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12,662 results for “linking”
JSTOR plant type specimens linked to GBIF occurrences
<p>A mapping between URLs for type specimens in JSTOR Global Plants and the corresponding occurrence in the Global Biodiversity Information Facility (GBIF).</p><p>Guide to fields:</p><ul><li><strong>doi</strong>: JSTOR identifier</li><li><strong>code</strong>: Barcode:</li><li><strong>gbif</strong>: GBIF occurrence id</li><li><strong>occurrenceUrl</strong>: URL to specimen in original herbarium database</li><li><strong>occurrenceID</strong>: occurrenceID stored in GBIF</li><li><strong>title</strong>: Title of specimen in JSTOR</li><li><strong>resource_type</strong>: Type of resource</li><li><strong>canonical</strong>: Canonical taxonomic name</li><li><strong>stored_under_name</strong>: Taxonomic name specimen is stored under</li><li><strong>type_status</strong>: What kind of type</li><li><strong>family</strong>: Family plant species belongs to</li><li><strong>collector</strong>: Collector</li><li><strong>date</strong>: Date of collection</li><li><strong>country</strong>: Country of collection</li><li><strong>herbarium</strong>: Herbarium where specimen is stored</li><li><strong>names</strong>: All taxonomic names associated with specimen as JSON array</li><li><strong>url</strong>: JSTOR URL</li><li><strong>thumbnailUrl</strong>: URL to thumbnail of image in JSTOR</li></ul>
Data from: warming and top-down control of stage-structured prey: linking theory to patterns in natural systems
<p>Warming has broad and often nonlinear impacts on organismal physiology and traits, allowing it to impact species interactions like predation through a variety of pathways that may be difficult to predict. Predictions are commonly based on short-term experiments and models, and these studies often yield conflicting results depending on the environmental context, spatiotemporal scale, and the predator and prey species considered. Thus, the accuracy of predicted changes in interaction strength, and their importance to the broader ecosystems they take place in, remain unclear. Here, we attempted to link one such set of predictions generated using theory, modeling, and controlled experiments to patterns in the natural abundance of prey across a broad thermal gradient. To do so, we first predicted how warming will impact a stage-structured predator-prey interaction in riverine rock pools between Pantala spp. dragonfly nymph predators and Aedes atropalpus mosquito larval prey. We then described temperature variation across a set of hundreds of riverine rock pools (n = 775) and leveraged this natural gradient to look for evidence for or against our model's predictions. Our model's predictions suggested that warming should weaken predator control of mosquito larval prey by accelerating their development and shrinking the window of time that aquatic dragonfly nymphs could consume them in. This was consistent with data collected in rock pool ecosystems, where the negative effects of dragonfly nymph predators on mosquito larval abundance were weaker in warmer pools. Our findings provide additional evidence to substantiate our model-derived predictions, while emphasizing the importance of assessing similar predictions using natural gradients of temperature whenever possible.</p>
Computationally directed manipulation of cross-linked covalent organic frameworks for membrane applications - PCCP
<p>The dataset uploaded herein is associated with the paper published under the title "<i>Computationally directed manipulation of cross-linked covalent organic frameworks for membrane applications</i>" with the Royal Society of Chemistry - Physical Chemistry Chemical Physics Journal. This dataset includes the .vasp files for all modeled structures, an example dftb_in.hsd file, which is the instructional file for geometry optimization with DFTB+, an Excel spreadsheet with atom number densities and total energy values for all modeled geometries, and, finally, a Python script that was used to calculate the Enthalpy of Formation and Cohesive Energies for all structures. This data has been made available to the scientific community in the interest of open-source and accessible data. The authors request that you please cite the associated paper and Zenodo dataset if used.</p><p><strong>Abstract</strong></p><p>Two-dimensional covalent organic frameworks (2D-COFs) exhibit characteristics ideal for membrane applications, such as high stability, tunability and porosity along with well-ordered nanopores. However, one of the many challenges with fabricating these materials into membranes is that membrane wetting can result in layer swelling. This allows molecules that would be excluded based on pore size to flow around the layers of the COF, resulting reduced separation. Cross-linking between these layers inhibits swelling to improve the selectivity of these membranes. In this work, computational models were generated for a quinoxaline-based COF cross-linked with oxalyl chloride (OC) and hexafluoroglutaryl chloride (HFG). Enthalpy of formation and cohesive energy calculations from these models show that formation of these COFs is thermodynamically favorable and the resulting materials are stable. The cross-linked COF with HFG was synthesized and characterized with Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis with differential scanning calorimetry (TGA-DSC), and water contact angles. Additionally, these frameworks were fabricated into membranes for permeance testing. The experimental data supports the presence of cross-linking and demonstrates that varying the amount of HFG used in the reaction does not change the amount of cross-linking present. Computational models indicate that the effect of varying cross-linking concentration on the framework stability is negligible and less cross-linking still results in stable materials. This work sheds light on the nature of the cross-linking in these 2D-COFs and their application in membrane separations.</p>
Linking provenance and its metadata for an AI-based computation using CPM and RO-Crate
<p>This dataset is a prototype implementation of a mechanism for linking provenance information and its metadata, also called provenance of provenance or meta-provenance. This dataset is an <a href="https://www.researchobject.org/ro-crate/">RO-Crate</a> that bundles artifacts of an AI-based computational pipeline. The resulting RO-Crate contains (directly or by a reference) artifacts of the pipeline execution, such as input dataset, intermediate and final results, configuration files, pipeline implementation, log files, or provenance files. The RO-Crate is based on the <a href="https://w3id.org/cpm/ro-crate/0.2">CPM RO-Crate profile</a>, which integrates the <a href="https://doi.org/10.1038/s41597-022-01537-6">Common Provenance Model</a> (CPM) and <a href="https://w3id.org/ro/wfrun/process/0.2">Process Run Crate profile</a>. The description of the AI pipeline and an explanation of how the CPM RO-Crate profile is applied to bundle the pipeline execution artifacts is provided in our <a href="https://doi.org/10.5281/zenodo.7676924">previous work</a>.</p> <p>As this dataset aims to demonstrate the mechanism for linking provenance and meta-provenance, the input dataset used for the AI model training and testing is reduced only to a few images, as the size of the input dataset does not affect the mechanism. The images used in the input are from the <a href="http://gigadb.org/dataset/100439">Camelyon16 dataset</a>.</p> <p> </p>
Artifact of 'Unification for Subformula Linking under Quantifiers'
<p>This is the artifact for the CPP '24 paper 'Unification for Subformula Linking under Quantifiers'. It contains formalizations of section 3.3 and section 4, as well as patches for Iris's improved version of iFrame.</p>
FIGURE 16 Periclimenes incertus Borradaile, 1915 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 16 Periclimenes incertus Borradaile, 1915, ovigerous female, RMNH.CRUS.D.53946. A, left major second pereiopod; B, idem, chela; C, right minor second pereiopod; D, idem Downloaded, chelafrom. Scale Brill. bar com: A,12 C/= 121/mm 2023; 03:02:30PM B, D = 0.2 mm. via Open Access. This is an open access article distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
FIGURE 14 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 14 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, telson; B, idem, detail distal part; C, distolateral part of uropod exopod; D, right first pleiopod. Male paratype (pocl. 1.35 mm), RMNH.CRUS.D.57575. E, right first pleiopod; F, right second pleopod. Scale bar: A, C, E = 0.4 mm; B = 0.07 mm; D, F = 0.2 mm.
FIGURE 15 Periclimenes incertus Borradaile, 1915 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 15 Periclimenes incertus Borradaile, 1915, ovigerous female, RMNH.CRUS.D.53946. A, rostrum and anterior appendages, dorsal view; B, idem, lateral view; C, left first pereiopod; D, idem, chela; E, idem, proximal segments; F, fourth thoracic sternites and proximal segments of first pereiopods. Scale bar: A–C = 1 mm; D–E = 0.2 mm; F = 0.4 mm.
FIGURE 5 Periclimenes watamuae Bruce, 1976a, minor second pereiopod. A. male, 1.00 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 5 Periclimenes watamuae Bruce, 1976a, minor second pereiopod. A. male, 1.00 mm, left P2, RMNH.CRUS.D.57574, LEM.36; B, ovigerous female, pocl 1.45 mm, right P2, RMNH.CRUS.D.57574, LEM.36; C, ovigerous female, pocl. 1.40 mm, right P2, RMNH.CRUS.D.57574, GenBank MK843275. Scale bar = 0.4 mm.
FIGURE 12 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 12 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, left major second pereiopod; B, idem fingers of chela; C, idem, tip of fingers, setae omitted; D, right minor second pereiopod; E, idem, fingers of chela. Scale bar: A, D = 1 mm; B, E = 0.2 mm; C = 0.07 mm.
FIGURE 11 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 11 Periclimenes subcorallum sp. nov., ovigerous female paratype (pocl. 1.45 mm), RMNH.CRUS.D.57575. A, left second maxiliped; B, left third maxilliped; C, left first pereiopod; D, idem, proximal segments; E, idem, chela. Scale bar: A, D, E = 0.2 mm; B = 0.4 mm; C = 1 mm.
FIGURE 6 Periclimenes diversipes Kemp, 1922, ovigerous female. A, stn LEM.07 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 6 Periclimenes diversipes Kemp, 1922, ovigerous female. A, stn LEM.07, on Danafungia scruposa; B, stn Downloaded from Brill.com 12/12/2023 03:02:30PM LEM.07, on Lithophyllon via repanda; Open C, stn AccessLEM..18 This, onis an Sandalolitha open accessrobustaarticle. distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
FIGURE 4 Periclimenes watamuae Bruce, 1976a, major second pereiopod. A in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 4 Periclimenes watamuae Bruce, 1976a, major second pereiopod. A, male, pocl 1.00 mm, right P2, RMNH. CRUS.D.57574, LEM.36; B, ovigerous female, pocl 1.45 mm, left P2, RMNH.CRUS.D.57574, LEM.36; C, ovigerous female, pocl. 1.40 mm, left P2, RMNH.CRUS.D.57574, GenBank MK843275. Scale bar = 0.4 mm.
FIGURE 3 Periclimenes diversipes Kemp, 1922, minor second pereiopod. A in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 3 Periclimenes diversipes Kemp, 1922, minor second pereiopod. A, male, pocl 1.38 mm, left P2, RMNH.CRUS.D.57553, GenBank MK843283; B, ovigerous female pocl. 1.25 mm, left P2, RMNH. CRUS.D.57547, GenBank MK843284; C, idem, lateral aspect chela; D, female pocl. 1.25 mm, right P2, RMNH.CRUS.D.57548, GenBank MK843295; E, ovigerous female pocl. 1.63 mm, right P2, RMNH. CRUS.D.57551, GenBank MK843282. Scale bar = 0.4 mm.
FIGURE 9 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 9 Periclimenes subcorallum sp. nov., ovigerous female holotype (pocl. 1.50 mm), MZB CRU 4968. Habitus. Scale = 2 mm.
FIGURE 2 Periclimenes diversipes Kemp, 1922, major second pereiopod. A, ovigerous female pocl. 1.63 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 2 Periclimenes diversipes Kemp, 1922, major second pereiopod. A, ovigerous female pocl. 1.63 mm, left P2, RMNH.CRUS.D.57551, GenBank MK843282; B, ovigerous female pocl. 1.25 mm, right P2, RMNH. CRUS.D.57547, GenBank MK843284; C, female pocl. 1.25 mm, left P2, RMNH.CRUS.D.57548, GenBank MK843295; D, male, pocl 1.38 mm, right P2, RMNH.CRUS.57553, GenBank MK843283. Downloaded from Brill.com 12/12/2023 03:02:30PM Scale bar = 0.4 mm. via Open Access. This is an open access article distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
FIGURE 8 in Shrimps of the genus Periclimenes (Crustacea, Decapoda, Palaemonidae) associated with mushroom corals (Scleractinia, Fungiidae): linking DNA barcodes to morphology
FIGURE 8 Mushroom coral cladogram based on published phylogenetic analyses (Gittenberger et al., 2011; Benzoni et al., 2012). The host relations of five Periclimenes species (table 3) are projected on the phylogeny reconstruction as well as the morphological traits "attached vs. free-living mode of life" (A = attached / F = free-living) and maximum recorded corallum size (Hoeksema, 1991, 2012a, 2014; Gittenberger et al., 2011) with size categories (S = small, <15 cm; M = medium, ≥15 cm and <25 cm; L = large, ≥25 cm). P. div = Periclimenes diversipes, P. gon = Periclimenes gonioporae Downloaded, P. jug = from Brill Periclimenes.com 12/ jugalis 12/, P 2023. wat03=:02:30PM Periclimenes watamuae, P. sub via=Open Periclimenes Access. This subcorallum is an sp open. nov. access article distributed under the terms of the prevailing CC-BY license at the time of publication. https://creativecommons.org/licenses/by/4.0/
Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer
<p>Data supporting the findings of "<a href="https://doi.org/10.1158/2326-6066.CIR-23-0873" target="_blank" rel="noopener">Machine learning links T cell function and spatial localization to neoadjuvant immunotherapy and clinical outcome in pancreatic cancer</a>" publication. Files include patient and tissue region metadata (in metadata folder) and output of multiplex immunohistochemistry computational image processing workflow for each tissue region (in mIHC_files folder). The code used to produce the results of this study is available at: <a href="https://github.com/kblise/PDAC_mIHC_paper">https://github.com/kblise/PDAC_mIHC_paper</a>.</p>
An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion
<ol> <li>Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitive subordinates like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. </li> <li>Wild dogs in Zambia's Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors, due to spatial variation in illegal offtake.</li> <li>We used long-term data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity, and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated.</li> <li>The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, <em>Kobus vardonii</em>, and impala, <em>Aepyceros</em> <em>melampus</em>), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density, and intermediate in the two regions with intermediate prey density. The population growth rate (λ) was positive for the population as a whole, strongly positive in the region with the highest prey density, and strongly negative in the region with the lowest prey density.</li> <li>It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.</li> </ol>
Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
<p>A better understanding of the relationship between plant specialized metabolism and traditional medicine has the potential to aid in bioprospecting and untangling of cross-cultural use patterns. However, given the limited information available for metabolites in most plant species, understanding medicinal use-metabolite relationships can be difficult. The order Caryophyllales has a unique pattern of lineages of tyrosine- or phenylalanine-dominated specialized metabolism, represented by mutually exclusive anthocyanin and betalain pigments, making Caryophyllales a compelling system to explore the relationship between medicine and metabolites by using pigment as a proxy for tyrosine- vs phenylalanine-dominant metabolism. We compiled a list of medicinal species in select tyrosine- or phenylalanine-dominant families of Caryophyllales (Nepenthaceae, Polygonaceae, Simmondsiaceae, Microteaceae, Caryophyllaceae, Amaranthaceae, Limeaceae, Molluginaceae, Portulacaceae, Cactaceae, and Nyctaginaceae) by searching scientific literature until no new medicinal uses were recovered. We then tested for phylogenetic clustering of uses using a "hot nodes" approach. To test potential non-metabolite drivers of medicinal use, like how often humans encounter a species (apparency), we repeated the analysis using only North American species across the entire order and performed phylogenetic generalized least squares regression (PGLS) with occurrence data from the Global Biodiversity Information Facility (GBIF). We hypothesized families with tyrosine-enriched metabolism would show clustering of different types of medicinal use compared to phenylalanine-enriched metabolism. Instead, wide-ranging, apparent clades in Polygonaceae and Amaranthaceae are overrepresented across nearly all types of medicinal use. Our results suggest that apparency is a better predictor of medicinal use than metabolite profile, although metabolism type may still be a contributing factor.</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.