Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
258
datasets available to search
ShareScore release 0.9.0
Dataset results
258 results for “caging”
Salt Marsh Crab Caging Experiment, Virginia 2021
Herbivore fronts can alter plant traits (chemical and/or morphological features) and performance via grazing. Yet, herbivore-driven trait alterations are rarely considered when assessing how these fronts shape ecosystems, despite the critical role that plant performance plays in ecosystem functioning. We evaluated herbivore fronts created by the purple marsh crab, Sesarma reticulatum, as it consumes the cordgrass, Spartina alterniflora, in Virginian salt marshes. Sesarma fronts form at the head of tidal creeks and move inland, creating a denuded mudflat between the tall-form Spartina low marsh (trailing edge) and the short-form Spartina high marsh (leading edge). We quantified Sesarma front migration rate, tested if Sesarma herbivory altered geomorphic processes and Spartina traits at the trailing and leading edges, and examined how these trait changes persisted through the final 8 weeks of the growing season. Sesarma front migration in our region is two times slower than fronts in the Southeast U.S., and Spartina retreat rate at the leading edge is greater than the revegetation rate at the trailing edge. Sesarma fronts lowered elevation, and decreased sediment shear strength at the trailing edge, while having no impact on soil organic matter and bulk density at either edge. At the leading edge, Sesarma grazing reduced Spartina growth traits and defensive ability, and trait changes persisted through the remaining growing season. At the trailing edge, however, Sesarma grazing promoted belowground biomass production, and had limited to no effect on growth or defensive traits. We show that herbivore fronts negatively impact saltmarsh plant traits at their leading edge, potentially contributing to front propagation. In contrast, plants at the trailing edge were more resistant to herbivore grazing, and may enhance resilience through elevated belowground biomass production. Future work should consider herbivore-driven plant trait alterations in the context of herbivore fr
Random-Phase Approximation in Many-Body Noncovalent Systems: Methane in a Dodecahedral Water Cage
<p>Supplementary information and raw data for Random-Phase Approximation in Many-Body Noncovalent Systems: Methane in a Dodecahedral Water Cage. </p>
Transcription initiation peaks based on FANTOM5 CAGE data on hg38 and mm10
<p><strong>Overview</strong></p> <p>Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the re-processed (re-aligned) FANTOM5 data, upon hg38 (GRCh38) and mm10 (GRCm38), obtained from below:</p> <ul> <li>http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v1/basic/</li> <li>http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/</li> </ul> <p>The same parameters to the ones used in the previous paper (Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014) was used.</p> <p> </p> <p><strong>Data files</strong></p> <p>Four data files per assembly are prepared as below.</p> <ol> <li>tag cluster in the original definition (*.tc.bed.gz)</li> <li>full set of DPI peaks (*.tc.decompose_smoothing_merged.bed.gz)</li> <li>permissive set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz)</li> <li>robust set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz)</li> </ol> <p> </p> <p><strong>Acknowledgement</strong></p> <p>This data set is supported by Research Grant from MEXT to RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.</p>
Fracture Caging in a Porous Lab Fault: Complementary Data
<p>This dataset is complementary experiment data to the already published dataset (doi.org/10.5281/zenodo.10951458) related to fracture caging in shear. It includes the viscosity and flow rate variables in fracture caging study in a porous lab fault. The ReadMeFirst.txt file contains the necessary information to understand the data structure. </p> <p>Three more experiments are added to this complementary experiment dataset. Details are provided. </p>
Datasets underlying the paper 'Chemotactic self-caging in active emulsions'
<p>Datasets supporting the figures 3-5 in 'Chemotactic self-caging in active emulsions' (in press, see also https://arxiv.org/abs/2012.05170)</p>
Mice infected with High shedder S. mansoni parasites from cross A - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 2/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with High shedder S. mansoni parasites from cross A - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with S. mansoni High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 3/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p> <p> </p>
Mice infected with High shedder S. mansoni parasites from cross B - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 6/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross A - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 5/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross A - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 4/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.1 / 2C.2 / 2C.3).
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.1/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.</p>
Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.4 / 2C.5).
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.2/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.</p>
Mice infected with High shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 7/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 9/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross B - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 8/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Near-miss Symmetric Polyhedral cages off files
<p>The file contains the coordinates of the nodes and faces of the all the near-miss symmetric p-cages with polygonal faces ranging from hexagon to 20-gon. The off file can be viewed using tools such as geomview or antiview.</p>
Salamander survival and growth cage experiment at the Coweeta Hydrologic Laboratory, Otto, NC
Climate change is predicted to alter biotic communities and, as a result, cause changes in ecosystem processes. Such predictions assume that future communities will lack species capable of compensating for the loss of other species. In southern Appalachian headwater streams, abundant larval Black-bellied Salamanders (Desmognathus quadramaculatus) represent a significant standing crop of nitrogen (N) and phosphorus (P). Desmognathus quadramaculatus are projected to be extirpated from the southern Appalachian highlands under most climate change scenarios, which would result in the loss of most salamander standing crop of limiting nutrients unless other species compensate for the loss of D. quadramaculatus biomass. Eurycea cirrigera, which has an abundant congener Eurycea wilderae already in the headwaters, and Gyrinophilus porphyriticus, which currently occurs in low densities in the headwaters, are projected to remain within southern Appalachian highlands. We used field cages to measure (1) the amount of compensatory survival and growth Eurycea would show in the absence of the larger, predatory D. quadramaculatus, and (2) whether replacement of D. quadramaculatus by G. porphyriticus, which is known to be a more efficient predator, would reduce Eurycea and total salamander biomass.
Transcription initiation peaks based on FANTOM5 CAGE data on rn6, canFam3, and galGal5
<p><strong>Overview</strong></p> <p>Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the FANTOM5 data of rat (rn3), dog (canFam3), and chicken (galGal5):</p> <ul> <li>https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/</li> </ul> <p>The same parameters to the ones used in the previous paper (Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014) was used.</p> <p><strong>Data files</strong></p> <p>Four data files per assembly are prepared as below.</p> <ol> <li>tag cluster in the original definition (*.tc.bed.gz)</li> <li>full set of DPI peaks (*.tc.decompose_smoothing_merged.bed.gz)</li> <li>permissive set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz)</li> <li>robust set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz)</li> </ol> <p><strong>Acknowledgement</strong></p> <p>This data set is supported by Research Grant from MEXT to RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Integrative Medical Sciences, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.</p>
Figures 14–15. Leaf beetle rearing cages. 14 in Biology of the sineguelas leaf beetle, Podontia quatuordecimpunctata (L.) (Chrysomelidae: Galerucinae: Alticini), on Spondias purpurea L. (Anacardiaceae) in the Philippines
Figures 14–15. Leaf beetle rearing cages. 14) Sineguelas leaf beetle rearing cage with sineguelas (Spondias purpurea (L., 1767) seedling as food and soil at the base of the twig for pupation. 15) Rearing cages where the study of its biology was conducted. (Photographs courtesy of SLB project).
FIGURE 8 in Comparison between Atlantic salmon Salmo salar post-smolts reared in open sea cages and in the Preline raceway semi-closed containment aquaculture system
FIGURE 8 Mean (S.E.; n = 30) relative gene transcription values for (a) mef2c () Reference, and () Preline, (b) gata4 () Reference, and () Preline and (c) vegf () Reference, and () Preline using ef1α as standard in Salmo salar heart, both in fresh water and after rearing in Preline semiclosed containment system (S-CCS;) and reference group open pen () for 4 months in seawater. Significant differences between groups are indicated by different lower-case letters
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.