Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Computed tomography scanning as a tool for linking the skeletal and otolith-based fossil records of teleost fishes

Micro-computed tomography scanning (µCT scanning) now represents a standard tool for non-destructive study of internal or concealed structure in fossils. Here we report on otoliths found in situ during routine µCT scanning of three-dimensionally preserved skulls of Palaeogene and Cretaceous fishes. Comparisons are made with isolated otolith-based taxa in order to attempt correlations between the body fossil and otolith fossil records. In situ otoliths previously extracted mechanically from specimens of Apogon macrolepis and Dentex laekeniensis match our µCT models. In some cases, we find a high degree of congruence between previously independent taxonomic placements for otolith and skeletal remains (Rhinocephalus, Osmeroides, Hoplopteryx). Unexpectedly, in situ otoliths of the aulopiform Apateodus match isolated otoliths of Late Cretaceous age previously interpreted as belonging to gempylids, a group of percomorph fishes that do not appear in the body fossil record until the Palaeogene. This striking example of convergence suggests constraints on otolith geometry in pelagic predators. The otoliths of Apateodus show a primitive geometry for aulopiforms and lack the derived features of Alepisauroidea, the lizardfish clade to which the genus is often attributed. In situ otoliths of Early Cretaceous fishes (Apsopelix) are not well preserved, and we are unable to identify clear correlations with isolated otolith morphologies. We conclude that the preservation of otoliths suitable for µCT scanning appears intimately connected with the taphonomic history, lithological characteristics of surrounding matrix, and syn- and postdepositional diagenetic effects.

opencc-zeroJul 2021View details →

Data from: Pro-inflammatory immune response is linked to wintering habitat in a migratory shorebird

Migratory shorebirds (Charadrii) show a strong dichotomy in their breeding and wintering strategies: Arctic-breeding species typically spend the wintering season in marine habitats, while more southerly breeding species tend to do so in freshwater habitats where pathogens and parasites, particularly vector-borne blood parasites, are generally more abundant. Thus, it has been hypothesized that the former group may reduce their investment in immunity, but experimental data supporting this hypothesis are lacking. Moreover, whether this contrasting habitat selection can shape investments in immunocompetence among populations within a species is uncertain. We experimentally tested the hypothesis that there is a significant association between habitat occupancy and the strength of a pro-inflammatory immune response in Dunlins Calidris alpina, a widely distributed long-distance migratory shorebird that breeds in (sub-)arctic areas and winters mainly, but not exclusively, in coastal habitats. Overwintering Dunlins occupying inland freshwater and marine habitats at a similar latitude were captured and acclimated under identical conditions in outdoor aviaries. After an acclimation period, they were challenged with phytohemagglutinin to assess the pro-inflammatory immune response and its associated energetic costs, measured by basal metabolic rate (BMR) and body mass changes. We found that freshwater Dunlins exhibited a higher (63%) pro-inflammatory immune response than marine Dunlins. Although this difference did not involve significant BMR changes, the time course of body mass response differed between freshwater and marine individuals. Our findings point to the existence of different pro-inflammatory immune and energetic strategies associated to the wintering habitat. These intraspecific differences are likely due to population adaptation rather than phenotypic plasticity, where not only disease risk but also physiological adaptations to different salinity levels could play an important role.

opencc-by-4.0Aug 2021View details →

Data and code for figures: Coherent Terahertz-to-Microwave Link Using Electro-Optic-Modulated Turing Rolls

This dataset contains the figures and data presented in the paper <Coherent Terahertz-to-Microwave Link Using Electro-Optic-Modulated Turing Rolls>.

opencc-zeroAug 2021View details →

Data from: A tale of two seasons: the link between seasonal migration and climatic niches in passerine birds.

The question of whether migratory birds track a specific climatic niche by seasonal movements has important implications for understanding the evolution of migration, the factors affecting species' distributions and the responses of migrants to climate change. Despite much research, previous studies of bird migration have produced mixed results. However, whether migrants track climate is only one half of the question, the other being why residents remain in the same geographic range year-round. We provide a literature overview and test the hypothesis of seasonal niche tracking by evaluating seasonal climatic niche overlap across 437 migratory and resident species from eight clades of passerine birds. Seasonal climatic niches were based on a new global dataset of breeding and non-breeding ranges. Overlap between climatic niches was quantified using ordination methods. We compared niche overlap of migratory species to two null expectations, 1) a scenario in which they do not migrate and 2) in comparison to the overlap experienced by closely related resident species, while controlling for breeding location and range size. Partly in accordance with the hypothesis of niche tracking, we found that the overlap of breeding vs. non-breeding climatic conditions in migratory species was greater than the overlap they would experience if they did not migrate. However, this was only true for migrants breeding outside the tropics and only relative to the overlap species would experience if they stayed in the breeding range year-round. In contrast to the hypothesis of niche tracking, migratory species experienced lower seasonal climatic niche overlap than resident species, with significant differences between tropical and non-tropical species. Our study suggests that in seasonal non-tropical environments migration away from the breeding range may serve to avoid seasonally harsh climate; however, different factors may drive seasonal movements in the climatically more stable tropical regions.

opencc-by-4.0Jun 2021View details →

Adopt a Pixel 3 km: A Multiscale Data Set Linking Remotely Sensed Land Cover Imagery with Field Based Citizen Science Observation

These datasets were used in an article submitted to the journal Frontiers in Climate in 2021: <a href="https://www.frontiersin.org/articles/10.3389/fclim.2021.658063/full">https://www.frontiersin.org/articles/10.3389/fclim.2021.658063/full</a> Further supplemental links (including general information about GLOBE data) can be accessed at <a href="https://observer.globe.gov/get-data/mosquito-habitat-data">https://observer.globe.gov/get-data/mosquito-habitat-data</a>.

opencc-by-4.0Oct 2021View details →

Data linked to the "Liana optical traits increase tropical forest albedo and reduce ecosystem productivity" paper

Data necessary to reproduce the findings of the aforementionned paper

opencc-by-4.0Sep 2021View details →

A neural circuit linking two sugar sensors regulates satiety-dependent fructose drive in Drosophila (raw data)

This is the raw numerical data used in Musso et al., 2021, A neural circuit linking two sugar sensors regulates satiety-dependent fructose drive in Drosophila.

opencc-by-4.0Nov 2020View details →

Tough Tables: Carefully Evaluating Entity Linking for Tabular Data

Tough Tables (2T) is a dataset designed to evaluate table annotation approaches in solving the CEA and CTA tasks. The dataset is compliant with the data format used in <a href="https://www.cs.ox.ac.uk/isg/challenges/sem-tab/2019/index.html">SemTab 2019</a>, and it can be used as an additional dataset without any modification. The target knowledge graph is DBpedia 2016-10. Check out the <a href="https://github.com/vcutrona/tough-tables">2T GitHub repository</a> for more details about the dataset generation. New in v3.0: We release the updated version of 2T! The target knowledge graphs are DBpedia <a href="http://downloads.dbpedia.org/wiki-archive/downloads-2016-10.html">2016-10</a> and Wikidata <a href="https://zenodo.org/record/6643443">20220521</a>. Starting from this version, the dataset is split into valid and test sets. This work is based on the following paper: <blockquote> Cutrona, V., Bianchi, F., Jimenez-Ruiz, E. and Palmonari, M. (2020). Tough Tables: Carefully Evaluating Entity Linking for Tabular Data. ISWC 2020, LNCS 12507, pp. 1–16. </blockquote> Note on License: This dataset includes data from the following sources. Refer to each source for license details: - Wikipedia https://www.wikipedia.org/ - DBpedia https://dbpedia.org/ - Wikidata https://www.wikidata.org/ - SemTab 2019 https://doi.org/10.5281/zenodo.3518539 - GeoDatos https://www.geodatos.net - The Pudding https://pudding.cool/ - Offices.net https://offices.net/ - DATA.GOV https://www.data.gov/ THIS DATA IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Changelog: v3.0 <ul> <li>Both datasets require SemTab2020 CEA format (tab_id, row_id, col_id, entity). <ul> </ul> </li> <li>Tables IDs and artificial noise values differ from previous versions.</li> <li>Datasets are split into Valid and Test sets of tables.</li> <li>New GT for ToughTables-WD (2T_WD) <ul> <li>Entities Q23772518 and Q7327323 have been removed because they are no longer represented in WD</li> <li>Updated ancestor/descendant hierarchies to evaluate CTA.</li> </ul> </li> <li>Evaluation scripts are provided with the data sets.</li> </ul> v2.0 <ul> <li>New GT for 2T_WD <ul> <li>A few entities have been removed from the CEA GT, because they are no longer represented in WD (e.g., dbr:Devonté points to wd:Q21155080, which does not exist)</li> <li>Tables codes and values differ from the previous version, because of the random noise.</li> <li>Updated ancestor/descendant hierarchies to evaluate CTA.</li> </ul> </li> </ul> v1.0 <ul> <li>New Wikidata version (2T_WD)</li> <li>Fix header for tables CTRL_DBP_MUS_rock_bands_labels.csv and CTRL_DBP_MUS_rock_bands_labels_NOISE2.csv (column 2 was reported with id 1 in target - NOTE: the affected column has been removed from the SemTab2020 evaluation)</li> <li>Remove duplicated entries in tables</li> <li>Remove rows with wrong values (e.g., the Kazakhstan entity has an empty name "''")</li> <li>Many rows and noised columns are shuffled/changed due to the random noise generator algorithm</li> <li>Remove row "Florida","Floorida","New York, NY" from TOUGH_WEB_MISSP_1000_us_cities.csv (and all its NOISE1 variants)</li> <li>Fix header of tables: <ul> <li>CTRL_WIKI_POL_List_of_current_monarchs_of_sovereign_states.csv</li> <li>CTRL_WIKI_POL_List_of_current_monarchs_of_sovereign_states_NOISE2.csv</li> <li>TOUGH_T2D_BUS_29414811_2_4773219892816395776___videogames_developers.csv</li> <li>TOUGH_T2D_BUS_29414811_2_4773219892816395776___videogames_developers_NOISE2.csv</li> </ul> </li> </ul> v0.1-pre <ul> <li>First submission. It contains only tables, without GT and Targets.</li> </ul>

opencc-zeroJan 2023View details →

Biomass data to accompany Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance

<ul> <li>The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance.</li> <li>Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multi-level analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations.</li> <li>We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost.</li> <li>Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD and that the fitness cost associated with resistance in this species is likely a by-product of genetic-hitchhiking.</li> </ul>

opencc-zeroJan 2023View details →

Data from: Observed and dark diversity dynamics over millennial time scales: Fast-life history traits linked to expansion lags of plants in northern Europe

Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity—the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.

opencc-zeroFeb 2023View details →

Linked Data Transformation archivischer Metadaten

Die Daten gehören zu einer Masterarbeit mit dem Titel "<a href="https://doi.org/10.18452/27976" target="_blank" rel="noopener">Linked Data Transformation archivischer Metadaten</a>", die im Rahmen des gemeinsamen Studienganges  "Digitales Datenmanagement" der Humboldt-Universität zu Berlin und der Fachhochschule Potsdam erstellt wurde. Der Datensatz enthält archivischen Metadaten von zwei Beständen des <a href="https://www.bundesarchiv.de/">Bundesarchivs </a>als XML- und RDF-Dateien. Die XML-Dateien werden vom Bundesarchiv im Format EAD(DDB) öffentlich abrufbar bereitgestellt. Die RDF-Dateien wurden unter Verwendung der Ontologie <a href="https://www.ica.org/standards/RiC/ontology.html">RiC-O</a> im Rahmen der Masterarbeit erzeugt. Das der Transformation zugrunde liegende Mapping zwischen EAD(DDB) und RiC-O ist ebenfalls Bestandteil des Datensatzes. Zusätzlich umfasst der Datensatz je eine maschinenlesbare sowie je eine menschenlesbare Dokumentation der aus XML- und RDF-Dateien bestehenden Datensammlung. Weitere Informationen zu den einzelnen Datensätzen sind in der readme.md enthalten.

opencc-by-4.0Mar 2023View details →

Data from: Balanced mitochondrial function at low temperature is linked to cold adaptation in Drosophila species

Data from: Balanced mitochondrial function at low temperature is linked to cold adaptation in Drosophila species

opencc-zeroMar 2023View details →

Data for: Link between glucose metabolism and EMT drives triple negative breast cancer migratory heterogeneity

Intracellular and environmental cues result in heterogeneous cancer cell populations with different metabolic and migratory behaviors. While glucose metabolism and EMT have previously been linked, we aim to understand how this relationship fuels cancer cell migration. We show that while glycolysis drives single-cell migration in confining microtracks, fast and slow cells display different migratory sensitivities to glycolysis and oxidative phosphorylation inhibition. Phenotypic sorting of highly and weakly migratory subpopulations (MDA+, MDA-) reveals that more mesenchymal, highly migratory MDA+ preferentially use glycolysis while more epithelial, weakly migratory MDA- utilize mitochondrial respiration. These phenotypes are plastic and MDA+ can be made less glycolytic, mesenchymal, and migratory and MDA- can be made more glycolytic, mesenchymal, and migratory via modulation of glucose metabolism or EMT. These findings reveal an intrinsic link between EMT and glucose metabolism that controls migration. Identifying mechanisms fueling phenotypic heterogeneity is essential to develop targeted metastatic therapeutics.

opencc-by-4.0Apr 2023View details →

Data Collection Template linking MAED to OSeMOSYS

Data Collection Template linking MAED to OSeMOSYS

opencc-by-4.0Jun 2023View details →

Data and code for Keller et al. (2023) "Links between large igneous province volcanism and subducted iron formations," published in Nature Geoscience

Data and computer code used to generate results for Keller et al. (2023) "Links between large igneous province volcanism and subducted iron formations." A readme file in the folder gives a description for each file. Data may also be accessed from the article link on the publisher's website.

FIGURE 16. Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

FIGURE 16. Austroniscus brandtae n. sp., manca stage 1 (SMF 57955, R7R). Confocal laser scanning microscopy images. A, habitus, dorsal view. B, habitus, ventral view. C, habitus, lateral view. Scale bars: A–C = 200 µm.

FIGURE 14. Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

FIGURE 14. Austroniscus brandtae n. sp., paratype female (SMF 57930, R4E). Confocal laser scanning microscopy images. A, habitus, dorsal view. B, habitus, ventral view. C, habitus, lateral view. Scale bars: A–C = 200 µm.

FIGURE 12. Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

FIGURE 12. Austroniscus brandtae n. sp.; A–I, paratype female (SMF 57930, R4E). A, habitus, dorsal view, detail: rostrum and pereonite 1 lateral margin. B, habitus, lateral view. C, Antennula. D, Operculum. E, Pleotelson, ventral view. F, Uropod. G, Pleopod III, H, Pleopod IV. I, Pleopod V. Scale bar: A–B, E = 200 µm, C–D, F–I = 100 µm.

FIGURE 13. Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

FIGURE 13. Austroniscus brandtae n. sp.; A–I, paratype female (SMF 57930, R4E). A, habitus, dorsal view. B, habitus, lateral view. C–I, Pereopods I–VII (pereopod V ischium with epibiont ciliates exemplary illustrated on ventral margin). Scale bar: A–B = 200 µm, C–I = 100 µm.

FIGURE 15. Austroniscus brandtae n in Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench

FIGURE 15. Austroniscus brandtae n. sp., paratype female (SMF 57930, R4E). Confocal laser scanning microscopy images. A, cephalothorax, dorsal view. B, cephalothorax, ventral view. C, Pleotelson and Operculum, ventral view. D, right uropod, ventral view. E, left uropod, ventral view. Scale bars: A–E = 200 µm.