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518 results for “cycling data”
Analysis of Padlet in the educational process on the rock cycle through Data Science
<p><strong><span>Analysis of Padlet in the educational process on the rock cycle through Data Science</span></strong></p>
No increase is detected and modelled for the seasonal cycle amplitude of δ13C of atmospheric carbon dioxide: scripts and data to prepare figures
<p>The file contains the scripts and data to plot the graphics displayed in Joos et al., No increase is detected and modelled for the seasonal cycle amplitude of δ13C of atmospheric carbon dioxide, Biogeosciences, in press, November 2024.</p>
Data from: Is tropical montane forest heterogeneity promoted by a resource-driven feedback cycle? Evidence from nutrient relations, herbivory and litter decomposition along a topographical gradient
1. Ridges of tropical mountains often differ strikingly from neighbouring ravines in terms of forest structure, productivity, and species composition. This heterogeneity is poorly understood despite its critical role in biodiversity maintenance, carbon and nutrient budgets. 2. We examined measures of tree biomass and productivity, foliage and litter quality (nutrient concentrations, specific leaf mass, phenolics), herbivory and leaf litter decomposition in each six plots laid out in upper and lower slope position in a tropical montane moist forest in southeastern Ecuador. 3. Productivity, quality of foliage and litter and herbivory were significantly lower in upper slope position and closely correlated with soil nutrient concentrations and accumulated humus. The decomposition of upper slope leaf litter (decomposition rate k) was substantially lower than in litter from lower slope forest, whereas the site of decomposition (slope position) only had a marginal effect on the decomposition rate. 4. Our results suggest that the differences in stand structure, productivity, foliar quality, herbivory and decomposition between slope positions are ultimately due to stronger nutrient limitations in upper slope forest. We propose a general conceptual model that explains origin and maintenance of contrasting forest types along topographical gradients through down-slope fluxes of nutrients and water, and a nutrient-driven positive feedback cycle.
Data from: Plasticity in leaf litter traits partly mitigates the impact of thinning on forest floor carbon cycling
1. Reducing stand density by thinning intensification has been emphasized as an efficient strategy of forest adaptation to climate change as it improves stand resistance to drought. Yet, it is still unclear how it could affect litter C cycling processes. Recent evidence indicates that the plasticity of an oak tree species can lead to a decline in its leaf litter quality and decomposability following thinning. The consequences for litter decomposition and forest floor C storage at the ecosystem-scale remain largely unexplored. 2. In this study, we took advantage of a regional-scale, multi-site network of long-term thinning experiments in temperate oak (Quercus petraea) forests to address this issue. We measured ecosystem properties related to forest floor C cycling in 19 plots across eight experimental sites covering a large gradient of stand density and age. Though we expected thinning to affect in situ litter decomposition by altering oak leaf litter quality, we conducted complementary experiments exploring additional mechanisms, i.e. alterations of microenvironmental conditions and soil faunal activity. 3. Thinning intensification induced a strong decline in tree canopy leaf area index, aboveground tree litter production and forest floor decomposition rate in early 'aggradation' stage of forest development. This slower litter decomposition was mainly driven by plasticity of oak trees that produced leaf litter of poorer quality and decomposability following thinning, e.g. litter richer in secondary metabolites such as condensed tannins. Change in microenvironmental conditions also contributed to the slowdown of litter decomposition, likely as a result of the less buffered microclimate associated with larger tree canopy opening. No change in soil faunal effect induced by thinning was found. 4. Thinning resulted in a limited decrease in forest floor C stock. Indeed, the slower litter decomposition offset nearly half of the forest floor C loss associated to the reduced litterfall in 'aggradation' stage. 5. Our study demonstrated that phenotypic plasticity in leaf litter traits of a dominant tree species can strongly affect ecosystem functioning by slowing forest floor decomposition following thinning intensification, in turn partly mitigating the negative effect of thinning on forest floor C storage.
Data from: Soil nitrogen-cycling responses to conversion of lowland forests to oil palm and rubber plantations in Sumatra, Indonesia
Rapid deforestation in Sumatra, Indonesia is presently occurring due to the expansion of palm oil and rubber production, fueled by an increasing global demand. Our study aimed to assess changes in soil-N cycling rates with conversion of forest to oil palm (Elaeis guineensis) and rubber (Hevea brasiliensis) plantations. In Jambi Province, Sumatra, Indonesia, we selected two soil landscapes – loam and clay Acrisol soils – each with four land-use types: lowland forest and forest with regenerating rubber (hereafter, "jungle rubber") as reference land uses, and rubber and oil palm as converted land uses. Gross soil-N cycling rates were measured using the 15N pool dilution technique with in-situ incubation of soil cores. In the loam Acrisol soil, where fertility was low, microbial biomass, gross N mineralization and NH4+ immobilization were also low and no significant changes were detected with land-use conversion. The clay Acrisol soil which had higher initial fertility based on the reference land uses (i.e. higher pH, organic C, total N, effective cation exchange capacity (ECEC) and base saturation) (P≤0.05–0.09) had larger microbial biomass and NH4+ transformation rates (P≤0.05) compared to the loam Acrisol soil. Conversion of forest and jungle rubber to rubber and oil palm in the clay Acrisol soil decreased soil fertility which, in turn, reduced microbial biomass and consequently decreased NH4+ transformation rates (P≤0.05–0.09). This was further attested by the correlation of gross N mineralization and microbial biomass N with ECEC, organic C, total N (R=0.51–0. 76; P≤0.05) and C:N ratio (R=-0.71 – -0.75, P≤0.05). Our findings suggest that the larger the initial soil fertility and N availability, the larger the reductions upon land-use conversion. Because soil N availability was dependent on microbial biomass, management practices in converted oil palm and rubber plantations should focus on enriching microbial biomass.
Data from: Using a full annual cycle model to evaluate long-term population viability of the conservation-reliant Kirtland's warbler after successful recovery
Long-term management planning for conservation-reliant migratory songbirds is particularly challenging because habitat quality in different stages and geographic locations of the annual cycle can have direct and carry-over effects that influence the population dynamics. The Neotropical migratory songbird Kirtland's warbler Setophaga kirtlandii (Baird 1852) is listed as endangered under the U.S. Endangered Species Act and Near Threatened under the IUCN Red List. This conservation-reliant species is being considered for U.S. federal delisting because the species has surpassed the designated 1000 breeding pairs recovery threshold since 2001. To help inform the delisting decision and long-term management efforts, we developed a population simulation model for the Kirtland's warbler that incorporated both breeding and wintering grounds habitat dynamics, and projected population viability based on current environmental conditions and potential future management scenarios. Future management scenarios included the continuation of current management conditions, reduced productivity and carrying capacity due to the changes in habitat suitability from the creation of experimental jack pine Pinus banksiana (Lamb.) plantations, and reduced productivity from alteration of the brown-headed cowbird Molothrus ater (Boddaert 1783) removal programme. Linking wintering grounds precipitation to productivity improved the accuracy of the model for replicating past observed population dynamics. Our future simulations indicate that the Kirtland's warbler population is stable under two potential future management scenarios: (i) continuation of current management practices and (ii) spatially restricting cowbird removal to the core breeding area, assuming that cowbirds reduce productivity in the remaining patches by ≤41%. The additional future management scenarios we assessed resulted in population declines. Synthesis and applications. Our study indicates that the Kirtland's warbler population is stable under current management conditions and that the jack pine plantation and cowbird removal programmes continue to be necessary for the long-term persistence of the species. This study represents one of the first attempts to incorporate full annual cycle dynamics into a population viability analysis for a migratory bird, and our results indicate that incorporating wintering grounds dynamics improved the model performance.
Supporting data for Optimal closed-loop wake steering, Part 2: Diurnal cycle atmospheric boundary layer conditions
<p>Supporting data for "Optimal closed-loop wake steering, Part 2: Diurnal cycle atmospheric boundary layer conditions" by Michael F. Howland, Aditya S. Ghate, Jesús Bas Quesada, Juan José Pena Martínez, Wei Zhong, Felipe Palou Larrañaga, Sanjiva K. Lele, and John O. Dabiri</p> <p>See README for data description.</p> <p>The code is available at: https://github.com/FPAL-Stanford-University/PadeOps</p>
Removing the effects of cell cycle genes data
<p>This data is used for the Galaxy Training Network tutorial 'Removing the effects of cell cycle genes'. It includes lists of cell cycle genes in mice and a dataset that is also used in the GTN tutorial 'Filter, Plot and Explore Single-cell RNA-seq Data'.</p> <p>The original dataset can be found here: Bacon, Wendi Anne. (2022). AnnData object for case study tutorials [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.7053673">https://doi.org/10.5281/zenodo.7053673</a> The version uploaded here has been processed according to the 'Filter, Plot and Explore Single-cell RNA-seq Data' tutorial up to the point of scaling the data. The data was published in Bacon, W. A., R. S. Hamilton, Z. Yu, J. Kieckbusch, D. Hawkes <em>et al.</em>, 2018 Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice. Frontiers in Immunology 9: <a href="https://doi.org/10.3389/fimmu.2018.02523">10.3389/fimmu.2018.02523</a></p> <p>The cell cycle gene lists were obtained from the Harvard Chan School: Bioinformatics Core tinyatlas (2017) cell_cycle/Mus_musculus via GitHub:<a href="https://github.com/hbc/tinyatlas/blob/master/cell_cycle/Mus_musculus.csv"> https://github.com/hbc/tinyatlas/blob/master/cell_cycle/Mus_musculus.csv</a> </p> <p> </p>
Measurement data for Condition assessment of cycle path roughness and evenness using a bicycle measurement trailer
<p>Dataset for measurements with the Bicycle Measurement Trailer (BMT) which form the basis for the article "Condition assessment of cycle path roughness and evenness using a bicycle measurement trailer"</p>
Data for "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis"
<p>This dataset was used to make tables and figures for the study entitled "Nitrogen availability mediates soil carbon cycling response to climate warming: a meta-analysis", which was submitted to Global Change Biology in October 2022. It contains a meta-analysis database focusing on the effects of warming on soil C storage, root biomass and soil respiration.</p>
Data for Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport
<p>Datasets containing derived data and results used by code in: https://github.com/AlexandraVallet/PVSflow for "Sleep cycle-dependent vascular dynamics and the predicted effects on perivascular cerebrospinal fluid flow and solute transport", Bojarskaite et al. 2023. Please see github for instructions. </p>
Data from: Effect of infection and gonotrophic cycle on Aedes aegypti behavior and preferences
<p><span>Targeting gravid females through chemical lures is a promising strategy in vector control; however, it requires the understanding of the factors susceptible to alter female oviposition behaviour. Here, we evaluated the effect of infection with chikungunya virus (CHIKV) and the number of gonotrophic cycles (GCs) on oviposition activity in <em>Ae. aegypti</em>. Dual choice oviposition assays were performed, where dodecanoic acid, pentadecanoic acid, n-heneicosane and a Sargasssum fluitans (Børgesen) Børgesen extract were tested in uninfected females and females infected with CHIKV, at the 1<sup>st</sup> and 2<sup>nd</sup> GC. Infected females displayed a lower percentage of oviposition and a higher number of eggs laid at the 1<sup>st</sup> GC. Then, combined effects of GC and CHIKV induced the preference towards the tested candidates to either increase or decrease with a chemical-dependent effect. These results allow a deeper understanding of the mechanisms involved in oviposition site selection and highlight the need for taking into account physiological stage changes to increase the control programs efficacy.</span></p>
Data to "Functional relationships reveal differences in the water cycle representation of global water models"
<p>This repository contains 30-year (climatological) averages (1975-2004) from 8 global water models, following the ISIMIP 2b protocol: CLM4.5, CWatM, H08, JULES-W1, LPJmL, MATSIRO, PCR-GLOBWB, and WaterGAP2.</p> <p>Variables included are precipitation (<em>pr</em>), temperature (<em>tas</em>), minimum temperature (<em>tasmin</em>), maximum temperature (<em>tasmax</em>), downwelling shortwave radiation (<em>rsds</em>), downwelling longwave radiation (<em>rlds</em>), net radiation (<em>netrad</em>), potential evapotranspiration (<em>potevap</em>), actual evapotranspiration (<em>evap</em>), groundwater recharge (<em>qr</em>), and total runoff (<em>qtot</em>). For details see <a href="https://www.isimip.org/">https://www.isimip.org/</a>.</p> <p><em>domains.csv </em>contains different definitions of the domains used in the paper (wet warm, wet cold, dry cold, dry warm).</p> <p><em>days_below_x.csv </em>contains the average fraction of days where the temperature is below <em>x</em> °C.</p>
Dominance of contrasting fungal functional groups influence nutrient cycling across four Japanese cool-temperate forest soils - Data repository
<p>Soil data related to the publication <strong>Dominance of contrasting fungal functional groups influence nutrient cycling across four Japanese cool-temperate forest soils.</strong></p>
All data used for thermochemical modeling of wet-dry cycles in Gale crater
<p>All data used for thermochemical modeling of wet-dry cycles in Gale crater including starting parameters, modeled and extrapolated results, and result comparisons.</p>
Treating the End of the Data Life Cycle as a First-Class Citizen in Data Engineering - Datasets
<p>Additional data for paper "Treating the End of the Data Life Cycle as a First-Class Citizen in Data Engineering".</p>
Data accompanying "Kinetics of the Xanthophyll Cycle and its Role in the Photoprotective Memory and Response"
<p>Data and code accompanying "Kinetics of the Xanthophyll Cycle and its Role in the Photoprotective Memory and Response".</p>
Data containing alitude profiles of Joule heating and Pedersen conductivity from EISCAT and TIE-GCM used for the research work "A comparative assessment of the distribution of Joule heating in altitude as estimated in TIE-GCM and EISCAT over one solar cycle"
<p>This archive contains the data used for the research work with title "A comparative assessment of the distribution of Joule heating in altitude as estimated in TIE-GCM and EISCAT over one solar cycle". The data represent Joule heating and Pedersen conductivity altitude profiles for the duration of the solar cycle 24 between the years 2009 and 2019. The information is separated by Magnetic Local Time, Kp index and altitude. There are data from the EISCAT incoherent scatter radar in Matlab format and from a TIE-GCM simulation executed at the Department of Electrical and Computer Engineering, Democritus University of Thrace in NetCDF format. </p>
Data from: Environmental heterogeneity amplifies behavioural response to a temporal cycle
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Data from: How do cold-adapted plants respond to climatic cycles? interglacial expansion explains current distribution and genomic diversity in Primula farinosa L.
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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.