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885 results for “data strategy”
Data from: A real data-driven simulation strategy to select an imputation method for mixed-type trait data
<p>Missing observations in trait datasets pose an obstacle for analyses in myriad biological disciplines. Considering the mixed results of imputation, the wide variety of available methods, and the varied structure of real trait datasets, a framework for selecting a suitable imputation method is advantageous. We invoked a real data-driven simulation strategy to select an imputation method for a given mixed-type (categorical, count, continuous) target dataset. Candidate methods included mean/mode imputation, k-nearest neighbour, random forests, and multivariate imputation by chained equations (MICE). Using a trait dataset of squamates (lizards and amphisbaenians; order: Squamata) as a target dataset, a complete-case dataset consisting of species with nearly completed information was formed for the imputation method selection. Missing data were induced by removing values from this dataset under different missingness mechanisms: missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR). For each method, combinations with and without phylogenetic information from single gene (nuclear and mitochondrial) or multigene trees were used to impute the missing values for five numerical and two categorical traits. The performances of the methods were evaluated under each missing mechanism by determining the mean squared error and proportion falsely classified rates for numerical and categorical traits, respectively. A random forest method supplemented with a nuclear-derived phylogeny resulted in the lowest error rates for the majority of traits, and this method was used to impute missing values in the original dataset. Data with imputed values better reflected the characteristics and distributions of the original data compared to complete-case data. However, caution should be taken when imputing trait data as phylogeny did not always improve performance for every trait and in every scenario. Ultimately, these results support the use of a real data-driven simulation strategy for selecting a suitable imputation method for a given mixed-type trait dataset.</p>
Data for: Allometry reveals trade-offs between Bergmann's and Allen's rules, and different avian adaptive strategies for thermoregulation
<p>Animals tend to decrease in body size (Bergmann's rule) and elongate appendages (Allen's rule) in warm climates. However, it is unknown whether these patterns depend on each other or constitute independent responses to thermal environment. Here, based on a global phylogenetic comparative analysis across 99.7% of the world's bird species, we show that the way in which the relative length of unfeathered appendages co-varies with temperature depends on body size and vice versa. First, the larger the body, the greater the increase in beak length with temperature. Second, the temperature-based increase in tarsus length is apparent only in larger birds, whereas in smaller birds, tarsus length decreases with temperature. Third, body size and the length of beak and tarsus interact each other to predict the species' temperature preferences. These findings suggest that the animals' body size and shape are products of an evolutionary compromise that reflects distinct alternative thermoregulatory adaptations.</p>
Large-scale saliva pooling as a screening strategy to control transmission_raw data
<p>This dataset include the raw data of our experience after building a bespoke laboratory to control critical areas by pooling samples of saliva. From August 2020 to February 2022; 928,528 individual self-samples of saliva were processed in 52,580 pools, 4,935 of which were positive and helped us detect 5,806 nonsymptomatic individuals. </p> <p>The dataset was collected directly from the laboratory information system and was processed to delete the columns with sensitive information.</p> <p>The Dataset was charged as XLSX file and only need a compatible software.</p> <p>To facilitate the understanding of the data set, which uses the Galician language and an internal nomenclature of our laboratory, we include a sheet named "description" and a README file in which it defines the terms used and their equivalence with those used in the article.</p>
Data from: Unique drought resistance strategies occur among monkeyflower populations spanning an aridity gradient
<p>This data repository contains the metadata and data to produce all results found in the manuscript titled: "<em>Unique drought resistance strategies occur among monkeyflower populations spanning an aridity gradient</em>". This repository includes two different datasets as well as associated readme files. One dataset (fileA) contains phenotype data from an experimental manipulation experiment taking place in growth chambers at the University of Louisiana, Lafayette. The second dataset contains data from a common garden experiment that contained offspring from the well-watered treatment of the experimental manipulation from fileA. This dataset contains both offspring and midparent values for the same phenotypes measured in the experimental manipulation. Datasets are both uploaded as .csv files. Please read the readme files for descriptions of the data in each .csv file.</p>
Climatic forcing and individual heterogeneity in a resident mountain bird: legacy data reveal effects on reproductive strategies
<p><span>Optimization of clutch size and timing of reproduction </span><span>have substantial effects on lifetime reproductive success in vertebrates, and b</span><span>oth </span><span>individual quality and </span><span>environmental variation may impact </span><span>life history strategies</span><span>. </span><span>We tested hypotheses related to maternal investment and timing of reproduction</span><span>, using 17 years (1978-1994) of individual-based life history data on willow ptarmigan (<em>Lagopus l. lagopus</em>, </span><span>n=290 breeding females with n=319 breeding attempts</span><span>) in central Norway. We analysed whether climatic variation and individual state variables (age and body mass) affected number of offspring and timing of reproduction, and individual repeatability in strategies</span><span>. The results suggest that willow ptarmigan share a common optimal clutch size that is largely independent of measured individual states. While we found no clear direct weather effects on clutch size, higher spring temperatures advanced onset of breeding, and early breeding was followed by an increased number of offspring. Warmer springs were positively related to maternal mass, and mass interacted with clutch size in production of hatchlings. Finally, clutch size and timing of reproduction were highly repeatable within individuals, indicating that individual quality guided trade-offs in reproductive effort. Our results demonstrate how climatic forcing and individual heterogeneity in combination influenced life history traits in a resident montane keystone species.</span></p>
Data for: Adaptive plasticity to drought of Grime's CSR strategies
<p>Grime's strategies (Competitor, Stress tolerator, Ruderal; CSR) represent viable trait combinations with which species deal with environmental conditions. CSR strategies are broadly used to understand plant adaptation to the environment, yet their plastic responses have received little attention. A globally-calibrated tool (StrateFy) estimates CSR strategies using specific leaf area (SLA), leaf dry matter content (LDMC) and leaf area (LA) data, but these three traits can hardly characterise whole-plant responses to the environment individually. CSR strategies reflect trade-offs among growth, survival and reproduction, at both leaf and whole-plant levels, thus integrating several functions. We hypothesised that CSR strategies and the three constituent traits would show independent plasticity patterns, and that CSR strategies would be more likely to show adaptive responses, i.e., to fit expected functional responses to environmental gradients. We compared phenotypic plasticity to drought in single traits (SLA, LDMC and LA) with the integrated plasticity of the resulting CSR strategy. The study species was the invasive plant <em>Mesembryanthemum crystallinum</em>, which is distributed in arid and semiarid Chile. We found that trait plasticity was rather idiosyncratic and contrary to what would be expected from a functional adjustment to drought: LDMC did not change (expected response: increase) and SLA increased (expected response: decrease). Conversely, plastic responses of CSR strategy and LA were consistent with functionally adaptive responses to drought in all populations: S-strategy increased, while C-strategy and LA decreased. We advocate the use of Grime's CSR theory as an integrative approach to further our understanding of adaptive plasticity in plants.</p>
Data from "Optimizing the baiting strategy for oral vaccine delivery to wild boar"
<p>Data from the paper "Optimization of the baiting strategy for the administration of oral vaccines to wild boar". These data are from experiments done in field work based on the baiting preference of different animal species.</p>
Data from: Virus community structuring is shaped by habitat heterogeneity and resource utilisation strategies
<p><span>After decades of disconcerted research, we still recognise large gaps in the understanding of mechanisms that govern disease dynamics in complex biological communities. To determine how spatial structuring of plant communities caused by anthropic disturbance affects resource utilisation traits of viruses, we combine high-throughput, network, and metacommunity approaches. We find that the disturbance gradient corresponded to network modules and habitat specificity exhibited by a majority of viruses. Communities were connected through key hub species of either generalist viruses or high potential host reservoirs. Spatial dependencies were evident in regression models of species richness and correlations between metacommunity structure and both host range and transmission mode at finer spatial resolutions. We propose that virus community assembly is influenced by variation in niche opportunities. Distinctions in virus community composition caused by resource compartmentalisation can be used to track ecological traits important in forecasting transmission risk.</span></p>
Supplementary data and material, Global strategy for the conservation and use of eggplants.
<p>Supplementary data and material from</p> <p>Solberg, S., van Zonneveld, M., Rakha, M. T. , Taher, D. I. , Prohens, J., Jarret, R. van Dooijeweert, W., and Peter Giovannini. 2022. Global strategy for the conservation and use of eggplants. Global Crop Diversity Trust. Bonn, Germany.</p>
Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia
<p><span>Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus <em>Clarkia</em>. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other <em>Clarkia </em>taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa – a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.</span></p>
Data from: A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1
<p>The relative positions of viral DNA genomes to the host intranuclear environment play critical roles in determining virus fate. Recent advances in the application of chromosome conformation capture-based sequencing analysis (3C technologies) have revealed valuable aspects of the spatiotemporal interplay of viral genomes with host chromosomes. However, to elucidate the causal relationship between the subnuclear localization of viral genomes and the pathogenic outcome of an infection, manipulative tools are needed. Rapid repositioning of viral DNAs to specific subnuclear compartments amid infection is a powerful approach to synchronize and interrogate this dynamically changing process in space and time. Herein, we report an inducible CRISPR-based two-component platform that relocates extrachromosomal DNA pieces (5 kb to 170 kb) to the <strong>nu</strong>clear <strong>p</strong>eriphery <strong>in</strong> minutes (CRISPR-nuPin). Based on this strategy, investigations of herpes simplex virus 1 (HSV-1), a prototypical member of the human herpesvirus family, revealed unprecedently reported insights into the early intranuclear life of the pathogen: I) Viral genomes tethered to the nuclear periphery upon entry, compared with those freely infecting the nucleus, were wrapped around histones with increased suppressive modifications and subjected to stronger transcriptional silencing and prominent growth inhibition. II) Relocating HSV-1 genomes at 1 hour post infection significantly promoted the transcription of viral genes, termed an "Escaping" effect. III) Early accumulation of ICP0 was a sufficient but not necessary condition for "Escaping". IV) Subnuclear localization was only critical during early infection. Importantly, the CRISPR-nuPin tactic, in principle, is applicable to many other DNA viruses.</p>
Using Data-Driven Implementation Strategies to Improve the Quality of Cirrhosis Care
ClinicalTrials.gov study NCT04178096. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Evolved phenological cueing strategies show variable responses to climate change
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Data from: Recognition of endophytic Trichoderma species by leaf-cutting ants and their potential in a Trojan-horse management strategy
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Survey questionnaire and data of health management strategies of resilient honey bee stock throughout Southern California
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Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem
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Data from: Mate choice strategies in a spatially-explicit model environment
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Data from: Diet variability among insular populations of Podarcis lizards reveals diverse strategies to face resource-limited environments
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Data from: Nest attendance by tropical and temperate passerine birds: same constancy, different strategy
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Termite trait data from: Continental-scale shifts in termite diversity and nesting and feeding strategies
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ScienceDex guides
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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.