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1,548 results for “Trajectories”
Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech
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Crowdsourced dataset of firefly trajectories obtained by automated stereo calibration of 360-degree cameras
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Data for: ‘Drifting’ Buchnera genomes track the microevolutionary trajectories of their aphid hosts
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Explaining the divergence of population trajectories for two interacting waterfowl species
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Data from: Distinct developmental trajectories for risky and impulsive decision-making in chimpanzees
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Genetic differentiation and demographic trajectory of the insular Formosan and Orii’s flying foxes
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Data from: Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)
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A large dataset of detection and submeter-accurate 3-D trajectories of juvenile Chinook salmon
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Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory
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Estimates of Forest Structure, Successional Trajectory, and Carbon and Nitrogen Pools Across the 2004 Wildfire Network Sites
This dataset contains stand structure and ecosystem carbon and nitrogen pool data measured in 2005 and 2006. It includes in situ measurements of post-fire residual above and belowground carbon and nitrogen pools, reconstructions of pre-fire pools and estimates of losses. Successional trajectory was calculated from measurements of tree seedling density and biomass made in 2017.
Land Change Trajectories across Four Watersheds in the Upper Little Tennessee River Basin
These data were collected to reconstruct spatially explicit land use/land cover change trajectories that were temporally consistent and at very high accuracies for a selection of watersheds in Macon County, NC: Cartoogechaye, Coweeta, Skeenah and Watauga. Buildings (points) and roads (lines) were digitized from historic maps and aerial photographs and aligned where necessary for temporal consistency. Land cover was simultaneously classified across all years for each 25x25m pixel (1/16 ha) in order to maximize temporal consistency.
The Salinity and phosphorus mesocosm experiment in freshwater sawgrass wetlands: Determining the trajectory and capacity of freshwater wetland ecosystems to recover carbon losses from saltwater intrusion (FCE LTER), Florida, USA from 2015 to 2018
In experimental wetland mesocosms located at Florida Bay Interagency Science Center, Key Largo, Florida, researchers continuously added salinity (approximately 6.9 g salt d-1) and phosphorus ( approximately 0.5 mg P d-1) to Cladium jamaicense peat monoliths from February 2015 to February 2017 and quantified changes in carbon partitioning. Several studies, focusing on the functional roles of marsh, soil, periphyton and microbe in the sawgrass-peat ecosystem, summarized detailed methodology and results (Wilson et al. 2019; Servais et al. 2019; Mazzei et al. in press). Briefly, salinity was increased (~10 ppt) and phosphorus was added (0.45 mg P d-1) to simulate four treatment effects (n = 24 plots): i) freshwater and no-added phosphorus, ii) freshwater and added phosphorus, iii) saltwater and no-added phosphorus, and iv) saltwater and added phosphorus. Upon the termination of manipulation study (early February 2017), containers holding water and peat-sawgrass cores were drained, rinsed, and refilled with only freshwater without any added nutrient and salt. Then, we experimentally restored freshwater to previous treatment and control mesocosms from February 2017 to June 2018 to examine the capacity of wetland ecosystems to recover carbon losses from saltwater intrusion. Note that FCE1226_Water_quality.csv summarizes water quality during both the manipulation and restoration study; however, all other files in the Dataset Title section only summarize results from the restoration study. Detailed methodology is provided below.
Simulated trajectories of city population: Levy walks along Buffalo, NY, street network
<p>Simulated trajectories of the full 2000 census population of Buffalo, New York. Each simulated person was placed randomly along a road within his or her census tract of residence and then independently performed road-network-constrained, truncated Lévy walks for 8 hours of simulated time, moving at 4 km per hour. The trajectories were then sampled at 30 minute intervals. The original dataset was created for studying indexes of activity-space segregation. It is archived at <a href="https://zenodo.org/record/2865830#.XpYviKsza00">https://zenodo.org/record/2865830#.XpYviKsza00</a> and described more fully in Palmer (2013), Activity-Space Segregation: Understanding Social Divisions in Space and Time (http://arks.princeton.edu/ark:/88435/dsp01k643b130h).</p> <p>This version has been created to aid in testing contact-tracing apps and mobility analysis tools. The fields are:</p> <p>latitude: latitude</p> <p>longitude: longitude</p> <p>time: UNIX time in milliseconds</p> <p>ID: random ID assigned to each individual</p>
Simulated trajectories of city population: Levy walks along Utica, NY, street network
<p>Simulated trajectories of the 2000 census population of Utica, New York. Each of 53,971 simulated people was placed randomly along a road within his or her census tract of residence and then independently performed road-network-constrained, truncated Lévy walks for 8 hours of simulated time, moving at 4 km per hour. The trajectories were then sampled at 30 minute intervals. The original dataset was created for studying indexes of activity-space segregation. It is archived at <a href="https://zenodo.org/record/2865830#.XpYviKsza00">https://zenodo.org/record/2865830#.XpYviKsza00</a> and described more fully in Palmer (2013), Activity-Space Segregation: Understanding Social Divisions in Space and Time (http://arks.princeton.edu/ark:/88435/dsp01k643b130h).</p> <p>This version has been created to aid in testing contact-tracing apps and mobility analysis tools. The fields are:</p> <p>latitude: latitude</p> <p>longitude: longitude</p> <p>time: UNIX time in milliseconds</p> <p>ID: random ID assigned to each individual</p>
SIRAH-CoV2 initiative: UPDATED TRAJECTORY of SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)
<p>This dataset contains an updated trajectory of a four microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). It substitutes the previous one on the same system, which was performed in the absence of disulfide bridges.</p> <p>Simulations have been performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, 6M17_SIRAHcg_rawdata_2-3.tar, and 6M17_SIRAHcg_rawdata_3-4.tar contain all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6M17_SIRAHcg_4us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_4us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6M17_SIRAHcg_4us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD 1.9.3 using the command line:</p> <p>vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_4usprot_skip.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Data from: Specialized breeding in plants affects diversification trajectories in Neotropical frogs
<p>Many animals breed exclusively in plants that accumulate rainwater (phytotelma; e.g., bromeliad, bamboo, fruit husk, and tree hole), to which they are either physiologically or behaviorally specialized for this microhabitat.<b> </b>Of the numerous life-history modes observed in frogs, few are as striking or potentially consequential as the transition from pond- or stream-breeding to the deposition of eggs or larvae in phytotelmata. Such specialization can increase offspring survivorship due to reduced competition and predation, representing potential ecological opportunity for adaptive radiation, yet few lineages of phytotelma-breeding frogs appear to have diversified extensively after such a transition, at least in the New World. We use a phylogeny of Neotropical frogs and data on breeding microhabitat to understand the evolutionary transitions involved with specialized phytotelma-breeding. First, we find that phytotelma-breeding is present in at least 168 species in 10 families of frogs. Across the phylogeny, we estimate 14 origins of phytotelma-breeding and 115 reversals, showing that phytotelma-breeding is a highly labile character. Second, phytotelma-breeding lineages overall have higher net diversification than non-phytotelma-breeding ones. This specialization represents an ecological opportunity resulting in increased diversification in most families with phytotelma-breeding lineages, whereas phytotelma-breeding toads have restricted diversification histories.</p>
Data from: Carnivorous mammals from the middle Eocene Washakie Formation, Wyoming, USA, and their diversity trajectory in a post-warming world
The middle Eocene Washakie Formation of Wyoming, USA, provides a rare window, within a single depositional basin, into the faunal transition that followed the early Eocene warming events. Based on extensive examination, we report a minimum of 27 species of carnivorous mammals from this formation, more than doubling the previous taxic count. Included in this revised list are a new species of carnivoraform, <i>Neovulpavus mccarrolli</i>, and up to ten other possibly new taxa. Our cladistic analysis of early Carnivoraformes incorporating new data clarified the array of middle Eocene taxa that are closely related to crown-group Carnivora. These anatomically relatively derived carnivoraforms collectively had an intercontinental distribution in North America and east Asia, exhibiting notable variations in body size and dental adaptation. This time period also saw parallel trends of increase in body-size and dental sectoriality in distantly-related lineages of carnivores spanning a wide range of body sizes. A new, model-based Bayesian analysis of diversity dynamics accounting for imperfect detection revealed a high probability of substantial loss of carnivore species between the late Bridgerian and early Uintan North American Land Mammal 'Ages', coinciding with the disappearance of formerly common mammals such as hyopsodontids and adapiform primates. Concomitant with this decline in carnivore diversity, the Washakie vertebrate fauna underwent significant disintegration as measured by patterns of coordinated detection of taxa at the locality level. These observations are consistent with a major biomic transition in the region in response to climatically-induced opening-up of forested habitats.
Simplified Event Logs for Sepsis Patient Trajectories
<p>This dataset contains a simplified excerpt from a real event log that tracks the trajectories of patients admitted to a hospital to be treated for sepsis, a life-threatening condition. The log has been recorded by the Enterprise Resource Planning of the hospital. Additionally, the dataset contains three synthetic logs that increase the number of trajectories within the original log timespan, while maintaining other statistical characteristics.</p> <p>In total, the dataset contains four files in .zip format and a companion that describes the statistical method used to synthesize the logs as well as the dataset content in detail. The dataset can be used in testing the performance of event-based process-mining and log (runtime) monitoring tools against an increasing load of events.</p>
Multiple genetic trajectories to extreme abiotic stress adaptation in Arctic Brassicaceae
<p>Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. The Arctic is one of the most hostile environments on Earth, and the few plant species inhabiting this region typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic, and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general. </p>
Epigenetic Profiling of Social Communication Trajectories and Co-occurring Mental Health Problems: A Prospective, Methylome-wide Association Study
<p>While previous studies suggest that both genetic and environmental factors play an important role in the development of autism-related traits, little is known about potential biological mechanisms underlying these associations. Using data from the Avon Longitudinal Study of Parents and Children (ALSPAC), we examined prospective associations between DNA methylation (DNAm: N-birth=804, N-age7=877) and trajectories of social communication deficits (8-17 years). Methylomic variation at three loci across the genome (false discovery rate=0.048) differentiated children following high (n=80) versus low (n=724) trajectories of social communication deficits. This differential DNAm was specific to the neonatal period and not observed at age 7. Associations between DNAm and trajectory membership remained robust after controlling for co-occurring mental health problems (i.e., hyperactivity/inattention, conduct problems). The three loci identified at birth were not replicated in the Generation R Study. However, to the best of our knowledge, ALSPAC is the only study to date that is prospective enough to examine DNAm in relation to longitudinal trajectories of social communication deficits from late childhood to late adolescence. Although the present findings might point to potentially novel sites that differentiate between a high versus low trajectory of social communication deficits, the results should be considered tentative until further replicated.</p> <p>This dataset contains summary statistics for the methylome-wide association study using DNAm data collected from individuals at birth.</p> <p>Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a zenodo DOI generated for you go to ewascatalog.org/upload</p>
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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.