AND METHODS. We applied bi-directional Mendelian randomization (MR) to assess causality between type 2 diabetes and self-reported depression. Using the UK biobank, we performed 1) GWAS, separately, and 2) multi-phenotype GWAS (MP–GWAS) of type 2 diabetes (cases=19,344, controls=463,641) and depression, using two depression definitions–clinically diagnosed major depressive disorder (MDD, cases=5,262, controls=86,275) and self–reported depressive symptoms (PHQ-9, n=153,079). The FinnGen study was used for replication for MDD (n=23,424) and type 2 diabetes (n=32,469). Based on the results, we analyzed expression quantitative trait loci (eQTL) data from public databases to identify target genes in relevant tissues. RESULTS. MR demonstrated a significant causal effect of depression on type 2 diabetes (OR=1.18[1.06–1.32], p=0.0024), but not in the reverse direction. GWAS of type 2 diabetes and depressive symptoms did not identify any shared loci between them, whereas MP-GWAS identified seven shared loci mapped to TCF7L2, CDKAL1, IGF2BP2, SPRY2, CCND2-AS1, IRS1, CDKN2B-AS1. MDD did not yield genome-wide significant loci in either GWAS or MP-GWAS. We found that most MP-GWAS loci had an eQTL, including SNPs implicating the cell cycle gene CCND2 in pancreatic islets and brain, and key insulin signaling gene IRS1 in adipose tissue, suggesting a multi-tissue and pleiotropic underlying mechanism. CONCLUSION. Our study reveals the complexity in the depression-diabetes relationship and our results have important implications for a more efficient prevention of type 2 diabetes from early adulthood when depressive symptoms usually occur.
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Background There has been increasing demand for aesthetic surgery procedures in the United States, highlighting the critical importance of competence of plastic surgery residents and rigorous methods of aesthetic surgery training. Objectives The objective of this study was to review procedures and outcomes from our plastic surgery resident aesthetic clinic. Outcomes and costs were compared to national averages and reports from the literature. Methods A retrospective chart review identified all adult patients who presented to the Resident Aesthetic Surgery Clinic at NYU Langone Health in 2021. Patient demographics, comorbidities, procedural data, postoperative complications, revisions, and surgeon fees were compiled. A brief confidence survey was distributed to participating residents before and after their clinic rotation. Data were analyzed using IBM SPSS software (Armonk, NY). Results In 2021, 144/379 consultations led to an operation (38.0% conversion rate), resulting in 420 distinct surgical procedures. The majority (53.3%) of procedures involved the head and neck. Complication and revision rates were 5.5% and 1.0%, respectively, with surgeon fees consistently below national average. Residents reported being significantly more confident performing face lifts, rhinoplasties, and aesthetic surgery in general following their clinic rotation. Conclusions These data represent the largest annual reported study of plastic surgery resident aesthetic procedures and outcomes, demonstrating the high volume and productivity of the NYU Resident Aesthetic Surgery Clinic. These results further support resident aesthetic clinics as a robust training modality.
Thesis
Viele Erkrankungen und altersabhängige Prozesse wie die AMD gehen mit Veränderungen der Steifigkeit des Umgebungsgewebes sowie der zellulären Differenzierung und Funktionalität einher. In der vorliegenden Arbeit wurde der Einfluss biomechanischer Umgebungsbedingungen auf die miRNA-Expression in RPE untersucht. Ziel des Projektes war es, den Einfluss der Steifigkeit zellulärer Umgebungen auf die Expression von miRNAs und ihre Auswirkungen auf möglicherweise pathogenetisch relevante Signalwege in RPE zu charakterisieren. Hierzu wurden ARPE-19-Zellen auf Substraten unterschiedlicher Steifigkeit kultiviert. Mittels NGS wurde das zelluläre Transkriptom mit besonderem Fokus auf die Fraktion der miRNAs als Teil des Genregulationsnetzwerkes untersucht. Mithilfe von In-silico-Analysen wurden mögliche Einflüsse steifigkeitsabhängig exprimierter miRNAs auf für die Differenzierung und Funktionalität von RPE relevante Signalwege prognostiziert und mittels qPCR sowie WB validiert. Steifigkeitsabhängige Mechanismen der Mechanotransduktion beeinflussen die Expression kleiner, nicht-codierender RNAs in ARPE-19-Zellen. Die miRNA-Fraktion der kleinen, nicht-codierenden RNAs ist auf Umgebungen erhöhter Substratsteifigkeit insgesamt verstärkt exprimiert, wobei einige miRNAs eine substratabhängige differenzielle Expression aufweisen. Die Transkriptomdaten unterstützen die kürzlich postulierte gewebehomöostatische Funktion und feinregulatorische Wirkung von miRNAs. Beim Wnt/b-Catenin-Signalweg zeigte sich hingegen keine Stabilisierung, sondern eine Veränderung der Expression durch mechanosensitive miRNAs in ARPE-19-Zellen. So sind auf Umgebungen höherer Steifigkeit eine Aktivierung des Wnt/b-Catenin-Signalweges und eine verstärkte Expression von MITF und Dicer zu beobachten, die wiederum eine verstärkte Expression der miRNA-Fraktion begünstigen könnten. Im Alter und im Zuge von Erkrankungen auftretende Veränderungen der Gewebesteifigkeit könnten so miRNA-vermittelt die Differenzierung und Funktionalität sowie das Adhäsionsverhalten von RPE beeinflussen und auf diese Weise pathologische Gewebeveränderungen induzieren. Mithilfe von Untersuchungen des isolierten Einflusses einzelner diskutierter miRNAs und Proteine könnte die Etablierung möglicherweise neuer gezielter Ansätze in der Therapie altersassoziierter Erkrankungen wie der AMD gelingen.
Article
Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.
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Facial bristles are one of the least described feather types and have not yet been systematically studied across phylogenetically diverse avian species. Consequently, little is known about their form, function and evolutionary history. Here we address this knowledge gap by characterising the evolution of facial bristles for the first time. We especially focus on rictal bristle presence and their associations with foraging behaviour, diet and habitat preferences in 1022 avian species, representing 91 families in 29 orders. Results reveal that upper rictal, lower rictal and interramal bristles were likely to be present in the most recent common ancestor of this avian phylogeny, whereas narial bristles were likely to be absent. Rictal bristle presence, length and shape varied both within and between avian orders, families and genera. Rictal bristles were gained or lost multiple times throughout evolution, which suggest that the different morphologies observed within species might not be homologous. Phylogenetic relatedness is also not likely to be the only driver of rictal bristle presence and morphology. Rictal bristle presence and length were associated with species-specific ecological traits, especially nocturnality. Our findings suggest that species foraging in low-light conditions are likely to have longer rictal bristles, and that rictal bristles are likely to have evolved in early birds.
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Background Conventional preclinical models often miss drug toxicities, meaning the harm these drugs pose to humans is only realized in clinical trials or when they make it to market. This has caused the pharmaceutical industry to waste considerable time and resources developing drugs destined to fail. Organ-on-a-Chip technology has the potential improve success in drug development pipelines, as it can recapitulate organ-level pathophysiology and clinical responses; however, systematic and quantitative evaluations of Organ-Chips’ predictive value have not yet been reported. Methods 870 Liver-Chips were analyzed to determine their ability to predict drug-induced liver injury caused by small molecules identified as benchmarks by the Innovation and Quality consortium, who has published guidelines defining criteria for qualifying preclinical models. An economic analysis was also performed to measure the value Liver-Chips could offer if they were broadly adopted in supporting toxicity-related decisions as part of preclinical development workflows. Results Here, we show that the Liver-Chip met the qualification guidelines across a blinded set of 27 known hepatotoxic and non-toxic drugs with a sensitivity of 87% and a specificity of 100%. We also show that this level of performance could generate over $3 billion annually for the pharmaceutical industry through increased small-molecule R&D productivity. Conclusions The results of this study show how incorporating predictive Organ-Chips into drug development workflows could substantially improve drug discovery and development, allowing manufacturers to bring safer, more effective medicines to market in less time and at lower costs.
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Whether intraspecific spatial patterns in body size are generalizable across species remains contentious, as well as the mechanisms underlying these patterns. Here we test several hypotheses explaining within‐species body size variation in terrestrial vertebrates including the heat balance, seasonality, resource availability and water conservation hypotheses for ectotherms, and the heat conservation, heat dissipation, starvation resistance and resource availability hypotheses for endotherms. Global. 1970–2016. Amphibians, reptiles, birds and mammals. We collected 235,905 body size records for 2,229 species (amphibians = 36; reptiles = 81; birds = 1,545; mammals = 567) and performed a phylogenetic meta‐analysis of intraspecific correlations between body size and environmental variables. We further tested whether correlations differ between migratory and non‐migratory bird and mammal species, and between thermoregulating and thermoconforming ectotherms. For bird species, smaller intraspecific body size was associated with higher mean and maximum temperatures and lower resource seasonality. Size–environment relationships followed a similar pattern in resident and migratory birds, but the effect of resource availability on body size was slightly positive only for non‐migratory birds. For mammals, we found that intraspecific body size was smaller with lower resource availability and seasonality, with this pattern being more evident in sedentary than migratory species. No clear size–environment relationships were found for reptiles and amphibians. Within‐species body size variation across endotherms is explained by disparate underlying mechanisms for birds and mammals. Heat conservation (Bergmann's rule) and heat dissipation are the dominant processes explaining biogeographic intraspecific body size variation in birds, whereas in mammals, body size clines are mostly explained by the starvation resistance and resource availability hypotheses. Our findings contribute to a better understanding of the mechanisms behind species adaptations to the environment across their geographic distributions.
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The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in ‍specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.
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Background Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, show confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Results We chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn’s Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Conclusions Gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.
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Increasing evidence has proven that spatial distance has stronger effects on root-associated microbiomes. However, the effect of spatial distance on the composition of plant endophytic microbiomes has been poorly understood. Meanwhile, whether aboveground endophytes can regulate the accumulation of secondary metabolites in the roots of medicinal plants remains unclear. To explore the effect of the endophytic microbiome of the medicinal plant Astragalus membranaceus (Fisch.) Bunge var.mongholicus (A. mongholicus) on secondary metabolites, we investigated the endophytic community structure of A. mongholicus from Tanchang county in Gansu province, Hunyuan county in Shanxi province and Zizhou county in Shaanxi province in China using the high-throughput sequencing. The results demonstrated that regional variation had a greater effect on the endophytic community than plant compartments, especially on leaf endophytic bacteria and root endophytic fungi. The endophytic network patterns showed distinct co-occurrence patterns and niche differentiation, especially the root network. In addition, the contents of secondary metabolites in endophytic compartments were also affected by regional variation. Correlation analysis and random forest model (RF) showed that endophytic bacteria of A. mongholicus grew in three regions exhibited a stronger correlation with secondary metabolite accumulation in plants. Interestingly, the keystone species in the pivotal modules were significantly related to secondary metabolites. Importantly, pot experiments verified that the aboveground microbiota were associated with the accumulation of secondary metabolites in roots. Taken together, our findings illustrate the importance and functionalities of plant microbiomes, highlight the role of key microbiota constituents in regulating plant secondary metabolites, and provide a basis for the application of prospective endophytic taxa to improve the quality and pharmaceutical value of A. mongholicus.
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Emergence of the colistin resistance gene, mcr-1, has attracted worldwide attention. Despite the prevalence of mcr-1-positive Escherichia coli (MCRPEC) strains in human carriage showed a significantly decrease between 2016 and 2019, genetic differences in MCRPEC strains remain largely unknown. We therefore conducted a comparative genomics study on MCRPEC strains from fecal samples from healthy human subjects in 2016 and 2019. We identified three major differences in MCRPEC between these two time points. (i) The insertion sequence ISApl1 was often deleted and the percentage of mcr-1-carrying IncI2 plasmids was increased. (ii) The antimicrobial resistance genes, aac(3)-IVa and blaCTX-M-1, emerged and coexisted with mcr-1 in 2019. (iii) MCRPEC strains in 2019 contain more virulence genes, resulting in an increase in the proportion of mcr-1 in extraintestinal pathogenic E. coli (ExPEC) strains (36.1%) compared to commensal E. coli strains (10.5%), implying that these strains could occupy intestinal ecological niches by competing with other commensal bacteria. Our data suggest that despite the significant reduction in the prevalence of MCRPEC strains in human subjects, mcr-1 is now associated with more stable genetic structures and widespread IncI2 plasmid. Furthermore, mcr-1 has an increased coexistence with other clinically important antibiotic resistance genes, and is increasingly associated with ExPEC strains, thus posing a potential public health threat.
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Objective: The transition to parenthood might negatively influence health-related behavior and can result in increased adiposity. The aim of this study was to investigate how body composition in mother-father dyads changes from pregnancy up to 6 months post partum. Methods: Anthropometrics were collected from 144 nulliparous couples at 12 weeks of gestation (PG12) and 6 weeks (PP6WK) and 6 months (PP6M) post partum. A longitudinal dyadic confirmatory factor analysis model was used to analyze changes in body composition. Body composition was treated as a latent variable using BMI, body fat percentage, and waist circumference as indicators. Results: For women, latent means increased at 6 weeks post partum (PP6WK - PG12: +1.115, SE: 0.117, p < 0.001), decreased again at 6 months post partum (PP6M - PP6WK: -0.368, SE: 0.107, p < 0.001), but remained above baseline levels (PP6M - PG12: +0.747; SE: 0.115, p < 0.001). For men, the latent means at follow-up were higher than at baseline (PP6WK-PG12: +0.370, SE: 0.075; PP6M-PG12: +0.366, SE: 0.084, both p < 0.001). Conclusions: Increases in latent means correspond to unfavorable changes in BMI, body fat percentage, and waist circumference. These changes were observed from the beginning of pregnancy up to 6 months post partum. Weight management for both women and men during pregnancy and the early postpartum period is recommended and fathers should be included in pre- and postnatal standard care.
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Teleost fish of the genus Danio are excellent models to study the genetic and cellular bases of pigment pattern variation in vertebrates. The two sister species Danio rerio and Danio aesculapii show divergent patterns of horizontal stripes and vertical bars that are partly caused by the evolution of the potassium channel gene kcnj13. In D. rerio, kcnj13 is required in melanophores for interactions with xanthophores and iridophores, which cause location-specific pigment cell shapes and thereby influence colour pattern and contrast. Here, we show that cis-regulatory rather than protein coding changes underlie kcnj13 evolution between the two species. D. aesculapii express lower kcnj13 levels and exhibit low-contrast patterns similar to D. rerio mutants. Our results suggest that homotypic and heterotypic interactions between the pigment cells and their shapes diverged between species by quantitative changes in kcnj13 expression during pigment pattern diversification.
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Microorganisms residing within the gastrointestinal tract are implicated in the onset and progression of Alzheimer’s disease (AD) through the mediation of inflammation, exchange of small-molecules across the blood-brain barrier, and stimulation of the vagus nerve. Unfortunately, most animal models for AD are housed under conditions that do not reflect real-world human microbial exposure and do not sufficiently account for (or meaningfully consider) variations in the microbiome.
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Juvenile stages of fishes are frequently bottlenecks to recruitment. Habitat use of early life stages and the extent to which fish rely on local resources may affect how they respond to habitat loss and alterations, with important implications for habitat management. To investigate the potential for prolonged reliance on local resources, we quantified stable isotope ratios (δ13 carbon, δ15 nitrogen, δ18 oxygen and δ2 hydrogen) of young‐of‐year (YOY) largemouth bass Micropterus salmoides and isotope ratios of locally collected water and potential prey across three study components, a controlled pond experiment, a multi‐lake survey and a detailed single‐lake survey. Across study components, we observed habitat and site fidelity of YOY largemouth bass in mid‐summer, demonstrated by distinct spatial differences in young bass stable isotope ratios. Additionally, we observed significant, positive correlations between δ13C of YOY largemouth bass and δ13C of locally collected invertebrates and small bluegill Lepomis macrochirus in the single lake survey, suggesting localised foraging. Later in summer, spatial differences in largemouth bass stable isotope ratios were not apparent, indicating a transition to more spatially integrated foraging. Prior to switch to piscivory, YOY largemouth bass rely on local resources indicating that they may be more susceptible, both positively and negatively, to hyper‐local changes in forage availability or disturbances. This study demonstrates that stable isotope ratios allow for differentiating environmental experiences among young fish in relatively close proximity in small freshwater systems. Moreover, high spatial variation of consumer stable isotope ratios demonstrates the importance of considering spatial heterogeneity in stable isotope studies.
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The Arenig Fawr area of North Wales constitutes the type area for the British Lower to Middle Ordovician Arenig Series and is complemented by sections in the Carmarthen and Whitland areas of South Wales. We describe chitinozoan assemblages from both areas in order to aid correlation of the Arenig Series in its type region with the global Ordovician series and stages. Chitinozoans recorded from Arenig Fawr provide permissive rather than conclusive evidence but suggest that the Henllan Ash Member correlates with the upper Floian Stage Slice Fl3 or lower Dapingian Stage Slice Dp1. Better results were obtained from South Wales where six chitinozoan assemblages are distinguished, ranging in age from late Tremadocian to middle Darriwilian (early Llanvirn). Most species are known from South China, Gondwana and/or Baltica where there are controls on ranges. They show that much of the lower Arenig (Moridunian) succession in South Wales correlates with the upper Floian Stage (Fl3). Correlatives of the lower and middle Floian Stage (Fl1, Fl2), if present, must be represented by the Ogof Hên Formation and lowest Carmarthen Formation. Chitinozoan assemblages from the upper Arenig Series (Fennian Stage) are more readily correlated with Gondwanan biozones and indicate correlation of the Fennian Stage with the Dapingian and lower Darriwilian (Dw1) stages. The middle Arenig Whitlandian Stage is constrained in South Wales to an interval from the uppermost Floian Stage to the basal Dapingian Stage, resulting in an inferred increased rate of sediment accumulation.
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Eriocheir sinensis is an euryhaline crab found from East Asia to Europe and North America. This species can live in freshwater and seawater due to the unique physiological characteristics of their life cycle, which allows them to adapt and inhabit different habitats in a wide range of environments. Despite the wealth of studies focusing on adaptation mechanism of E. sinensis to specific environmental factors, the adaptation mechanisms to wild habitats with coexisting environmental factors are not well understood. In this study, we conducted a transcriptome analysis to investigate gene expression differences related to habitat adaptation of E. sinensis from two wild habitats with different environmental factors in the Han River, Korea. A total of 138,261 unigenes were analyzed, of which 228 were analyzed as differentially expressed genes (DEGs) between the two wild habitats. Among 228 DEGs, 110 DEGs were annotated against databases; most DEGs were involved in energy metabolism, immunity, and osmoregulation. Moreover, DEG enrichment analysis showed that upregulated genes were related to biosynthesis, metabolism, and immunity in an habitat representing relatively high salinity whereas downregulated genes were related to ion transport and hypoxia response in habitats with relatively low salinity and dissolved oxygen. The present findings can serve as foundation for future E. sinensis culture or conservation approaches in natural conditions.
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