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15,519 results for “r”
Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus
<p>Using flow cytometry and microsatellite DNA analysis (MSDA), we studied hybrids between Rubus caesius and various other Rubus species, with an emphasis on Sweden. We show that hybrids between Rubus caesius and Rubus sect. Corylifolii arise easily. They show a large variation in morphology, but can normally be recognised by a number of characters. They are typically hexaploids, but ~13% of the hybrids are pentaploids and ~8% tetraploids. With MSDA, they are harder to identify than hybrids with R. idaeus, partly because all Corylifolii species have themselves arisen from R. caesius hybrids and therefore share many alleles with R. caesius, partly because hybridisation with R. caesius seems to give rise to some variation in microsatellite regions. Hybrids with species of R. sect. Rubus are much rarer in Sweden and we have only identified one such case. We show that R. cyclomorphus and R. tiliaster are not proper apomictic species, at least not in Sweden, but rather a collection of genetically unrelated hybrids between R. caesius and R. raduloides or R. tiliaster. MSDA analysis of R. slesvicensis and R. firmus shows that these species are problematic. We identify two distinct taxa, one from Skåne in Sweden, which we describe as a new species, R. ruboculus, and another from the neighbourhood of Viborg and Schleswig, although the latter is probably not identical with R. slesvicensis s.s. All the other samples form a diverse group of putative R. caesius hybrids at three different ploidy levels. Rubus glauciformis is uniform in Småland, Öland and Blekinge, but becomes harder to distinguish from various hybrids in Skåne. We conclude that once R. caesius and R. idaeus hybrids are properly identified, along with a small number of new apomictic species (often with a local distribution), the genus Rubus does not pose any serious taxonomical problems in Sweden.</p>
Data and R code for statistical analyses on trap experiments
<p>Data and R code for statistical analyses related to trap experiments used in the article titled "<strong>Attractant activity of host-related chemical blends on the Poultry Red Mite at different spatial scales".</strong></p> <p>Data are provided as two .csv files and codes as one .rmd file and one .R file as follows:</p> <p>- 6-trap laboratory experiments (data_PRM_lab_6-trap_experiments.csv and Lab_6-trap-experiments.rmd)</p> <p>- field experiments (data_PRM_field_trapping.csv and Field_trap_analyses.R).</p>
Evaluating drivers of female dominance in the spotted hyena: R code and data
<p><strong>Introduction</strong>: Dominance relationships in which females dominate males are rare among mammals. Mechanistic hypotheses explaining the occurrence of female dominance suggest that females dominate males because 1) they are intrinsically more aggressive or less submissive than males, and/or 2) they have access to more social support than males.</p> <p><strong>Methods</strong>: Here, we examine the determinants of female dominance across ontogenetic development in spotted hyenas (<em>Crocuta crocuta</em>) using 30 years of detailed behavioral observations from the Mara Hyena Project to evaluate these two hypotheses.</p> <p><strong>Results</strong>: Among adult hyenas, we find that females spontaneously aggress at higher rates than males, whereas males spontaneously submit at higher rates than females. Once an aggressive interaction has been initiated, adult females are more likely than immigrant males to elicit submission from members of the opposite sex, and both adult natal and immigrant males are more likely than adult females to offer submission in response to an aggressive act. We also find that adult male aggressors are more likely to receive social support than adult female aggressors, and that both adult natal and immigrant males are 2-3 times more likely to receive support when attacking a female than when attacking another male. Across all age classes, females are more likely than males to be targets of aggressive acts that occur with support. Further, receiving social support does slightly help immigrant males elicit submission from adult females compared to immigrant males acting alone, and it also helps females elicit submission from other females. However, adult females can dominate immigrant males with or without support far more often than immigrant males can dominate females, even when the immigrants are supported against females.</p> <p><strong>Discussion</strong>: Overall, we find evidence for both mechanisms hypothesized to mediate female dominance in this species: 1) male and female hyenas clearly differ in their aggressive and submissive tendencies, and 2) realized social support plays an important role in shaping dominance relationships within a clan. Nevertheless, our results suggest that social support alone cannot explain sex-biased dominance in spotted hyenas. Although realized social support can certainly influence fight outcomes among females, adult females can easily dominate immigrant males without any support at all.</p>
AI-SPRINT SPACE4AI-R Local Search
<p>This repository includes the source code and the evaluation data and results for the Local Search algorithm implemented for the SPACE4AI-R Optimizer framework. An extended discussion is reported in the AI-SPRINT project deliverable "D3.3 - Second release and evaluation of the runtime environment".</p>
Data, sample sizes, and R code for analysis of: Variation in mutation (co)variances
<p>Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and, together with selection, are expected to shape standing genetic covariances between traits and eventual phenotypic divergence between populations. It is therefore important to find if the M matrix, describing mutational variances of each trait and covariances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in lines of two genotypes of the nematode <em>Caenorhabditis elegans </em>that accumulated mutations in a nearly-neutral manner for 250 generations. We find significant mutational variance along at least one phenotypic dimension of the M matrices, but neither their size nor their orientation had detectable differences between genotypes. The number of generations of mutation accumulation, or the number of MA lines measured, was likely insufficient to sample enough mutations and detect potentially small differences between the two M matrices. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a population derived by the hybridization of several genotypes, including the two measured for M, and domesticated to a lab-defined environment for 140 generations. We found that the M and G were different because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by linkage disequilibrium in the lab population. We further show that M matrices differed in their alignment with the lab population G matrix. If generalized to other founder genotypes of the lab population, these observations indicate that selection does not shape the evolution of the M matrix for locomotion behavior in the short-term of a few tens to hundreds of generations and suggests that the hybridization of <em>C. elegans </em>genotypes allows selection on new phenotypic dimensions of locomotion behavior.</p>
Data and R scripts for: Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix)
<p>While intensive hunting activities, such as commercial fishing and trophy hunting, can have profound influences on natural populations, less intensive recreational hunting can also have more subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse (<em>Lyrurus</em> <em>tetrix</em>) may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets. Furthermore, inbreeding in black grouse is mainly avoided through female-biased dispersal, so any disruptions to dispersal caused by hunting could lead to changes in gene flow, leading to an increasing risk of inbreeding. We therefore investigated the impact of hunting on genetic diversity, inbreeding and dispersal on a metapopulation of black grouse in Central Finland. We genotyped 1,065 adult males and 813 adult females from twelve lekking sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites (two hunted, five unhunted) at up to thirteen microsatellite loci. Our initial confirmatory analysis of sex-specific fine-scale population structure revealed little genetic structure in the metapopulation. Levels of inbreeding did not differ significantly between hunted and unhunted sites in both adults and chicks. However, immigration rates into hunted sites were significantly higher among adults compared to immigration into unhunted sites. We conclude that the influx of migrants into hunted sites may compensate for the loss of harvested individuals, thereby increasing gene flow and mitigating inbreeding. Given the absence of any obvious potential barriers to gene flow in Central Finland, a spatially heterogeneous matrix of hunted and unhunted regions may be crucial to ensure sustainable harvests into the future.</p>
Light-by-nitrogen greenhouse experiment dataset and R code (v2.1)
<p>Release corrects errors in some reported chlorophyll absorbance values in "data_sheets/LxN_phys_data.csv" and updates the "data_sheets/LxN_phys_metadata.csv" metadata file.</p>
SIMCor - R-Statistical Environment embedded in the SIMCor Virtual Research Environment
<p>Using RStudio, the capabilities of running statistical evaluations in a standardised manner directly on the SIMCor Virtual Research Environment (VRE) has been realised. Via a web frontend, scripts written in the R programming language can be directly evaluated on the data, such as the virtual cohorts, available at the VRE.</p>
Data and R scripts for: Ant invasions is associated with lower root density and different root distribution of a foundational savanna tree species
<p>Some invasive ants have worldwide distributions and impose substantial impacts on human society and native biodiversity. Yet we know little about how ants impact soil ecosystems in general, much less how soil ecosystems shift when invasive ants move in. We excavated the coarse roots of a monodominant savanna tree in invaded and uninvaded areas to test the hypothesis that the presence of invasive ants would be associated with changes in root distribution and biomass across the landscape. We found that in the presence of invasive ants, trees had a shifted distribution of lateral coarse roots, with proportionally less root biomass near the surface and far from tree stems. In addition, the density of lateral coarse-root biomass was ~20% lower for trees within invaded landscapes. Our results suggest that soil-nesting invasive ants can drive important changes in rooting strategy for a tree species that serves a foundational role in the biogeochemical cycles of vertisol savannas.</p>
Datasheets and R-codes for flood mortality and income inequality project
<p>This zipped folder contains the compiled datasheets, raw figures, tables and R-codes for the analysis conducted in 2023 by Sara Lindersson, as reported in the following preprint:</p> <p>Sara Lindersson, Elena Raffetti, Maria Rusca, Luigia Brandimarte, Johanna Mård and Giuliano Di Baldassarre. <em>The wider the gap between rich and poor, the higher the flood mortality.</em> 2023. PREPRINT (revised manuscript)</p> <ul> <li>Dataset v. 1.0 corresponds to the first version of the manuscript, submitted in 2022.</li> <li>Dataset v. 2.0 corresponds to the revised manuscript, submitted in 2023.</li> </ul>
Datasets and R script to replicate the theoretical modeling from the article entitled Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission
<p>Datasets and R script to replicate the theoretical modeling from the article entitled "<strong> </strong>Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission" by Vantaux A., Moiroux N., Dabire K. R., Cohuet A., Lefevre T. 2023</p>
Insect visits to cherry blossoms and wildflowers in sweet cherry orchards: datasets and R scripts
<p>This repository contains a number of datasets, all collected in commercial sweet cherry orchards in the West Midlands, UK between 2017-2019. Alleyways in these orchards were sown with native perennial plant species. Datasets include:</p> <p>- cherry blossom and wildflower visitors recorded on pollinator transect surveys.<br> - fruit set and quality (in 2019) from cherry blossoms which were either exposed to insects, insect-excluded, or hand-pollinated.</p> <p>Additionally, all the scripts to analyse these datasets using the software R are also included.</p>
Data and R code for: Temperature-induced multispecies cohort effects in sympatric snakes
<p>In reptiles, reproductive maturity is often determined by size rather than age. Consequently, growth early in life may influence population dynamics through effects on generation time and survival to reproduction. Because reproductive phenology and pre- and post-natal growth are temperature-dependent, environmental conditions may induce multi-species cohort effects on body size in sympatric reptiles. I present evidence of this using ten years of neonatal size data for three sympatric viviparous snakes, Dekay's Brownsnakes (<i>Storeria dekayi</i>), Red-bellied Snakes (<i>S. occipitomaculata</i>) and Common Gartersnakes (<i>Thamnophis sirtalis</i>). End-of-season neonatal size varied in parallel across species such that snout-vent length was 36-61% greater and mass was 65-223% greater in years when gestating females could achieve higher April-May (vs. June-July or August-September) operative temperatures. Thus, temperature had a larger impact during follicular enlargement and ovulation than during gestation or post-natal growth. Multi-species cohort effects like these may affect population dynamics and increase with climate change.</p>
Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird
<p>Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (<em>Pardalotus</em> <em>quadragintus</em>), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.</p>
R scripts for manuscript "The circulating phageome reflects bacterial infections"
<p>These are documents and an R script associated with the manuscript "The circulating phageome reflects bacterial infections".</p> <p>These include:</p> <p>1. allphagedf_seqids.csv which is a table including number of BLAST hits to unique phage Genbank IDs by sample. The samples used in this table are the 71 (61 septic, 10 asymptomatic controls) sequenced in this study. The rows of this table correspond to samples (rownames are library IDs) and columns correspond to all identified phage Genbank IDs from the blast output.</p> <p>2. Phageome Summaries.RMD which is an R markdown document which demonstrates i) processing of blast output into a new allphagedf_seqids document, ii) use of the phage dictionary to summarize representation of phage taxonomic families as well as host genuses, and iii) use of the coliphage dictionary to assess how E. coli phages represent known host bacterial characteristics across samples.</p> <p>3. Readme.txt which summarizes the above as well as provides links to other relevant data.</p>
R-script: Deterioration of respiratory health following changes to land cover and climate in Indonesia
<p>This file contains the R-script presented in "Santika, T., Muhidin, S., Haryanto, B. et al. (2023) Deterioration of respiratory health following changes to land cover and climate in Indonesia".</p> <p>** R-script.txt</p> <p>This is the main script used to produce the results of the paper, which contains three parts:</p> <ol> <li>Analysis of the change in rainfall patterns across regencies in Sumatra, Indonesia</li> <li>Analysis of the change in fire patterns across Sumatra by soil type and land cover/degradation</li> <li>Analysis of the link between respiratory illness prevalence and environmental and socio-economic variables</li> </ol>
Diversification and change in the R programming language
<p>Languages change over time, driven by creation of new words and cultural pressure to optimise communication. Programming languages resemble written language but communicate primarily with computer hardware rather than a human audience. I tested for changes over time in use of R, a mature, open-source programming language used for scientific computing. Across 393,142 GitHub repositories published between 2014 and 2021, I extracted 143,409,288 R functions, programming "verbs", and paired linguistic and ecological approaches to estimate change in the diversity and composition of function use over time. I found that the number of R functions in use increased and underwent substantial change, driven primarily by the popularity of the "tidyverse" collection of community-written extensions. I provide evidence that users can directly change the nature of programming languages, with patterns that match known processes from natural languages and genetic evolution. In the case of R, patterns suggested there are selective pressures for increased analytic complexity and R functions in decline but not extinct ("extinction debts"). R's evolution towards the tidyverse may also represent the start of a division into two distinct dialects, which may impact the readability and continuity of analytic and scientific inquiries codified in R, as well as the language's future.</p>
Dataset and R code for the manuscript: Interspecific facilitation favors rare species establishment and reduces performance disparities among adults
<p>The following directory contains the data necessary to replicate the results obtained in the manuscript entitled: <strong>Interspecific facilitation favors rare species establishment and reduces performance disparities among adults.</strong></p> <p>We provided an R workspace containing the data "Dataset1.RData", a "ReadMe.txt" archive with detailed information on the variables included in "Dataset1.RData", and the R code necessary to replicate the results ("Rcode1.txt")</p>
Data and R codes from: Effects of human disturbance on risk-taking behavior in painted turtles
<p>Animals are exposed to high levels of anthropogenic disturbance, which has profound consequences for population persistence. Individuals can adjust their behavior plastically when faced with perturbations in their environment and may show consistent differences in the way they perceive and respond to risky situations. Over time, this variability among individuals in response to risk can affect the dynamics of populations exposed to human disturbance. Thus, understanding how animals cope behaviorally with human disturbance is important, especially for species vulnerable to human perturbations, such as turtles. In this context, we evaluated whether risk-taking behaviors are consistent within individual painted turtles (<em>Chrysemys picta</em>) and assessed how these behaviors are related to the extent of human disturbance along the Rideau Canal, Ontario, Canada. Specifically, we conducted repeated measurements of the number of active defensive behaviors used during handling and the time taken to escape a floating platform for a total of 730 painted turtles (1117 observations) from 22 sites varying in human disturbance along the canal. We also quantified the emergence of the turtles from the water after escaping the platform. First, individual painted turtles showed consistent differences in all risk-taking behaviors. Second, painted turtles in areas with high boat activity displayed more active defensive behaviors, while turtles from sites in proximity to more houses with access to the canal used fewer. Our study highlights the importance of studying animal behavior to better understand the impact of human activities on animal populations.</p>
AccessFixer: Enhancing GUI Accessibility for Low Vision Users with R-GCN model
<p>Here is the relevant dataset and open-source code for the article titled "AccessFixer: Enhancing GUI Accessibility for Low Vision Users with RGCN-based Method"</p> <p><strong>Introduction</strong></p> <p>In this work, we designed and implemented a tool, named <strong>AccessFixer</strong>, capable of fixing GUI accessibility issues in terms of small size, narrow interval, and low color contrast. It can ensure the consistency of GUI visual effects in the repair process, and will not produce inconsistent components.</p> <p><strong>Functions</strong></p> <ol> <li><strong>Convert the GUIs screenshots to GUI-graphs. </strong>AccessFixer converts the GUIs into their corresponding GUI-graphs by parsing the XML file (in Graph_Presentation()), and meanwhile, our tool could remove all edges that connected the problematic nodes detected by Google Accessibility Scanner.</li> <li><strong>Pre-trained model based on Relational-Graph Convolutional Neural Network (R-GCN). </strong>Along with Capture_Signal(model), users can obtain the spectral signals of predicted links. Encoder and Decoder are responsible for generating new edges and scoring edges.</li> <li><strong>AccessFixer</strong> builds a mapping relationship between signal values and attribute values of GUI components in Attribute_Mapp(). Based on this mapping, it is possible to input a GUI to be repaired and generate repair strategies for its various components.</li> </ol> <p><strong>Environment</strong></p> <p>This tool can be run on an Android emulator based on Android 11.0 on a typical development machine, using Windows 11 with 2.4GHz core i7 CPU and 16 GB memory. The pre-trained RGCN model is run in PyCharm 4.5.4 with the packages of tensorflow, GraphConvolution, pandas, time, numpy, argparse, optimization, Parameter, and Module.</p> <p><strong>Installation</strong></p> <ol> <li>Using pip install package-name to install the required packages.</li> <li>Configure GCN model training in the same directory.</li> <li>Click the run button in PyCharm or use the command run-train.sh [configuration]</li> </ol> <p><strong>Frequently Asked Questions</strong></p> <ol> <li>Unable to install packages using pip</li> </ol> <p>Answer: It could be the version of the pip install command. Detailed solution could be found in https://stackoverflow.com/questions/17869101/unable-to-install-pygame-using-pip/74229901#74229901</p> <ol> <li>Some GUIs fail to build GUI-graphs</li> </ol> <p>Answer: To create GII-graphs, the user is required to provide the GUI screenshot and the layout file parsed by UIAutomator.</p> <p><strong>Contact Information</strong></p> <p>If you have any questions about this tool, you can contact the author of this work at <a href="mailto:zmxalakay@126.com">zmxalakay@126.com</a></p> <p><strong>Copyright</strong></p> <p>All copyright of the tool is owned by the author of the paper.</p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.