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.
10,735
datasets available to search
ShareScore release 0.9.0
Dataset results
10,735 results for “dependence”
Data from: Deer-mediated ecosystem service vs. disservice depends on forest management intensity
MANUSCRIPT ABSTRACT <p>As global terrestrial biodiversity declines via land-use intensification, society has placed increasing value on non-commercial species as providers of ecosystem services. Yet, many deer species and non-crop plants are perceived negatively when they decrease crop productivity, leading to reduced economic gains and human-wildlife conflict. We hypothesized that deer provide an ecosystem service in forest plantations by controlling competition and promoting crop-tree growth, although the effects of herbivory may depend on forest management intensity. If management negatively affects foraging habitat at local and landscape scales, then we expected browsing to shift to less-palatable crop trees. To test these hypotheses, we established a 5-year experiment that manipulated early forest management intensity via herbicide treatments and access of two deer species to vegetation via exclosures. Contrary to our hypothesis, deer provided an ecosystem service at high management intensities and a disservice occurred with low-intensity management. Crop-tree growth and survival was greatest when herbivory and herbicides suppressed broadleaf regeneration. In contrast, crop-tree growth was lowest when broadleaf vegetation was retained and crop-trees were subject to both browse damage and competition. We found a positive, yet variable, association between deer detections and stand- and landscape-scale broadleaf habitat, and despite initial reductions in forage, herbivory pressure was similar among management intensities. When broadleaf vegetation was suppressed by herbicides and herbivory, selection of herbaceous forage by deer intensified, likely aiding in the service. Overall, our findings indicate that the effects of vegetation management for promoting timber production are highly dependent on the presence of large herbivores.</p> <p>Synthesis and applications: Although deer are thought to reduce crop productivity in many systems, we found that herbivory switched from reducing crop tree growth where non-crop vegetation was retained, to promoting crop tree growth when both herbivory and herbicides suppressed competing vegetation. However, the provision of this ecosystem service is likely contingent on the amount of forage available in the landscape and subsequent foraging pressure. We conclude that nature's capacity to provide ecosystem services depends on the intensity of management at local and landscape scales.</p>
LabelGit: A dataset for software repositories classification using attributed dependency graphs
<p>A dataset for software repositories classification using attributed dependency graphs</p>
Supplementary material for "Investigating phoneme-dependencies of spherical voice directivity patterns"
<p>The .pdf file contains</p> <ul> <li>general information on the voice directivity files in the SOFA format</li> <li>information on the indices and names of the SOFA-files</li> </ul> <p> </p> <p>The .zip files contain</p> <ul> <li>voice directivities in the SOFA format sampled on the sparse measuring grid</li> <li>voice directivities in the SOFA format upsampled to a dense grid</li> </ul> <p> </p> <p>The Matlab script provides</p> <ul> <li>an example reading a dataset, performing spatial upsampling if required, and creating some basic plots. </li> </ul>
Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection
<p>Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community impact the susceptibility of amphibian hosts to infection by <em>Batrachochytrium</em> <em>dendrobatidis</em>, one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (<em>Acris</em> <em>crepitans</em>), prior to exposing these animals to <em>Batrachochytrium</em> <em>dendrobatidis</em> under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, <em>Stenotrophomonas</em> <em>maltophilia</em>, and one in which the frog's skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of <em>Bd</em> infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to <em>Bd</em> infection and chytridiomycosis. However, we also predicted that this interaction would be temperature-dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in <em>Bd</em>-exposed frogs. Whether temperature impacted survival, however, differed among our skin microbial treatment groups, with animals having more <em>S</em>. <em>maltophilia</em> on their skin surviving longer at 14 but not at 26 °C. Our results suggest that temperature was the predominant factor influencing <em>Bd</em>'s ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host's ability to survive (i.e., tolerate) a heavy <em>Bd</em> infection.</p>
Evolution under pH stress and high population densities leads to increased density-dependent fitness in the protist Tetrahymena thermophila
<p>Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species <em>Tetrahymena thermophila</em>, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (<em>r<sub>0</sub></em>). Overall, evolution at low pH led to the convergence of <em>r<sub>0</sub></em> and intraspecific competitive ability (<em>α</em>) across the four genotypes. Given the strong correlation between <em>r<sub>0</sub></em> and <em>α</em>, we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in <em>r<sub>0</sub></em> , or decrease of <em>α</em>, depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.</p> <p> </p>
Data from Churan et al. Action-dependent processing of self-motion in parietal cortex of macaque monkeys
<p><strong>Animals</strong></p> <p>Two adult male monkeys (macaca mulatta) participated in the study. Single-unit recordings were done using standard tungsten microelectrodes (FHC, Bowdoin, USA) with an impedance of ~2 MΩ at 1 kHz that were positioned by an hydraulic micromanipulator (MO-95, Narishige, Tokyo, Japan). A stainless-steel guiding tube was used for transdural penetration and support of the electrode. The neuronal signal was processed using a commercial system (Alpha Omega, Nof HaGalil, Israel). It was band-pass filtered (cut-off frequencies at 500 Hz and 8000 Hz) and sampled at 44 kHz.</p> <p><strong>Apparatus</strong></p> <p>During recordings, the monkeys were sitting head-fixed in a primate chair in a dark room, and their eye-position was monitored at 1000 Hz using a video-based eye tracker (EyeLink 1000, SR Research, Ottawa, Canada). The chair was positioned at a distance of 97 cm from a semi-transparent screen (size 160 cm x 90 cm, subtending the central 79 deg x 50 deg of the visual field) on which the visual stimuli were back-projected using a PROPixx-projector (VPixx Technologies, St-Bruno de Montarville, Canada) running at a resolution of 1920 x 1080 pixels and at a frame rate of 100 Hz. A custom-made touch sensor (length 10 cm, diameter 1 cm) was integrated into the monkey chair in front of the monkey and its status was monitored online at a sampling rate of 1 kHz.</p> <p><strong>Data processing</strong></p> <p>Single units were isolated using a semi-manual spike sorter (Plexon Inc, Dallas, Texas). To this end we used a threshold on the electrode signal that was set manually to separate the action potentials from noise. The samples that exceeded the threshold were further analyzed using principal components as well as other features that were derived from the signal (like local maxima and minima). Then clusters of samples with similar properties were identified visually and each defined as representing a single unit. For a detailed description of the sorting process see the offline User Guide (Plexon, 2020).</p> <p>Further description of the Methods, see: Churan et al. 2021, doi: 10.1152/jn.00049.2021</p> <p><strong>Data:</strong></p> <p>The file '<strong>data_active_passive.mat</strong>' contains following variables:</p> <p>monkey: code for the tested monkey (1=monkey S, 2=monkey O)</p> <p>baseline: Mean and standard deviation of the activity in a time window of 150 ms to 20 ms before the press of the button.</p> <p>reaction: Mean time between the switch of the color of the fixation point from red to green and the time of the button press.</p> <p>anti_p: Significance of a one sided t-test between the baseline activity and activity 200 ms to 0 ms prior to the onset of stimulus motion.</p> <p>p_win (a (1-3),b (1-3),c (1-3),n(1-110)): 4D matrix containing p-values of t-tests</p> <p>a:</p> <p>1: Was preparatory activity significantly higher in the passive relative to the active condition?</p> <p>2: Was preparatory activity significantly lower in the passive relative to the active condition?</p> <p>3: Was the tonic motion response (200 ms to 500 ms after motion onset) significantly different between the active and the passive conditions?</p> <p>b:</p> <p>1: Calculation was made based on all motion directions</p> <p>2: Calculation was made based on the preferred motion direction</p> <p>3: Calculation was made based on the flanking motion directions</p> <p>c:</p> <p>1: Calculation was made based on all presented delays</p> <p>2: Calculation was made based on the shorter set of delays (500 ms to 700 ms)</p> <p>3: Calculation was made based on the longer set of delays (701 ms to 1000 ms)</p> <p>n: number of the investigated neuron</p> <p>psth_alldir: cell array containing the PSTHs (obtained by convolving each spike with a Gaussian as described in the manuscript) in a time window between 1000 ms before and 800 ms after the onset of motion (in 1 ms steps). PSTHs were calculated based on data from all tested directions. Each cell array consists of 4 elements containing different conditions:</p> <p>1: active condition</p> <p>2: passive condition shorter set of delays (500 ms to 700 ms)</p> <p>3: passive condition longer set of delays (701 ms to 1000 ms)</p> <p>4: passive condition all delays</p> <p>psth_bestdir: same as above - using only the preferred direction</p> <p>psth_nbestdir: same as above - using only the flanking directions</p> <p>d_alldir: cell array containing the continuous d-prime (as described in the manuscript) in a time window between 1000 ms before and 800 ms after the onset of motion (in 1 ms steps). d' were calculated based on data from all tested directions. Each cell array consists of 4 elements containing different conditions:</p> <p>1: active condition</p> <p>2: passive condition shorter set of delays (500 ms to 700 ms)</p> <p>3: passive condition longer set of delays (701 ms to 1000 ms)</p> <p>4: passive condition all delays</p> <p>d_bestdir: same as above - using only the preferred direction</p> <p>d_nbestdir: same as above - using only the flanking directions</p> <p>The file '<strong>timecourse_preparatory.mat</strong>' contains the cell array 'd_alldir_preparatory' that consists of 201 elements. Each of the elements contains PSTHs of 23 neurons that have exhibited significant preparatory activity in the passive condition in a time window 1000 ms to 0 ms before the motion onset. Each of the 201 elements describes a specific range of delays between button press and motion onset. This delay range is always a 100 ms wide sliding window, e.g. the element 1 represents delays between 500 and 600 ms, in element 2, the delays are between 501 and 601 ms and so on with the last element (201) representing delays between 700 and 800 ms.</p> <p>Some example code that re-creates most of the figures from the manuscript and that may serve as a starting point for further exploration of the data is available on request from the corresponding author.</p>
Conversion of fluoride and chloride catalized by SAM-dependent fluorinase in Nocardia brasiliensis
<p>Data sets show the following reactions:</p> <p>- Fluorinase catalized conversion of fluoride and SAM to 5'-FDA and L-methionine (Explanation file: Figure 2).</p> <p>- Fluorinase catalyzed conversion of chloride and SAM to 5’-ClDA and L-methionine in the presence of L-amino acid oxidase (Explanation file: Figure 3).</p>
QD-AMVA: Evaluating Systems with Queue-Dependent Service Requirements - Data
<p>The data part of this release support the results <br /> presented in the paper <br /> "QD-AMVA: Evaluating Systems with Queue-Dependent Service<br /> Requirements", by G. Casale, J. F. Perez, and W. Wang, accepted <br /> to IFIP Performance 2015. </p> <p>When referring to the dataset or scripts please cite the paper above. </p> <p>The scripts released with the above paper can be found at https://zenodo.org/record/18887</p> <p> </p>
Supporting data: Grain-dependent responses of mammalian diversity to land-use and the implications for conservation set-aside
<p>Camera trap and live trap datasets underlying the analyses in an <em>Ecological Applications </em>paper (http://onlinelibrary.wiley.com/doi/10.1890/15-1363/abstract), provided in .csv format. Each row consists of a single trap night at a given location, with species in different columns. Old-growth forest, logged forest and oil palm plantation locations have the prefixes "Old", "Log" and "Palm", respectively. Values in each cell are the number of independent captures, as defined in the paper. </p>
X-ray diffraction images for the H145E mutant of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis.
<p>X-ray diffraction images of the H145E mutant (prefixed h145e) which were collected in October 1995 using a graphite-monochromated copper K-alpha rotating anode source (wavelength 1.5418 Å) with a Marresearch 90 cm image plate detector at a distance of 120 mm from the crystal. The data were collected at room temperature in two passes, each consisting of 100 one degree rotations of the crystal. Each image had an exposure time of 20 minutes. The crystal was rotated in the capillary tube prior to collection of the second pass in order to record the 'blind' region of the diffraction pattern and this set of images is prefixed h145eb. </p>
X-ray diffraction images for the H145Q mutant of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis.
<p>X-ray diffraction images collected from one crystal at room temperature using a rotating anode copper source (wavelength 1.5418 Å) and a 30 cm Marresearch image plate detector. The crystal-to-detector distance was 150 mm and a 90 mm image plate scan radius was used. Each of the 60 images had an exposure time of 20 minutes and corresponds to a 3 degree phi-rotation of the crystal. Diffraction extends to about 3.3 Å resolution. </p>
Data + Analyses: "Gaze-dependent Coding of Somatosensory Reach Targets after Effector Movement: Testing the Impact of Online Information, Movement Timing, and Target Distance"
<p>This upload contains the experiment scripts (written in Presentation), data, and analyses (performed with MATLAB and SPSS) underlying the publication<strong> </strong>by Mueller & Fiehler (2017). <em>PloS one</em>. doi:<strong>10.1371/journal.pone.0180782</strong></p>
Research data supporting "Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils"
<p>Research data supporting the publication:</p> <p>Wang, S.-T. et al., 2017, Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils, ACS Nano, http://dx.doi.org/10.1021/acsnano.7b02325</p>
Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context
<p><span>The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with frontotemporal dementia increase tau aggregation propensity and disrupt its endogenous microtubule-binding activity. However, the structural relationship between aggregation propensity and biological activity remains unclear. We employed a multi-disciplinary approach, including computational modeling, NMR, cross-linking mass spectrometry, and cell models to engineer tau sequences that modulate its structural ensemble. Our findings show that substitutions near the conserved 'PGGG' </span><span>β</span><span>-turn motif informed by tau isoform context reduce tau aggregation in vitro and cells and can even counteract aggregation from disease-associated proline-to-serine mutations. Engineered tau sequences maintain microtubule binding and explain why 3R isoforms exhibit reduced pathogenesis compared to 4R. We propose a simple mechanism to reduce the formation of pathogenic tau species while preserving biological function, thus offering insights for therapeutic strategies aimed at reducing tau protein misfolding in neurodegenerative diseases.</span></p> <p><strong>Description of Source Data and Supplementary Data</strong>: All MD, NMR (peptide and tauRD), ThT, XL-MS, MT stabilization, MT:tau modeling, and cell-based aggregation data are available in the Source_Data directory as Data S1, Data S2, Data S3, Data S4, Data S5, Data S6, Data S7, and Data S8, respectively. Supplementary Data for raw MD trajectory files, structure files for MSM modeling and validation file, and tau:MT modeling are available as "Supplementary_Data_MD_Trajectories_Structures", "Supplementary_Data_MSM_models_Structures" and "Supplementary_Data_MT-tau_complex_models", respectively."</p>
Package and Dependency Metadata for CZI Hackathon: Mapping the Impact of Research Software in Science
<p>A collection of useful datasets extracted from <a href="https://packages.ecosyste.ms">https://packages.ecosyste.ms</a> and <a href="https://repos.ecosyste.ms/">https://repos.ecosyste.ms</a> for use at the CZI Hackathon: Mapping the Impact of Research Software in Science.</p><p>All data is provided as NDJSON (new line delimited JSON), each line represents a valid JSON object, and they are separated by newline characters. There are <a href="https://pypi.org/project/ndjson/">python</a> and <a href="https://www.rdocumentation.org/packages/ndjson/versions/0.9.0/topics/stream_in">R</a> libraries for reading these files, or you can maually read each line and parse each line as a single JSON object.</p><p>Each ndjson file has been compressed with gzip (actual command: `tar -czvf`) to reduce download size, they expand to significantly bigger files after extraction.</p><h4>Package Data</h4><p>Package names from cran, bioconductor and pypi that have been parsed by the <a href="https://github.com/chanzuckerberg/software-mentions">software-mentions</a> project (data: <a href="https://datadryad.org/stash/dataset/doi:10.5061/dryad.6wwpzgn2c">https://datadryad.org/stash/dataset/doi:10.5061/dryad.6wwpzgn2c</a>) are collected together with their latest release at time of publishing along with the names of their dependencies, those dependency names have then also been recursively fetched with latest release and dependencies until the full list of transitive dependencies is included. </p><p>Note: This approach uses a simplified method of dependency resolution, always picking the latest version of each package rather than taking into account each dependencies specific version range requirements, this is primarily due to time constraints and allows all software ecosystems to be processed in the same way. A future improvement would be to use each package ecosystem's specific dependency resolution algorithm to compute the full transitive dependency tree for each mentioned software package.</p><h4>GitHub Data</h4><p>Two different approaches were taken for collecting data for referenced GitHub mentions:</p><p>1. `github.ndjson` is metadata for each repository from GitHub, including "manifest" files which are known files that contain dependency information for a project such as requirements.txt, DESCRIPTION and package.json, parsed using <a href="https://github.com/ecosyste-ms/bibliothecary">https://github.com/ecosyste-ms/bibliothecary</a>, which may include transitive dependencies that have been discovered in a `lockfile` within the repository.</p><p>2. `github_packages.ndjson` is metadata for each package that was found on any package manager that references the GitHub url as it's repository url/source/homepage, these packages, like the cran and pypi data above, include the latest release and their direct dependencies. There may be more than one package for each GitHub URL as it is a one to many relationship. `github_packages_with_transitive.ndjson` follows the same format but also includes the extra resolved transitive dependencies of all packages using the same approach as with cran and pypi data above with the same caveats. </p><p>There are also many more ecosystems referenced in these files than just cran, bioconductor and pypi, https://packages.ecosyste.ms provides a standardized metadata format for all of them to enable comparison and simplification of automation.</p><h4>Contact</h4><p>If you would like any help, support or more data from Ecosyste.ms please do get in touch via email: hello@ecosyste.ms or open an issue on GitHub: https://github.com/ecosyste-ms/packages/issues</p>
Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
<p>Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation, and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity, and the fixation of maladaptive alleles, hindered adaptation, and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.</p>
Fig. 2 in Dependence of spermatophore size and sperm number on body weight in various cricket species (Insecta, Orthoptera)
Fig. 2: Linear regression analyses elucidating possible relationships between ampulla diameter and body weight (a) as well as between number of sperm and ampulla diameter (b). Data obtained for all investigated cricket species have been plotted (N = 80).
Fig. 1 in Dependence of spermatophore size and sperm number on body weight in various cricket species (Insecta, Orthoptera)
Fig. 1: General appearance of the spermatophore produced by males of the four cricket species investigated for this study (STURM 2003): (a) overview of a spermatophore with its spermcontaining ampulla (amp) and attachment plate (ap); (b) main components of the ampulla: apical papilla (pap), outer membrane (om), inner membrane (im), sperm mass (spm), and spermatphore tube (spt); (c) electron micrograph exhibiting the internal structure of a spermatophore (il: inner layer); (d) detailed view on the sperm mass included into the ampulla (spf: sperm flagella).
Video Supplement for "Understanding the dependence of mean precipitation on convective treatment and horizontal resolution in tropical aquachannel experiments"
<p>A time series of snapshots of precipitable water (shading) and rainfall rate (contour) in the tropical aquachannel simulations. </p>
Data for "Temperature dependence of charge conversion during NV-center relaxometry in nanodiamond"
<p>In this Zenodo repository, the data as plotted in "Temperature dependence of charge conversion during NV-center relaxometry in nanodiamond" is uploaded. The file consists of folders named after the figures in the manuscript, where each folder contains csv files and a readme file in which additional information can be found. If a fit function is plotted in a figure, the fit data is also given in a csv file.</p>
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.