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.
1,548
datasets available to search
ShareScore release 0.9.0
Dataset results
1,548 results for “Trajectories”
Data from: Three-dimensional trajectories and network analyses of group behaviour within chimney swift flocks during approaches to the roost
Chimney swifts (Chaetura pelagica) are highly manoeuvrable birds notable for roosting overnight in chimneys, in groups of hundreds or thousands of birds, before and during their autumn migration. At dusk, birds gather in large numbers from surrounding areas near a roost site. The whole flock then employs an orderly, but dynamic, circling approach pattern before rapidly entering a small aperture en masse. We recorded the three-dimensional trajectories of ≈1 800 individual birds during a 30 min period encompassing flock formation, circling, and landing, and used these trajectories to test several hypotheses relating to flock or group behaviour. Specifically, we investigated whether the swifts use local interaction rules based on topological distance (e.g. the n nearest neighbours, regardless of their distance) rather than physical distance (e.g. neighbours within x m, regardless of number) to guide interactions, whether the chimney entry zone is more or less cooperative than the surrounding flock, and whether the characteristic subgroup size is constant or varies with flock density. We found that the swift flock is structured around local rules based on physical distance, that subgroup size increases with density, and that there exist regions of the flock that are less cooperative than others, in particular the chimney entry zone.
Cyclist Actions: Motion History Images and Trajectories
<p>The dataset consists of over 1.1 million samples of labeled cyclists actions. Every sample consists of two motion history images (MHI), consisting of motion over the past second, from two different cameras, the past trajectory of the cyclist of the last second (50 past positions), and a label of the currently performed action.</p> <p>The samples were extracted from 1,639 video sequences of cyclists moving across an urban intersection at the University of Applied sciences in Aschaffenburg: <a href="https://www.th-ab.de/ueber-uns/organisation/labor/kooperative-automatisierte-verkehrssysteme/ausstattung/">https://www.th-ab.de/ueber-uns/organisation/labor/kooperative-automatisierte-verkehrssysteme/ausstattung/</a></p> <p>The uploaded files consist of a numpy file with MHI, trajectories and labels, and a json file containing 5-fold cross validation/test split.</p> <p>Every MHI has a size 192x192x2. The two channels contain the separate motion contours of the bike and the cyclist.</p> <p>The manually created labels are:</p> <ul> <li>straight: cyclists is moving and not turning</li> <li>tr/tl: cyclist is turning left/right</li> <li>move: cyclist is moving with nearly constant velocity and not turning</li> <li>start: cyclist was standing and starts moving</li> <li>starting_movement: first movement of cyclist before starting</li> <li>stop: cyclist was moving/starting and slows down to a halt</li> <li>wait: cyclist is standing</li> <li>hand_signal_left/right: cyclist indicates a turn by hand signal</li> <li>shoulder_check_left/right: cyclist looks over left/right shoulder</li> <li>out_of_saddle: cyclist is standing</li> </ul> <p>The numpy file consists of python dictionaries with scenes of the form:</p> <pre><code class="language-python">{SCENE_NAME: 'mhi_hk1/2': [...], # list of zip compressed, python pickled mhi from cameras 1 and 2 'x/y/z_tracked': [...], # tracked cyclists positions in x/y/z directions, 'x/y/z_smoothed': [...], # smoothed (by rts smoother) cyclists positions in x/y/z directions, 'orientation': [...], # orientation of the cyclists estimated by kalman filters 'ts': [...], # utc timestamps in micro seconds LABEL_NAME: [...], # labels of different actions (0 or 1)}</code></pre> <p>The zipped/pickled mhi can be decompressed using:</p> <pre><code class="language-python">import numpy as np import pickle import zlib d = np.load('mhi_dataset_0,1,2,3,4,6,9,13,18,26,33,41,49.npy', allow_pickle=True, encoding='latin1').item() for scene_name in d: for i in range(len(d[scene_name]['mhi_hk1']) - 50): # ommit 50 first frames as they have no mhi mhi1 = pickle.loads(zlib.decompress(d[scene_name]['mhi_hk1'][49 + i].encode('latin1')), encoding='latin1') mhi2 = pickle.loads(zlib.decompress(d[scene_name]['mhi_hk2'][49 + i].encode('latin1')), encoding='latin1')</code></pre> <p> </p> <p>This work results from the project DeCoInt 2, supported by the German Research Foundation (DFG) within the priority program SPP 1835: "Kooperativ interagierende Automobile", grant numbers DO 1186/1-2, FU 1005/1-2, and SI 674/11-2. Additionally, the work is supported by "Zentrum Digitalisierung Bayern".</p> <p>Due to privacy laws in germany, we are not permitted to publish raw image data.</p>
Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files
<p>Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms</p>
Raw data for: Stable Isotope Trajectory Analysis (SITA): A new approach to quantify and visualize dynamics in stable isotope studies. Sturbois et al., in revision in Ecological Monographs
<p>These data sets are used as ecological applications in Sturbois et al., in revision, Stable Isotope Trajectory Analysis (SITA): A new approach to quantify and visualize dynamics in stable isotope studies. submitted in Ecological Monographs.</p> <p>- DataS1_furseals.Rdata originates from: Kernaléguen, L., Cazelles, B., Arnould, J.P.Y., Richard, P., Guinet, C., Cherel, Y., 2012. Long-Term Species, Sexual and Individual Variations in Foraging Strategies of Fur Seals Revealed by Stable Isotopes in Whiskers. PLoS ONE 7, e32916. https://doi.org/10.1371/journal.pone.0032916</p> <p>- DataS2_Pike.Rdata originates from: Cucherousset, J., Paillisson, J.-M., Roussel, J.-M., 2013. Natal departure timing from spatially varying environments is dependent of individual ontogenetic status. Naturwissenschaften 100, 761–768. https://doi.org/10.1007/s00114-013-1073-y</p> <p>- DataS4_GT1.Rdata and DataS5_GT2.Rdata originate from: Quillien, N., Nordström, M.C., Schaal, G., Bonsdorff, E., Grall, J., 2016. Opportunistic basal resource simplifies food web structure and functioning of a highly dynamic marine environment. Journal of Experimental Marine Biology and Ecology 477, 92–102.</p> <p>- DataS6_Lakes.Rdata originates from: Zhao, T., Villéger, S., Cucherousset, J., 2019. Accounting for intraspecific diversity when examining relationships between non-native species and functional diversity. Oecologia 189, 171–183. https://doi.org/10.1007/s00442-018-4311-3</p> <p>Information about respective sampling strategies and sample preparation are available in these original articles. All use of this data sets must cite original article as well as the SITA article.</p>
Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression.
<p>This file contains vst-normalized gene expression data along with annotations which can be used to reproduce our findings.</p>
Data from: Historical human activities reshape evolutionary trajectories across both native and introduced ranges
<p>The same vectors that introduce species to new ranges could move them among native populations, but how human‐mediated dispersal impacts native ranges has been difficult to address because human‐mediated dispersal and natural dispersal can simultaneously shape patterns of gene flow. Here, we disentangle human‐mediated dispersal from natural dispersal by exploiting a system where the primary vector was once extensive but has since ceased. From 10th to 19th Centuries, ships in the North Atlantic exchanged sediments dredged from the intertidal for ballast, which ended when seawater ballast tanks were adopted. We investigate genetic patterns from RADseq‐derived SNPs in the amphipod <i>Corophium volutator</i> (<i>n</i> = 121; 4,870 SNPs) and the annelid <i>Hediste diversicolor</i> (<i>n</i> = 78; 3,820 SNPs), which were introduced from Europe to North America, have limited natural dispersal capabilities, are abundant in intertidal sediments, but not commonly found in modern water ballast tanks. We detect similar levels of genetic subdivision among introduced North American populations and among native European populations. Phylogenetic networks and clustering analyses reveal population structure between sites, a high degree of phylogenetic reticulation within ranges, and phylogenetic splits between European and North American populations. These patterns are inconsistent with phylogeographic structure expected to arise from natural dispersal alone, suggesting human activity eroded ancestral phylogeographic structure between native populations, but was insufficient to overcome divergent processes between naturalized populations and their sources. Our results suggest human activity may alter species' evolutionary trajectories on a broad geographic scale via regional homogenization and global diversification, in some cases precluding historical inference from genetic data.</p>
The effect of captivity on cranial and postcranial ontogenetic trajectories in wild boar
<p>R for Zenodo: script containing all the analyses (can be open in R or RStudio or any text reader)</p> <p>Landmark coordinates: Raw coordinates for all specimens</p> <p>Metadata CSV: files containing all the information of the specimens</p>
"Structural and Functional Diversity among Agonist-Bound States of the GLP-1 Receptor" - MD trajectories
<p>Topology (.psf) and coordinates (.xtc) files of:</p> <p>- Ex4 WT, D-Ala Ex4, and L-Ala Ex4 (all simulated in water - without receptor)</p> <p>- Partial unbinding and binding simulations of Ex4 WT, D-Ala Ex4 and L-Ala Ex4 from GLP-1R </p> <p>Water molecules, lipids, and ions have been removed.</p> <p> </p>
Data from: Resource availability affects seasonal trajectories of population-level learning
<p>Environmental effects on learning are well known, such as cognition that is mediated by nutritional consumption. Less known is how seasonally variable environments affect phenological trajectories of learning. Here, we test the hypothesis that nutritional availability affects seasonal trajectories of population-level learning in species with developmentally plastic cognition. We test this in bumble bees (Apidae: Bombus), a clade of eusocial insects that produce individuals at different time points across their reproductive season and exhibit organ developmental plasticity in response to nutritional consumption. To accomplish this, we develop a theoretical model that simulates learning development across a reproductive season for a colony parameterized with observed life history data. Our model finds two qualitative seasonal trajectories of learning: (1) an increase in learning across the season and (2) no change in learning across the season. We also find these two qualitative trajectories revealed by empirical learning data; the proportion of workers successfully completing a learning test increases across a season for two bumble bee species (Bombus auricomus, Bombus pensylvanicus), but does not change for another three (Bombus bimaculatus, Bombus griseocollis, Bombus impatiens). This study supports the novel consideration that resources affect seasonal trajectories of population-level learning in species with developmentally plastic cognition.</p>
Trajectories from "A glutamine-based single ɑ-helix scaffold to target globular proteins" Escobedo et al. 2022
<p>Trajectories from the manuscript "A glutamine-based single ɑ-helix scaffold to target globular proteins" Escobedo et al. 2022.</p> <p>https://www.biorxiv.org/content/10.1101/2022.05.06.490931v1</p>
Progeny Project Gromacs input and trajectories of a C12E6 surfactant model at the vacuum-water interface
<p>This is gromacs 2021.2 input and output for an all-atom C12E6 surfactant molecule at the water-vacuum<br> interface with TIP4P-ew and SPC/E water models.</p>
Data from: Hedging at the rear edge: Intraspecific trait variability drives the trajectory of marginal populations in a widespread boreal tree species
<p>Rear-edge populations at the warm margin of species distribution are small, isolated and face environmental conditions at the limit of species bioclimatic envelope. Intraspecific phenotypic variation contributing to the persistence of peripheral populations is expected to become increasingly important under future climate conditions in order to avoid local extirpation where range shifts lag behind climate change velocity.</p> <p>We investigated the putative role of intraspecific phenotypic variation for the maintenance of rear-edge populations of fire-prone jack pine (<em>Pinus banksiana</em>), an obligate pyriscent boreal species. We assessed whether variation in cone serotiny is associated with the population trajectory of marginal stands located south of the boreal biome, in the temperate forest where natural wildfires are infrequent and unpredictable. To this end, we estimated stand-scale serotiny, minimal age and tree size structure in 26 jack pine stands from the rear edge (n = 17 sites) and the core (n = 9 sites) of the species' range in eastern Canada.</p> <p>On average, rear-edge jack pine populations are less serotinous albeit more variably compared to range-core populations where serotiny is more uniformly high. Rear-edge stands are generally older and display reverse J-shape tree size structure indicative of a multi-aged demographic equilibrium, whereas range-core stands are younger and show a unimodal stand structure depicting a single aging cohort generally lacking interfire recruitment. Eco-evolutionary dynamics shifts from a dependency on wildfires in range-core populations to stands that can regenerate and persist without recurrent fires at the rear edge, where stand-scale serotiny reaches values below 85%.</p> <p>Synthesis: Unlike range-core populations, rear-edge jack pine populations can locally rely on a dual life-history strategy to ensure both steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience and resistance of jack pine populations as global changes alter fire dynamics of the boreal forest. More generally, unique intraspecific phenotypic variation in rear-edge populations contributes to long-term species persistence in marginal environmental conditions that might scale up with global changes. The conservation of rear-edge populations and their genetic legacy appears crucial for the resilience of species.</p>
Global-scale modeling of early factors and country-specific trajectories of COVID-19 incidence: a cross-sectional study of the first 6 months of the pandemic
<p><span>Studies examining factors responsible for COVID-19 incidence </span><span>are</span><span> mostly focused at the national or sub-national level. A global-level characterization of contributing factors and temporal trajectories of disease incidence is lacking. Here we conducted a global-scale analysis of COVID-19 infections to identify key factors associated with early disease incidence. Additionally, we compared longitudinal trends of COVID-19 incidence at a per-country level and classified countries based on COVID-19 incidence trajectories and effects of lockdown responses. </span><span>Univariate analysis identified</span> <span>eleven variables as independently associated with COVID-19 infections at a global level (p<1e-05). Multivariable analysis identified a 4-variable model as optimal for explaining global variations in COVID-19 (p<0.01). COVID-19 case trajectories for most countries were best captured by a log-logistic model, as determined by AIC estimates. Six predominant country clusters were identified when characterizing the effects of lockdown intervals on variations in COVID-19 new cases per country.</span> <span>Globally, economic and meteorological factors are important determinants of early COVID-19 incidence. Analysis of longitudinal trends and lockdown effects on COVID-19 highlights important nuances in country-specific responses to infections. These results </span><span>provide valuable insights into disease incidence at a per-country level, possibly allowing for more informed decision making by individual governments in future disease outbreaks.</span></p>
Extracting interaction potentials from trajectories: code and a set of 30 simulated contest trajectories
<p>Dataset and code provided as supporting materials for the manuscript "Modeling animal contests based on spatio-temporal dynamics". See the Supporting Information of the manuscript for detailed instructions of use.</p>
Synthetic vehicle trajectory dataset for the metropolitan city of Los Angeles using DDTG
<p>The analysis of trajectory datasets has numerous applications ranging from urban planning to human mobility understanding, but to protect the privacy of individuals trajectory datasets are rarely released to researchers. And even when they are, they are limited in size and spatio-temporal coverage. To address these issues a number of methods for generating synthetic yet realistic trajectory datasets have been proposed. These existing methods either require a lot of complex parameters to be calibrated (simulators) or rely on existing trajectory datasets (generative models). We use our proposed, and recently published at IEEE BigData 2022 conference, Data-Driven Trajectory Generator, dubbed DDTG, to generate a synthetic vehicle trajectory dataset in the metropolitan city of Los Angeles. The dataset consists of 1.5 million trajectories spanning the first two weeks of December 2019.</p>
Landscape structure, predictability of forest regeneration trajectories, and recovery rate on secondary forests
<p>Abandonment of agricultural lands promotes the global expansion of secondary forests, which are critical for preserving biodiversity and ecosystem functions and services. Such roles largely depend, however, on two essential successional attributes, trajectory and recovery rate, which are expected to depend on landscape-scale forest cover in non- linear ways. This dataset is the synthesis outcome of 22 independent databases from studies of woody plant species recovery as part of the research project entitled "Impacts of landscape structure on secondary tropical forest regeneration". This work aimed to understand the effect of landscape-level disturbance on forest regeneration, specifically through the predictability of trajectories and the recovery rate of these forests.</p> <p>Using a multiscale approach and a large vegetation dataset (843 plots, 3511 tree species) from 22 secondary forest chronosequences distributed across the Neotropics, we show that successional trajectories of woody plant species richness, stem density, and basal area are less predictable in landscapes (4-km radius) with intermediate (40-60%) forest cover than in landscapes with high (>60%) forest cover. This supports theory suggesting that high spatial and environmental heterogeneity in intermediately deforested landscapes can increase the variation in key ecological factors for forest recovery (e.g. seed dispersal, seedling recruitment), increasing the uncertainty of successional trajectories. Regarding the recovery rate, only the species richness is positively related to forest cover in relatively small (1-km radius) landscapes. These findings highlight the importance of using a spatially-explicit landscape approach in restoration initiatives and suggest that these initiatives can be more effective in more forested landscapes, especially if implemented across spatial extents of 1-4 km radius. </p>
Out of Asia? Expansion of Eurasian Lyme borreliosis causing genospecies display unique evolutionary trajectories
<p>Vector-borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host and vector shifts can lead to geographic expansion of infectious agents and the emergence of new diseases in susceptible individuals. Three bacterial genospecies (<em>Borrelia</em> <em>afzelii</em>, <em>Borrelia</em> <em>bavariensis</em>, and <em>Borrelia</em> <em>garinii</em>) predominantly utilize two distinct tick species as vectors in Asia (<em>Ixodes</em> <em>persulcatus</em>) and Europe (<em>Ixodes</em> <em>ricinus</em>). Through these vectors, the bacteria can infect various vertebrate groups (e.g. rodents, birds) including humans where they cause Lyme borreliosis, the most common vector-borne disease in the Northern hemisphere. Yet, how and in which order the three <em>Borrelia</em> genospecies colonized each continent remains unclear including the evolutionary consequences of this geographic expansion. Here, by reconstructing the evolutionary history of 142 Eurasian isolates, we find evidence that the ancestors of each of the three genospecies likely have an Asian origin. Even so, each genospecies studied displayed a unique sub-structuring and evolutionary response to the colonization of Europe. The pattern of allele sharing between continents is consistent with the dispersal rate of the respective vertebrate hosts, supporting the concept that adaptation of <em>Borrelia</em> genospecies to the host is important for pathogen dispersal. Our results highlight that Eurasian Lyme borreliosis agents are all capable of geographic expansion with host association influencing their dispersal; further displaying the importance of host and vector association to the geographic expansion of vector-borne pathogens and potentially conditioning their capacity as emergent pathogens.</p>
100ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the DES-Amber Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the DES-Amber force field published by Maxwell et al. The simulation was run for 100 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
25ns REST2 MD Simulation Trajectory of Wild-Type Alpha-Synuclein using the a99SB-disp Forcefield
<p>Molecular dynamics simulation trajectory and for wild-type acylated alpha-Synuclein (Ac-AS) using the REST2 algorithm. The system was parameterised with the a99SB-disp force field published by Maxwell et al. The simulation was run for 25 nanoseconds using GROMACS on the Forschungszentrum Jülich JUWELS supercomputer. The reposited trajectory is the lowest temperature replica at 300 K from 32 replicas between 300-500 K.</p> <p>This work was partially performed as part of the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE) and received funding from the Helmholtz Association of German Research Centers.</p> <p>The authors gratefully acknowledge the Gauss Centre for Supercomputing e.V. (www.gauss-centre.eu) for funding this project by providing computing time through the John von Neumann Institute for Computing (NIC) on the GCS Supercomputer JUWELS at Jülich Supercomputing Centre (JSC).</p>
Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference [Datasets]
<p>This repository contains processed single-cell dataset files for DELAY.</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.