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722 results for “use case”
Supplementary tables for "Inconsistencies and opacity in retraction notices: Snapshot using 50 cases from Elsevier journals"
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Using Multi-Modal Path-Specific Transit Trips in Transportation Social Sustainability Analysis: Case Study in Atlanta, GA
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Installationsübersicht der lokalen Sensorik in den AIR-Use Cases
<p>Die Excel-Datei bietet eine Übersicht über alle lokal installierten Sensoren in den AIR-Use Cases, inklusive der jeweiligen Installationsdaten. <br>DOI: 10.5281/zenodo.14091807</p>
Data from: Using biogeographic history to inform conservation: the case of Preble's meadow jumping mouse
The last Pleistocene deglaciation shaped temperate and boreal communities in North America. Rapid northward expansion into high latitudes created distinctive spatial genetic patterns within species that include closely related groups of populations that are now widely spread across latitudes, while longitudinally adjacent populations, especially those near the southern periphery, often are distinctive due to long-term disjunction. Across a spatial expanse that includes both recently colonized and long-occupied regions, we analyzed molecular variation in zapodid rodents to explore how past climate shifts influenced diversification in this group. By combining molecular analyses with species distribution modeling and tests of ecological interchangeability, we show that the lineage including the Preble's meadow jumping mouse (Zapus hudsonius preblei), a US federally listed taxon of conservation concern, is not restricted to the southern Rocky Mountains. Rather, populations along the Front Range are part of a single lineage that is ecologically indistinct and extends to the far north. Of the 21 lineages identified, this Northern lineage has the largest geographic range and low measures of intra-lineage genetic differentiation, consistent with recent northward expansion. Comprehensive sampling combined with coalescent-based analyses and niche modeling lead to a radically different view of geographic structure within jumping mice and indicates the need to re-evaluate their taxonomy and management. This analysis highlights a premise in conservation biology, that biogeographic history should play a central role in establishing conservation priorities.
Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as sub-fossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established Maximum Likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a 'crown-giant' ecomorph anole hypothesized to have once been found throughout the Spanish, U.S., and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.
Data from: Metapopulation vicariance, age of island taxa and dispersal: a case study using the pacific plant genus Planchonella (Sapotaceae)
Oceanic islands originate from volcanism or tectonic activity without connections to continental landmasses, are colonized by organisms, and eventually vanish due to erosion and subsidence. Colonization of oceanic islands occurs through long-distance dispersals or metapopulation vicariance, the latter resulting in lineages being older than the islands they inhabit. If metapopulation vicariance is valid, island ages cannot be reliably used to provide maximum age constraints for molecular dating. We explore the relationships between the ages of members of a widespread plant genus (Planchonella, Sapotaceae) and their host islands across the Pacific to test various assumptions of dispersal and metapopulation vicariance. We sampled three nuclear DNA markers from 156 accessions representing some 100 Sapotaceae taxa, and analyzed these in BEAST with a relaxed clock to estimate divergence times and with a phylogeographic diffusion model to estimate range expansions over time. The phylogeny was calibrated with a secondary point (the root) and fossils from New Zealand. The dated phylogeny reveals that the ages of Planchonella species are, in most cases, consistent with the ages of the islands they inhabit. Planchonella is inferred to have originated in the Sahul Shelf region, to which it back-dispersed multiple times. Fiji has been an important source for range expansion in the Pacific for the past 23 myr. Our analyses reject metapopulation vicariance in all cases tested, including between oceanic islands, evolution of an endemic Fiji–Vanuatu flora, and westward rollback vicariance between Vanuatu and the Loyalty Islands. Repeated dispersal is the only mechanism able to explain the empirical data. The longest (8900 km) identified dispersal is between Palau in the Pacific and the Seychelles in the Indian Ocean, estimated at 2.2 Ma (0.4–4.8 Ma). The first split in a Hawaiian lineage (P. sandwicensis) matches the age of Necker Island (11.0 Ma), when its ancestor diverged into two species that are distinguished by purple and yellow fruits. Subsequent establishment across the Hawaiian archipelago supports, in part, progression rule colonization. In summary, we found no explanatory power in metapopulation vicariance and conclude that Planchonella has expanded its range across the Pacific by long-distance dispersal. We contend that this will be seen in many other groups when analyzed in detail.
Incipient speciation and the impact on taxonomic decision: a case study using a sky island sister species pair of stag beetle (Lucanus; Lucanidae)
<p class="BodyA">Species delimitation can be difficult when the divergence between focal taxa falls in the incipient stage of speciation, because conflicting results are expected among different data sets and the species limit may differ depending on the applied species concept. We studied the speciation history and investigated the impact on taxonomic decision when using different data types in a Taiwanese endemic sister species pair of stag beetle, <i>Lucanus miwai </i>and <i>L. yulaoensis</i>, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial <i>co1</i> lineages with pairwise sequence divergence > 3 %; however, <i>L. miwai</i> may not be monophyletic. Our multispecies coalescent based species delimitation result using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of genealogical divergence index (<i>gdi</i>) corresponded to the species delimitation ambiguous zone. We further showed that post divergence gene flow is unlikely. Our study demonstrates challenges in incipient species delineation, but shows the importance of understanding the speciation history and integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.</p>
FIGURE 1 in The histo structure of galls induced by aphids as a useful taxonomic character: the case of Rectinasus (Hemiptera, Aphididae, Eriosomatinae)
FIGURE 1. Galls induced by Rectinasus buxtoni. Microscopic structure. a Transverse section of the wall of the gall. Two vascular bundles are observed, one closer to the outside (Uvb) and the other closer to the inside of the gall (Lvb). Specifically, going from the outside (A) to the lumen (L) of the gall, the following is observed: epidermis-air (ea), storage parenchyma (pa), upper vascular bundle (Uvb), storage parenchyma, lower vascular bundle (Lvb), and epidermis-lumen (el). b–e Epidermis-air. b Uniseriate epidermis-air with thickened cuticle (c). Below storage parenchyma (pa) is observed, many cells of which have tannin inclusions. c View of the outer surface the gall. Between the epidermal cells a few stomata (s) are observed. d Detail of the foregoing. A stoma (s) and the presence of epicuticular waxes are observed in the epidermal cells. e Detail of the epicuticular waxes. f–i Vascular bundles. The vascular bundles are seen to be facing each other: the xylem of the upper bundle f–g is facing the xylem of the lower bundle h–i. f–g Upper vascular bundle. Xylem cells in f are the only ones that polarize light in g. h–i Lower vascular bundle. Xylem cells in h are the only ones that polarize light in i. The phloem is oriented towards the lumen (L) of the gall. j Detail of a vascular bundle: Closed collateral vascular bundle. Very characteristic of the vascular bundles of Pistacia sp. (and of the galls) is the presence of intraphloematic schizogenous ducts (sd). k–l Interior surface of the gall. k The interior surface of the gall has conspicuous dimples. l Detail of the foregoing. a b f h Safranin-Fast Green. Brightfield microscope. c d e k l SEM. g i Polarized light microscope. j Epifluorescence microscope. Abbreviations: A outside of the gall, c cuticle, ea epidermis-air, el epidermis-lumen, L lumen of the gall, Lvb lower vascular bundle, pa storage parenchyma, ph phloem, s stoma, sd intraphloematic schizogenous duct, Uvb upper vascular bundle, x xylem. Scale bars a 500 µm; b 50 µm; c f–k 100 µm; d l 20 µm; e 5 µm.
Data from: Ontogeny in the steinmanellines (Bivalvia: Trigoniida): an intra- and interspecific appraisal using the Early Cretaceous faunas from the Neuquén Basin as a case study
<p>Despite the paleontological relevance and paleobiological interest of trigoniid bivalves, our knowledge of their ontogeny –an aspect of crucial evolutionary importance– remains limited. Here, we assess the intra- and interspecific ontogenetic variations exhibited by the genus Steinmanella Crickmay (Myophorellidae: Steinmanellinae) during the early Valanginian – late Hauterivian of Argentina, and explore some of their implications. The (ontogenetic) allometric trajectories of seven species recognized for this interval were estimated from longitudinal data using 3D geometric morphometrics, segmented regressions and model selection tools, and then compared using trajectory analysis and allometric spaces. Our results show that within-species shell shape variation describes biphasic ontogenetic trajectories, decoupled from ontogenetic changes shown by sculpture, and with a gradual decay in magnitude as ontogeny progresses. The mode of change characterizing each phase (crescentic growth and anteroposterior elongation, respectively) is conserved across species, thus representing a feature of Steinmanella ontogeny; its evolutionary origin is inferred to be a consequence of the rate modification and allometric repatterning of the ancestral ontogeny. Among species, trajectories are more variable during early ontogenetic stages, becoming increasingly conservative at later stages. Trajectories' general orientation allows recognition of two stratigraphically-consecutive groups of species, hinting at a potentially higher genus-level diversity in the studied interval. In terms of functional morphology, juveniles had a morphology more suited for active burrowing than adults, whose features are associated with a sedentary lifestyle. The characteristic disparity of trigoniids could be related to the existence of an ontogenetic period of greater shell malleability betrayed by the presence of crescentic shape change.</p>
Use of Augmented Reality in the preservation of architectural heritage: case of aqueduct Kuru Kopru _Data set
<p>Architectural preservation embeds all the activities dealing with the physical sustainability of the built heritage<strong>,</strong> its diffusion and comprehension by a wide scope public. Representation and diffusion of heritage take a core place in that process. Nowadays, Augmented Reality (AR) is one of the most used digital tools in the diffusion of architectural heritage. This dataset embeds data used for the modeling of reconstruction models of the Roman aqueduct Kuru Kopru from the Roman-Byzantıne period to the year 2017 and those used for the development of two AR applications for the diffusion of the aforementioned aqueduct.</p>
FIGURE 5 in Using an Asteraceae checklist to understand collection history, species density and conservation implications: a case study in the state of Alagoas, Northeastern Brazil
FIGURE 5. Continental Protected Areas in the state of Alagoas. 1. Natural Monument of the São Francisco. 2. Wildlife Refuge of Morros do Craunã and Padre. 3. Ecological Station Curral do Meio. 4. Ecological Park Pedra do Sino. 5. Biological Reserve Pedra Talhada. 6. Environmental Protection Area Marituba do Peixe. 7. Environmental Protection Area of Piaçabuçu. 8. Extractive Reserve Jequiá. 9. Ecological Mangrove Reserve of Lagoa do Roteiro. 10. Ecological Reserve Saco da Pedra. 11. Environmental Protection Area of Santa Rita. 12. Environmental Protection Area of Catolé e Fernão Velho. 13. Municipal Park of Maceió. 14. Environmental Protection Area Patangy. 15. Environmental Protection Area of Murici. 16. Ecological Station of Murici. *RPPN
FIGURE 3 in Using an Asteraceae checklist to understand collection history, species density and conservation implications: a case study in the state of Alagoas, Northeastern Brazil
FIGURE 3. Results of the species richness (a) and collection density (b) analyses, and correlation between these two variables (c).
FIGURE 2 in Evaluating the taxonomy of macrofossils used in macroevolution: a case study of Artemisia (Asteraceae)
FIGURE 2. Leaf morphology of the macrofossils and extant Artemisia frigida leaves. A. Fossil leaf (redrawn from Zazula et al. 2003: Fig. 1d); B. Fossil leaf (redrawn from Zazula et al. 2007: Fig. 7i); C. Extant leaf central lobe of A. frigida; D. Extant upper leaf of A. frigida; E. Extant middle leaf of A. frigida; F. Extant lower leaf of A. frigida. Scale bar = 2 mm.
FIGURE 1 in Evaluating the taxonomy of macrofossils used in macroevolution: a case study of Artemisia (Asteraceae)
FIGURE 1. Leaf lobes and venation of Artemisia and its three closely related genera. A. A. igniaria; B. A. tridentata; C. A. chinensis; D. A. maritima; E. A. annua; F. A. stechmanniana; G. A. frigida; H. A. scoparia; I. Kaschgaria komarovii; J. Chrysanthemum indicum; K. Ajania pallasiana; L. fossil leaf (redrawn from Zazula et al. 2003); M. fossil leaf (redrawn from Zazula et al. 2007). Three pictures per species, 1 is the line drawing, 2 is the original image, and 3 is a partial enlarged view, showing the details of venation. Scale bar = 1 mm.
FIGURE 3 in Evaluating the taxonomy of macrofossils used in macroevolution: a case study of Artemisia (Asteraceae)
FIGURE 3. Corolla morphology of disc floret of extant Artemisia, its allies and the fossils. A. A. igniaria; B. A. tridentata; C. A. chinensis; D. A. maritima; E. A. annua; F. A. stechmanniana; G. A. frigida; H. A. scoparia; I. Kaschgaria komarovii; J. Chrysanthemum indicum; K. Ajania pallasiana; L. fossil (redrawn from Zazula et al. 2003: Fig. 1a). Scale bar = 1 mm.
FIGURE S1 in Evaluating the taxonomy of macrofossils used in macroevolution: a case study of Artemisia (Asteraceae)
FIGURE S1. Morphological comparison of Artemisia and its three closely related genera in the phylogenetic tree. The phylogenetic tree was summarized from Malik et al. (2017), Mei et al. (2016) and Sanz et al. (2008). The pictures in black boxes are A. A. igniaria; B. A. tridentata; C. A. chinensis; D. A. maritima; E. A. annua; F. A. stechmanniana; G. A. frigida; H. A. scoparia; and I. Kaschgaria komarovii; J. Chrysanthemum indicum; K. Ajania pallasiana; L1. fossil leaf (redrawn from Zazula et al. 2003); L2. fossil leaf (redrawn from Zazula et al. 2007); and L3. fossil corolla (redrawn from Zazula et al. 2003).
Dataset. Socio-ecological metabolism and rural livelihood conditions: two case studies on forest litter uses in France and Poland (1875-1910)
<p>This Datasets is the supplementary Material to the paper :"Socio-ecological metabolism and rural livelihoo conditions: two case studies on forest litter uses in France and Poland (1875-1910)".</p>
Software Analytics Use Cases
<p>Coded segments - software analytics use cases (IEEE Access paper: On Adopting Software Analytics for Managerial Decision-Making: A Practitioner's Perspective).</p>
Brief Communication: Monitoring active layer dynamic using a lightweight nimble Ground-Penetrating Radar system. A laboratory analog test case
<p>GPR dataset from Leger et al., 2023 (https://tc.copernicus.org/preprints/tc-2022-214/)</p> <p> </p>
Assessment of Temporomandibular Joint for Occurrence and Severity of Disorders in Adult Cases with Unilateral Cleft Lip and Palate and Non-Cleft Class I Using Helkimo Index
<p>master charts</p>
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.