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722 results for “use case”
Data from: Using full-length metabarcoding and DNA barcoding to infer community assembly for speciose taxonomic groups: a case study
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Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest
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Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
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Data from: Development of a sustainability assessment algorithm and its validation using case studies on cryogenic machining
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Dataset for: On the estimation of body mass in temnospondyls: A case study using the large-bodied Eryops and Paracyclotosaurus
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Data for: The role of ecdysis in repair of an attachment system: a case study using geckos
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Supporting material for: A multi-batch design to deliver robust estimates of efficacy and reduce animal use – a syngeneic tumour case study
<p>Underlying data, R scripts and subsequent figures are presented to deliver a replicable and transparent analysis for the manuscript "A multi-batch design to deliver robust estimates of efficacy and reduce animal use – a syngeneic tumour case study"</p> <p>Published in Scientific Reports</p> <p>See: <a href="https://protect-de.mimecast.com/s/kCQLCgpRGySlzOwmCNma6d?domain=rdcu.be">https://rdcu.be/b3vj2</a> </p> <p> </p> <p>This is version 2 of this data. This differs from version 1 in the following</p> <p>1. The number of simulation has increased from 300 to 2000 in each simulation cycle</p> <p>2. Script has been added to generate publication level figures</p> <p> </p> <p> </p> <p> </p>
Supplementary material 6 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S6. Average nucleotide diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 5 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S5. Average haplotype diversity for all four datasets of shared OTUs seperated according to sample sites and EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 7 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S7 – part 1. Haplotype network of the two most frequent EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 4 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S4. Average haplotype number per OTU for the four different datasets of shared OTUs. Datasets are split into EPT (Ephemeroptera, Plecoptera, Trichoptera) and PR ('Pollution Resistant') taxa
Supplementary material 3 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S3. Average haplotype number per OTU for the four different datasets of shared OTUs. Values are illustrated for all sample sites including all shared OTUs
Supplementary material 2 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S2. Four different datasets including shared OTUs between the different river systems (Emscher-Ennepe-Sieg, Emscher-Ennepe, Emscher-Sieg, Sieg-Ennepe). Number of OTUs is illustrated with taxonomic assignment on order level
Supplementary material 1 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Figure S1. Total number of aquatic macroinvertebrate individuals per sample and season plotted against the average haplotype number per OTU. Different colours indicate the three river systems
Data from: Phylogenomics in Cactaceae: a case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan/Sonoran Deserts
PREMISE OF THE STUDY: Although numerous phylogenetic studies have been conducted in Cactaceae, whole plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age and morphological evolution. METHODS: We developed a plastome dataset for most known diploid members of the chollas, 42 taxa, as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were referenced-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, which were used to build our plastome dataset that was analyzed using various methods. KEY RESULTS: Our plastome dataset resolved the phylogeny of the chollas, including most inter- and intraspecific relationships. Tribe Cylindropuntieae arose during the early Miocene in southern South America, ca. 18 mya, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya, and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series (e.g., spiny fruit) in Cylindropuntia are mostly homoplasious. CONCLUSIONS: This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although widespread throughout western North American deserts, the most recent common ancestor of the chollas s.l. likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, showing a strikingly similar pattern to other western North American Desert groups.
Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds
<p>1. Efforts to monitor and conserve populations and ecosystems in human-dominated landscapes can benefit from an empirical social-ecological systems approach.<br> 2. Here we illustrate how latent variable structural equation modelling of regional time series data can effectively describe interconnected drivers of population fluctuations in dynamic landscapes and can help to reveal previously unknown system drivers.<br> 3. Using a declining farmland-dependent bird species (Ammodramus savannarum) in the eastern United States (1994-2015) as a case study, our analysis reveals how farm management decisions drive population fluctuations (R<sup>2</sup> = 20%), while management is in turn highly influenced by climate (R<sup>2</sup> = 23-51%), but not by regional conservation spending.<br> 4. Synthesis and applications. Structural equation modelling revealed potential social-ecological pathways for halting regional population declines in a grassland bird, the Grasshopper Sparrow. Lower population growth rates followed years of higher hay yields (~4 percentage points per metric ton increase in hay yield) and later harvests (~2 percentage points per 10-day delay in harvest). Thus, one pathway for stabilising regional populations could involve compensating farmers for reducing hay harvests, potentially requiring a six-fold increase in current annual agri-environmental conservation spending.</p>
Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation
<p>Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation. For the model code, see https://github.com/YaleCIE/RECC-ODYM. The model results archived here were calculated by running the ODYM-RECC scripts of commit no. cb3a388 with the data in this archive.</p>
Smart Energy Use Case Clustering Dataset - II
<p>Cluster data set for multilayered and contextualized smart energy blockchain traces</p>
Taxonomic identification using virtual palaeontology and geometric morphometrics: a case study of Jurassic nerineoidean gastropods
<p><span>Taxonomic identification of fossils is fundamental to a wide range of geological and biological disciplines. Many fossil groups are identified based on expert judgment, which requires extensive experience and is not always available for the specific taxonomic group at hand. Nerineoideans, a group of extinct gastropods that formed a major component of Mesozoic shallow marine environments, have distinctive internal spiral folds that form the basis for their classification at the genus level. However, their identification is often inconsistent because it is based on a set of selected characters reliant upon individual interpretation. </span></p> <p><span>This study shows a non-destructive and quantitative method for their identification using micro-CT and geometric morphometrics. We examined and micro-CT-scanned nerineoidean specimens from five main families that dominated Europe, Arabia and Africa during the Middle-Late Jurassic. Optimal longitudinal slices were selected from the tomographic reconstructions or from images of polished cross-sections compiled from fossil collections, published work and online databases. Internal whorl outlines were represented by thirty evenly distributed sliding semilandmarks and shape variations were studied using the Procrustes-based geometric morphometrics method. Multivariate analysis shows that Ceritellidae and Ptygmatididae are distinct families, whereas Nerinellidae, Eunerineidae and Nerineidae fall within the same shape variance and cannot be distinguished based on internal whorl outlines. The suggested method can be applied to images from various sources as well as to poorly preserved specimens. Our case study demonstrates the importance of quantitatively re-evaluating taxonomy in the fossil record, promoting the future utility of large datasets. </span></p>
Data from: Influence of device accuracy and choice of algorithm for species distribution modelling of seabirds: a case study using black-browed albatrosses
Species distribution models (SDM) based on tracking data from different devices are used increasingly to explain and predict seabird distributions. However, different tracking methods provide different data resolutions, ranging from < 10m to >100km. To better understand the implications of this variation, we modeled the potential distribution of black-browed albatrosses Thalassarche melanophris from South Georgia that were simultaneously equipped with a Platform Terminal Transmitter (PTT) (high resolution) and a Global Location Sensor (GLS) logger (coarse resolution), and measured the overlap of the respective potential distribution for a total of nine different SDM algorithms. We found slightly better model fits for the PTT than for GLS data (AUC values 0.958±0.048 vs. 0.95±0.05) across all algorithms. The overlaps of the predicted distributions were higher between device types for the same algorithm, than among algorithms for either device type. Uncertainty arising from coarse-resolution location data is therefore lower than that associated with the modeling technique. Consequently, the choice of an appropriate algorithm appears to be more important than device type when applying SDMs to seabird tracking data. Despite their low accuracy, GLS data appear to be effective for analyzing the habitat preferences and distribution patterns of pelagic species.
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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.