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15,519 results for “r”
Ocurrencia de atropellamiento de especies de vertebrados silvestres en un tramo de 6 Km de carretera municipal, Dibulla, La Guajira, Colombia. R= Recorridos.
<p>Publicado en:</p> <p>Tamayo Lopez, I. Camargo-Gonzales, L. & Acuña-Vargas, J. (2022). Ocurrencias de atropellamiento de fauna silvestre en un tramo de carretera de Dibulla, La Guajira, Colombia. <em>Ciencia e Ingeniría</em>, 9 (1): e6722334. https://www.doi.org/10.5281/zenodo.6722334</p>
Tasa de atropellamiento de especies de vertebrados silvestres en un tramo de 6 Km de carretera municipal, Dibulla, La Guajira, Colombia. R= Recorridos; TA= Tasa de atropellamiento total; Tda= Tasa de atropellamiento por día de recorrido.
<p>Publicado en:</p> <p>Tamayo Lopez, I. Camargo-Gonzales, L. & Acuña-Vargas, J. (2022). Ocurrencias de atropellamiento de fauna silvestre en un tramo de carretera de Dibulla, La Guajira, Colombia. <em>Ciencia e Ingeniría</em>, 9 (1): e6722334. https://www.doi.org/10.5281/zenodo.6722334</p>
Extensive population-level sampling reveals clinal variation in (R)-(-)-linalool produced by the flowers of an endemic evening primrose, Oenothera harringtonii
<div></div> <div> <div> <p>The study of floral trait diversity has a long history due to its role in angiosperm diversification. While many studies have focused on visual traits including morphology and color, few have included floral scent despite its importance in pollination. Of the studies that have included floral scent, sampling has been limited and rarely explores variation at the population level. We studied geographic variation in the flowers of <em>Oenothera harringtonii</em>, a rare plant endemic to a vulnerable shortgrass prairie habitat, whose population structure and conservation status are well studied. The self-incompatible flowers of <em>O. harringtonii</em> open at dusk, produce nectar and a strong fragrance, and are pollinated by hawkmoths. We collected floral trait (morphology, scent chemistry and emission rates) data from 650 individuals from 19 wild populations to survey floral variation across the entire range of this species. Similarly, we collected floral data from 49 individuals grown in a greenhouse common garden, to assess whether variation observed in the field is consistent when environment factors (temperature, watering regime, soil) are standardized. We identified 35 floral volatiles representing 5 biosynthetic classes. Population differentiation was stronger for floral scent chemistry than floral morphology. (<em>R</em>)-(−)-linalool was the most important floral trait differentiating populations, exhibiting clinal variation across the distribution of <em>O. harringtonii</em> without any correlated shifts in floral morphology. Populations in the north and west produced (<em>R</em>)-(−)-linalool consistently, those in the east and south largely lacked it, and populations at the center of the distribution were polymorphic. Floral scent emissions in wild populations varied across four years but chemical composition was largely consistent over time. Similarly, volatile emission rates and chemical composition in greenhouse-grown plants were consistent with those of wild populations of origin. Our data set, which represents the most extensive population-level survey of floral scent to date, indicates that such sampling may be needed to capture potentially adaptive geographic variation in wild populations.</p> </div> </div>
Occurrence datasets, model outputs, and R script for 12 termite species used for niche modeling
<p>The advent of citizen-science databases in conjunction with museum specimen locality information has exponentially increased the power and accuracy of ecological niche modeling (ENM). Increased occurrence data has provided colossal potential to understand the distributions of lesser known or endangered species, including arthropods. Although niche modeling of termites has been conducted in the context of invasive and pest species, few studies have been performed to understand the distribution of basal termite genera. Using specimen records from the American Museum of Natural History (AMNH) as well as locality databases, we generated ecological niche models for 12 basal termite species belonging to six genera and three families. We extracted environmental data from the Worldclim 19 bioclimatic dataset v2, along with SoilGrids datasets and generated models using MaxEnt. We chose Optimal models based on partial Receiving Operating characteristic (pROC) and omission rate criterion and determined variable importance using permutation analysis. We also calculated response curves to understand changes in suitability with changes in environmental variables. Optimal models for our 12 termite species ranged in complexity, but no discernible pattern was noted among genera, families, or geographic range. Permutation analysis revealed that habitat suitability is affected predominantly by seasonal or monthly temperature and precipitation variation. Our findings not only highlight the efficacy of largely citizen-science and museum-based datasets, but our models provide a baseline for predictions of future abundance of lesser-known arthropod species in the face of habitat destruction and climate change.</p>
High-quality video file for Doekes, H.M. and Hermsen, R, "Multiscale selection in spatially structured populations" (2022)
<p>High-quality version of supplementary movie 1 as published with:</p> <p>Doekes, H.M. and Hermsen, R, "Multiscale selection in spatially structured populations" (to be submitted, 2022)</p>
Calibration data for IMACLIM-R electricity nexus - alpha version
<p>First release of the calibration data for the electricity nexus of IMACLIM-R (<a href="https://www.iamconsortium.org/resources/model-resources/imaclim-r/">https://www.iamconsortium.org/resources/model-resources/imaclim-r/</a>).</p> <p>Ongoing/missing:</p> <ul> <li>operation and maintenance costs</li> <li>installed capacity</li> </ul>
Edited DHS data for R training
<p>Edited DHS data for R training</p>
Synthetic data for R training
<p>Synthetic data for R training</p>
Data and R scripts for: Identifying existing management practices in the control of Striga asiatica within rice–maize systems in mid-west Madagascar
<p>Infestations by the parasitic weed genus <i>Striga</i> result in significant losses to cereal crop yields across sub-Saharan Africa. The problem disproportionately affects subsistence farmers who frequently lack access to novel technologies. Effective <i>Striga </i>management therefore requires the development of strategies utilising existing cultural management practices. We report a multi-year, landscape-scale monitoring project for <i>Striga</i> asiatica in the mid-west of Madagascar, undertaken over 2019-2020 with the aims of examining cultural, climatic and edaphic factors currently driving abundance and distribution. Long-distance transects were established across the middle-west region of Madagascar, over which <i>Striga asiatica</i> abundance in fields was estimated. Analysis of the data highlights the importance of crop variety and legumes in driving <i>Striga </i>density. Moreover, the dataset revealed significant effect of precipitation seasonality, mean temperature and altitude in determining abundance. A composite management index indicated the effect of a range of cultural practices on changes in <i>Striga </i>abundance<i>. </i>The findings support the assertion that single measures are not sufficient for the effective, long-term management of <i>Striga</i>. Furthermore, the composite score has potential as a significant guide of integrated <i>Striga </i>management beyond the geographic range of this study. </p>
Data and R script: Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era
<p>Raw data and R code necessary to reproduce the results of the paper entitled "Ecotourism impacts on reef fishes in a marine reserve during the COVID-19 era" published in Frontiers in Ecology and the Environment.</p> <p> </p>
Segmentation performance evaluation results and R scripts for generating figures and tables.
<p>This archive contains the evalutation results of 24 segmentation models and the R scripts to produce figures and tables published in Kloster et al. 2022: Improving deep learning-based segmentation of diatoms in gigapixel-sized virtual slides by object-based tile positioning and object integrity constraint.</p> <p>Please refer to the manuscript for further details.</p>
Data for testing the SIAMCAT R package
<p>Datasets needed for the vignettes of the <a href="https://siamcat.embl.de/">SIAMCAT</a> R package</p>
Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq
<p><em><span>Rattus norvegicus</span></em><span> and </span><em><span>Rattus tanezumi</span></em><span> are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored.</span><span> Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that </span><span><em>R</em>. <em>norvegicus</em></span><span> is widely distributed in China, </span><span>R. <em>tanezumi</em></span><span> is mainly distributed in southern China with currently invading northward; northeast China was the natal region of </span><span><em>R</em>. <em>norvegicus</em></span><span>, while the spread of </span><span><em>R</em>. <em>tanezumi</em></span><span> in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b‐RAD analyses. In the neighbor‐joining tree, individuals of </span><span><em>R</em>. <em>tanezumi</em></span><span> grouped into geographic‐specific branches, and populations from the southeast coast were ancestral groups, which confirmed the colonization route from the southeast coast to central and western China. However, individuals of </span><span><em>R</em>. <em>norvegicus</em></span><span> were generally grouped into two clusters instead of geographic‐specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that the spread history of </span><span><em>R</em>. <em>norvegicus</em></span><span> in China was complex; in addition to on‐land colonization, shipping transportation also played a great role. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the </span><span>R<em>.</em> <em>norvegicus</em></span><span> declined rapidly while the population of </span><span><em>R</em>. <em>tanezumi</em></span><span> continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation of phylogeography of two species in China.</span></p>
Supplementary material 1 from: Scacchetti P, Pansonato-Alves J, Utsunomia R, Oliveira C, Foresti F (2011) Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences. Comparative Cytogenetics 5(3): 223-235. https://doi.org/10.3897/compcytogen.v5i3.1375
Nexus file of aligned COI and COII nucleotide sequences.
Supplementary material 1 from: Virkkala R, Rajasärkkä A (2012) Preserving species populations in the boreal zone in a changing climate: contrasting trends of bird species groups in a protected area network. Nature Conservation 3: 1-20. https://doi.org/10.3897/natureconservation.3.3635
Mean densities and number of observations of species in 1981–1999 and in 2000–2009
Data and R codes used in Delory et al (2017) F1000Research
<p>This repository contains all the data and R codes used for the use cases presented in Delory et al archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems. The manuscript was submitted to F1000Research in December 2017.</p>
96 wells fluorescence reading and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the subsequent steps: To assess the secretion efficiency of the constructs, 96 colonies from the selection plates were evaluated using the workflow presented in Figure Workflow. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Fluorescence was measured at excitation 575/9 nm and emission 608/20 nm. Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p> </p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>barplot_R.R -> code to generate bar plot in R statistic 3.3.3</p> <p>boxplotv2.R -> code to generate boxplot in R statistic 3.3.3</p> <p>pRFU_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_+_bl.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_raw.csv -> supernatant mCherry fluorescence dataset of 96 colonies for each construct.</p> <p>who_+_bl2.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_raw.csv -> whole culture mCherry fluorescence dataset of 96 colonies for each construct.</p> <p>who_+_Chlo.csv -> whole culture chlorophyll fluorescence dataset of 96 colonies for each construct.</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>ANOVA_pRFU_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_sup_+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_who_+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>ANOVA_Chlo.doc -> ANOVA of whole culture chlorophyll fluorescence of all constructs, plus average and standard deviation values.</p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433</p> <p> </p> <p> </p>
Data supplementing the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal
<p>These data supplement the article "Avoiding quantification bias in metabarcoding: application of a cell biovolume correction factor in diatom molecular biomonitoring" V. Vasselon, A. Bouchez, F. Rimet, S. Jacquet, R. Trobajo, M. Corniquel, K. Tapolczai, I. Domaizon submitted to Methods in Ecology and Evolution journal</p> <p>The directory contains the following files:</p> <p>1<strong>5 fastq files raw reads (5 mock communities, 3 replicates)</strong><strong>.rar </strong>- contains the 15 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>15 fastq files information.xlsx</strong> :</p> <p>- contains the information relative to the 15 fastq files corresponding to the PGM raw data of the 5 mock communities (sequenced with 3 replicates), including: the ID of the fastq files, the mock community name, the replicate number, the final sample Id and the number of raw reads per fastq file.</p> <p>- contains the information of the proportion of the 8 diatoms species (%) used to create the 5 mock communities (estimated from microscopy).</p>
Seven Fluorescent proteins profile in Chlamydomonas reinhardtii and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the protocol described in dx.doi.org/10.17504/protocols.io.kfnctme. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>Analysis_Raw_FP.xlsx -> File with raw values organized in a spreadsheet </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii </em></p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>1. Molino JVD, de Carvalho JCM, Mayfield S. Evaluation of secretion reporters to microalgae biotechnology: blue to red fluorescent proteins. Algal Res. 2018;31: 252–261. doi:10.1016/j.algal.2018.02.018</p>
Extended Signal Events for LHCO2020 R&D Dataset
<p>These are the extended signal events for the LHCO2020 R&D dataset. It consists of the W'->X(qq)Y(qq) (2-prong decay) and the W'->X(qq)Y(qqq) (3-prong decay) events. The W' boson has a mass of 3.5 TeV, while the masses of particles X and Y form a grid ranging from 50 GeV to 600 GeV in 50 GeV increments. Each decay mode features 144 signal models, each with approximately 100,000 events. The events are produced using the same simulation settings as those of the <a href="https://doi.org/10.5281/zenodo.2629072">LHCO2020 R&D Dataset</a>.</p> <p>The dataset includes high-level features of the two highest pT jets. They are the 3-momenta, pT, eta, phi, invariant masses, number of jet constituents, and n-subjettiness variables tau1, tau2, and tau3 for the highest pT jet (j1) and the second highest pT jet (j2) as well as the invariant masses of X and Y:</p> <pre>'pxj1', 'pyj1', 'pzj1', 'ptj1', 'etaj1', 'phij1', 'mj1', 'Nj1', 'tau1j1', 'tau2j1', 'tau3j1',<br>'pxj2', 'pyj2', 'pzj2', 'ptj2', 'etaj2', 'phij2', 'mj2', 'Nj2', 'tau1j2', 'tau2j2', 'tau3j2',<br>'mx', 'my'</pre> <p>Notice that the n-subjettiness variables use a different normalization scheme to the LHCO2020 R&D Dataset, but the ratios of the variables should remain the same.</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.