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1,026 results for “Linked data”
Data from: On the link between functional traits and growth rate: meta-analysis shows effects change with plant size, as predicted
A plant's growth rate is seen as a central element of its ecological strategy, and as determined by its traits.Yet the literature is inconsistent about the empirical correlation between functional traits and growth, casting doubt on the capacity of some prominent traits to influence growth rate. We propose that traits should influence growth in a way that depends on the size of individual plants. We outline mechanisms and hypotheses based on new theoretical work, and test these predictions in tree species using a meta-analysis of 103 studies (> 500 correlations) for five traits (specific leaf area, wood density, maximum height, seed mass and maximum assimilation rate).We also recorded data for 14 other traits commonly used in the trait literature.To capture the effects of plant size, we tested for a shift in the direction of correlation between growth rates and each trait across three ontogenetic stages: seedling,sapling and adult. Results were consistent with predictions, although there were some limitations arising from unequal numbers of observation across ontogenetic stages.Specific leaf area was correlated with relative growth rate in seedlings but not in adult plants.Correlations of growth with wood density were not affected by ontogenetic stage. Seed mass, assimilation rate and maximum height were correlated with relative growth rate only in one ontogenetic stage category: seedlings,seedlings and adults,respectively. Although we were able to confirm several of our theoretical predictions,major knowledge gaps still exist in the trait literature.For example,for one third of the traits considered,the majority (> 75%) of reported correlations with growth came from the same ontogenetic stage. Synthesis: We show for some traits, how trait-growth correlations change in a predictable way with plant size.Our understanding of plant strategies should shift away from describing species as having a fixed growth strategy throughout their life (on a continuous axis from slow to fast growth), in favour of a size-dependent growth trajectories.
Data from: Differential female sociality is linked with the fine-scale structure of sexual interactions in replicate groups of red junglefowl, Gallus gallus
Recent work indicates that social structure has extensive implications for patterns of sexual selection and sexual conflict. However, little is known about the individual variation in social behaviours linking social structure to sexual interactions. Here, we use network analysis of replicate polygynandrous groups of red junglefowl (Gallus gallus) to show that the association between social structure and sexual interactions is underpinned by differential female sociality. Sexual dynamics are largely explained by a core group of highly social, younger females, which are more fecund and more polyandrous, and thus associated with more intense postcopulatory competition for males. In contrast, less fecund females from older cohorts, which tend to be socially dominant, avoid male sexual attention by clustering together and perching on branches, and preferentially reproduce with dominant males by more exclusively associating and mating with them. Collectively, these results indicate that individual females occupy subtly different social niches, and demonstrate that female sociality can be an important factor underpinning the landscape of intra-sexual competition and the emergent structure of animal societies.
Data from: An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles
Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of proteins encoded in genomes. Here we propose an improved phylogenetic profile-based method which considers the co-evolution of the reference genome to derive the basic similarity measure, the background phylogeny of target genomes for profile generation and assigning weights to target genomes. The ordering of genomes and the runs of consecutive matches between the proteins were used to define phylogenetic relationships in the approach. We used Escherichia coli K12 genome as the reference genome and its 4195 proteins were used in the current analysis. We compared our approach with two existing methods and our initial results show that the predictions have outperformed two of the existing approaches. In addition, we have validated our method using a targeted protein-protein interaction network derived from protein-protein interaction database STRING. Our preliminary results indicates that improvement in function prediction can be attained by using coevolution-based similarity measures and the runs on to the same scale instead of computing them in different scales. Our method can be applied at the whole-genome level for annotating hypothetical proteins from prokaryotic genomes.
Data from: Linking intra-specific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off
1.Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. 2.We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterized a trait dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. 3.Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r-squared of 34% to 57% and confirmed theoretical expectations of density dependent population growth and species interactions in the system. 4.Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. 5.Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics.
Data from: Macrophage migration inhibitory factor is involved in ectopic endometrial tissue growth and peritoneal-endometrial tissue interaction in vivo: a plausible link to endometriosis development
Pelvic inflammation is a hallmark of endometriosis pathogenesis and a major cause of the disease's symptoms. Abnormal immune and inflammatory changes may not only contribute to endometriosis-major symptoms, but also contribute to ectopic endometrial tissue growth and endometriosis development. A major pro-inflammatory factors found elevated in peritoneal fluid of women with endometriosis and to be overexpressed in peritoneal fluid macrophages and active, highly vascularized and early stage endometriotic lesions, macrophage migration inhibitory factor (MIF) appeared to induce angiogenic and inflammatory and estrogen producing phenotypes in endometriotic cells in vitro and to be a possible therapeutic target in vivo. Using a mouse model where MIF-knock out (KO) mice received intra-peritoneal injection of endometrial tissue from MIF-KO or syngeneic wild type (WT) mice and vice versa, our current study revealed that MIF genetic depletion resulted in a marked reduction ectopic endometrial tissue growth, a disrupted tissue structure and a significant down regulation of the expression of major inflammatory (cyclooxygenease-2), cell adhesion (αv and β3 integrins), survival (B-cell lymphoma-2) and angiogenic (vascular endothelial cell growth) factorsrelevant to endometriosis pathogenesis, whereas MIF add-back to MIF-KO mice significantly restored endometriosis-like lesions number and size. Interestingly, cross-experiments revealed that MIF presence in both endometrial and peritoneal host tissues is required for ectopic endometrial tissue growth and pointed to its involvement in endometrial-peritoneal interactions. This study provides compelling evidence for the role of MIF in endometriosis development and its possible interest for a targeted treatment of endometriosis.
Data from "Linked Coupled Cluster Monte Carlo"
<p>We consider a new formulation of the stochastic coupled cluster method in terms of the similarity transformed Hamiltonian. We show that improvement in the granularity with which the wavefunction is represented results in a reduction in the critical population required to correctly sample the wavefunction for a range of systems and excitation levels and hence leads to a substantial reduction in the computational cost. This development has the potential to substantially extend the range of the method, enabling it to be used to treat larger systems with excitation levels not easily accessible with conventional deterministic methods.</p>
Simulation data for "Tuning Adhesion and Energy Dissipation in Polymer Films between Solid Surfaces via Grafting and Cross-Linking"
<p>LAMMPS input and data files, Jupyter notebooks used for the analysis of the MD simulations.</p>
Data and R code linked to the paper "The human metatarsal from Sedia del Diavolo"
<p>Data and R code to reproduce the results reported in "The human metatarsal from Sedia del Diavolo"</p>
Data from: Linking radial growth patterns and moderate-severity disturbance dynamics in boreal old-growth forests driven by recurrent insect outbreaks: a tale of opportunities, successes, and failures
<p>In boreal landscapes, emphasis is currently placed on close-to-nature management strategies, which aim to maintain the biodiversity and ecosystem services related to old-growth forests. The success of these strategies, however, depends on an accurate understanding of the dynamics within these forests. This study aims to reconstruct the disturbance and post-disturbance dynamics in boreal old-growth forests that are driven by recurrent moderate-severity disturbances. We studied eight old-growth forests in Québec, Canada, that has recorded recurrent and moderate to severe spruce budworm (Choristoneura fumiferana [Clem.]) outbreaks over the 20th century. To reconstruct the disturbance history and the post-disturbance dynamics of the study sites, we used dendrochronological data and k-means clustering to identify growth releases and growth patterns in the studied trees. We identified nine growth patterns; these patterns represented trees differing in age, size, and canopy layer, and indicated different tree histories. Spruce budworm outbreaks caused recurrent moderate-severity disturbances within the study sites. The canopy gaps created by these disturbances were filled mainly by understorey trees, which responded by single and significant increases in radial growth and height. In contrast, overstorey trees had little influence on gap filling; thus, trees were mostly from the dominant and codominant canopy layers. Our study underlines the resistance of boreal old-growth forests to recurrent and moderate-severity disturbances, as understorey trees can rapidly fill the resulting gaps. However, trees that are unable to attain the canopy following the disturbance then tend to remain in the lower canopy layers. Therefore, reaching the canopy represents a once-in-a-lifetime opportunity, where success or failure depends on a relatively short window of time. This gap-filling dynamic produces, however, a vertical structure that is often similar to the expected structure in even-aged forests. Our results highlight the efficacy of identifying tree growth patterns to reconstruct stand disturbance dynamics and contribute to developing closer to nature forest management strategies.</p>
Teaser | Introduction to Linked Open Data in Linguistics
<p>Professor Julia Bosque-Gil (University of Zaragoza, Spain) introduces the course she will lecture with Professor Thierry Declerck (German Research Center for Artificial Intelligence) in <em>Lisbon Summer School in Linguistics 2021</em>: "Introduction to Linked Open Data in Linguistics".</p> <p>Further information: https://clunl.fcsh.unl.pt/en/lisbon-summer-school-in-linguistics-2021/</p>
Fedora4: The Open Linked Data Platform
<p>Presentation at Open Repositories 2015 (OR2015), the 10th International Conference on Open Repositories, Indianapolis, Indiana, in session P1A: Linked Open Data (LOD). Note that high quality video files for this talk were not obtainable, so some video quality problems may be noticed.</p> <p>Linked Open Data has moved from being a buzzword to a fundamental building block of modern repositories and information systems. Its explosion, taking in this domain the form of scholarly and scientific datasets, publications, annotations, cultural heritage descriptions and other repository-based content, offers unprecedented opportunity for scientific and societal advancement. It is the interconnections that integrate systems and resources, however, that turn disparate ideas into unanticipated solutions.</p> <p>The Open Repositories community largely understands the value of linked data. The trouble has been in answering the question of “how?” to do this together, rather than "why?" do it at all. In order to be effective, we need to have solid guidelines, common practices, and well specified toolsets and products. A confluence of developments has opened the door to exactly this.</p> <p>In October of 2012, the initial W3C working draft of the Linked Data Platform 1.0 (LDP) document was published[2]. In July of 2012, the demand for a next-generation Fedora platform was channeled into the Fedora 4 (F4) project, which at the time was termed Fedora Futures. The alignment of these two stars set in motion events that provided both requirements and solutions for the community.</p>
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Data from: White plumage color as an honest indicator: feather macrostructure links reflectance with reproductive effort and success
<p class="normal1">The structural condition of feathers may generally have a decisive role in shaping the color properties of the plumage. However, the information content of structurally mediated color differences is poorly known. This makes it particularly hard to determine the meaning of color variation in pigment-free white plumage patches. The white wing patch of the collared flycatcher (<em>Ficedula albicollis</em>) is an important sexual trait, and changes in its reflectance are partly due to macrostructural condition. We used two years of macrostructural, reflectance and breeding data from both sexes to examine whether wing patch macrostructure lends information content to actual reflectance in terms of reproductive effort and success. Macrostructure strongly predicted actual reflectance in males but only weakly in females. Furthermore, in males, feather vane width was related positively to current year reproductive effort, and negatively to previous year reproductive effort. This indicates that macrostructurally mediated reflectance attributes may inform the receiver not only of actual reproductive capacity but also of individual quality via reproductive costs.</p>
The link to raw data
<p>The link to raw data is saved in word file.</p>
Linked collectors and determiners for: Janet Cosh Herbarium (WOLL) AVH data.
Natural history specimen data linked to collectors and determiners held within, "Janet Cosh Herbarium (WOLL) AVH data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb">https://bionomia.net/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb">https://gbif.org/dataset/2002f5f5-a2b6-43ee-bcc7-44811ae22acb</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: New data on winter crane flies (Diptera: Trichoceridae) of Korea with description of a new species.
Natural history specimen data linked to collectors and determiners held within, "New data on winter crane flies (Diptera: Trichoceridae) of Korea with description of a new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/fb9d499d-fe53-4f29-b670-2b2bb67d6412">https://bionomia.net/dataset/fb9d499d-fe53-4f29-b670-2b2bb67d6412</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/fb9d499d-fe53-4f29-b670-2b2bb67d6412">https://gbif.org/dataset/fb9d499d-fe53-4f29-b670-2b2bb67d6412</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Zoologische Staatssammlung Muenchen - International Barcode of Life (iBOL) - Barcode of Life Project Specimen Data.
Natural history specimen data linked to collectors and determiners held within, "Zoologische Staatssammlung Muenchen - International Barcode of Life (iBOL) - Barcode of Life Project Specimen Data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661">https://bionomia.net/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661">https://gbif.org/dataset/f29ab192-5964-40ae-a397-fa48ffdf0661</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: First detection of the adventive large rove beetle Ocypus nitens (Schrank) in Canada and an update of its Nearctic distribution using data generated by the public.
Natural history specimen data linked to collectors and determiners held within, "First detection of the adventive large rove beetle Ocypus nitens (Schrank) in Canada and an update of its Nearctic distribution using data generated by the public". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e5e13b4c-e903-4507-9f00-47d764c2fe16">https://bionomia.net/dataset/e5e13b4c-e903-4507-9f00-47d764c2fe16</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e5e13b4c-e903-4507-9f00-47d764c2fe16">https://gbif.org/dataset/e5e13b4c-e903-4507-9f00-47d764c2fe16</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Studies in Guatemalan Ensifera: New Glaphyrosoma species (Orthoptera: Anostostomatidae) and additional data for other described species.
Natural history specimen data linked to collectors and determiners held within, "Studies in Guatemalan Ensifera: New Glaphyrosoma species (Orthoptera: Anostostomatidae) and additional data for other described species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b5964523-7b88-4cf5-8400-4d08f276e32e">https://bionomia.net/dataset/b5964523-7b88-4cf5-8400-4d08f276e32e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b5964523-7b88-4cf5-8400-4d08f276e32e">https://gbif.org/dataset/b5964523-7b88-4cf5-8400-4d08f276e32e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: NatureServe Network Species Occurrence Data.
Natural history specimen data linked to collectors and determiners held within, "NatureServe Network Species Occurrence Data". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/7fd12114-9010-4c13-8f46-990fe04ca882">https://bionomia.net/dataset/7fd12114-9010-4c13-8f46-990fe04ca882</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/7fd12114-9010-4c13-8f46-990fe04ca882">https://gbif.org/dataset/7fd12114-9010-4c13-8f46-990fe04ca882</a>. Formatted as a Frictionless Data package.
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.