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55 results for “spatial and temporal dynamics”
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Microbial Observatory at North Temperate Lakes LTER Spatial and temporal cyanobacterial population dynamics in Lake Mendota 2009 - 2011
Toxic cyanobacterial blooms threaten freshwaters worldwide but have proven difficult to predict because the mechanisms of bloom formation and toxin production are unknown, especially on weekly time scales. Water quality management continues to focus on aggregated metrics, such as chlorophyll and total nutrients, which may not be sufficient to explain complex community changes and functions such as toxin production. For example, nitrogen (N) speciation and cycling play an important role, on daily time scales, in shaping cyanobacterial communities because declining N has been shown to select for N fixers. In addition, subsequent N pulses from N2 fixation may stimulate and sustain toxic cyanobacterial growth. Herein, we describe how rapid early summer declines in N followed by bursts of N fixation have shaped cyanobacterial communities in a eutrophic lake (Lake Mendota, Wisconsin, USA), possibly driving toxic Microcystis blooms throughout the growing season. On weekly time scales in 2010 and *2011, we monitored the cyanobacterial community in a eutrophic lake using the phycocyanin intergenic spacer (PC-IGS) region to determine population dynamics. In parallel, we measured microcystin concentrations, N2 fixation rates, and potential environmental drivers that contribute to structuring the community.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format
The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Microbial Observatory at North Temperate Lakes LTER High-resolution temporal and spatial dynamics of microbial community structure in freshwater bog lakes 2005 - 2009 original format (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/344/6, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-ntl/349/4. The abstract below was extracted from the Level 0 data package and is included for context: The North Temperate Lakes - Microbial Observatory seeks to study freshwater microbes over long time scales (10+ years). Observing microbial communities over multiple years using DNA sequencing allows in-depth assessment of diversity, variability, gene content, and seasonal/annual drivers of community composition. Combining information obtained from DNA sequencing with additional experiments, such as investigating the biochemical properties of specific compounds, gene expression, or nutrient concentrations, provides insight into the functions of microbial taxa. Our 16S rRNA gene amplicon datasets were collected from bog lakes in Vilas County, WI, and from Lake Mendota in Madison, WI. Ribosomal RNA gene amplicon sequencing of freshwater environmental DNA was performed on samples from Crystal Bog, North Sparkling Bog, West Sparkling Bog, Trout Bog, South Sparkling Bog, Hell’s Kitchen, and Mary Lake. These microbial time series are valuable both for microbial ecologists seeking to understand the properties of microbial communities and for ecologists seeking to better understand how microbes contribute to ecosystem functioning in freshwater.
Sudden_Oak_Death_in_Oregon_Forests: Spatial and temporal population dynamics of the sudden oak death epidemic in Oregon Forests
<p>Release of code associated with the submitted manuscript</p> <p><strong>Authors</strong></p> <p>ZN Kamvar, MM Larsen, AM Kanaskie, EM Hansen, and NJ Grünwald.</p> <p><strong>Title</strong></p> <p>Spatial and temporal population dynamics of the sudden oak death epidemic in Oregon Forests.</p>
Data archive for Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics
<p>Data collected during annual sampling campaigns to the coastal oxygen minimum zone of Golfo Dulce, carried out in January-February 2018, 2019 and 2020. Methods and results are presented and discussed in Steinsdóttir et al. 2022. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environmental Microbiology, in press, doi: 10.1111/1462-2920.16003</p> <p>The content of files is as follows:</p> <p>nutrient_and_methane_concentrations.csv - Concentrations of methane, nitrite, nitrate, and ammonium.</p> <p>methane_oxidation_rates.csv - Rates of anaerobic methane oxidation.</p> <p>kinetics_of_anaerobic_methane_oxidation.csv - Kinetics of anaerobic methane oxidation, carried out in 2019.</p> <p>methylococcales.fa - Methylococcales 16S rRNA amplicon sequences</p> <p>methanofastidiosa.fa - Methanofastidiosa 16S rRNA amplicon sequences</p>
Data set for the publication entitled "Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis"
<p>Set of files containing data used for microbiota analysis by 16S rRNA amplicon sequencing.</p> <p>The study cohort included patients with idiopathic pulmonary fibrosis from four centres in Switzerland, treated with azithromycin or placebo, sampled sequentially by oropharyngeal swab.</p> <p>This work is available in medRxiv and has been submitted</p>
Drivers of spatial and temporal micro- and mesozooplankton dynamics in an estuary under strong anthropogenic influences (The Eastern Scheldt, Netherlands)
<p>Supplement to: Horn, H.G., van Rijswijk, P., Soetaert, K., van Oevelen, D. (2023): Drivers of spatial and temporal micro- and mesozooplankton dynamics in an estuary under strong anthropogenic influences (The Eastern Scheldt, Netherlands). J Sea Res. <a href="https://doi.org/10.1016/j.seares.2023.102357">https://doi.org/10.1016/j.seares.2023.102357</a></p> <p>This data set contains mesozooplankton and microzooplankton abundances, temperature, salinity, O2, DOC, Chl.a, SPM, and nutrient concentrations from eight stations in the Eastern Scheldt sampled in 2018. Phytoplankton growth and microzooplankton grazing rates from dilution experiments are also provided.</p>
Spatial, environmental, and functional distances among temporal ponds attenuate synchronization, stabilizing plant richness and biomass dynamics
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Temporal and spatial dynamics of Synechococcus clade II and other microbes in the eutrophic subtropical San Diego Bay
This data set comprises amplicon sequence variants (ASVs) from the nutrient-replete waters of San Diego Bay (SDB). Using 16S and 18S rRNA gene and internal transcribed spacer (ITS) region sequencing for Synechococcus, we analyzed multiple locations in San Diego Bay monthly for over a year (2021-2022) with additional samples dating back to 2015. San Diego Bay ITS region sequences were compared to nearby coastal samples collected from the Scripps Pier at Scripps Institution of Oceanography.
Spatial and temporal dynamics of space use by free-ranging domestic dogs Canis familiaris in rural Africa
<p>Variation in the spatial ecology of animals influences the transmission of infections and so understanding host behaviour can improve the control of diseases. Despite the global distribution of free-ranging domestic dogs <i>Canis familiaris</i> and their role as reservoirs for zoonotic diseases, little is known about the dynamics of their space use. We deployed GPS loggers on free-ranging dogs from six villages in rural Chad, and tracked the movements of 174 individuals in the dry season and 151 in the wet season. We calculated 95% and core home ranges using auto-correlated kernel density estimates (AKDE<sub>95</sub> and AKDE<sub>core</sub>), determined the degree to which their movements were predictable, and identified correlates of movement patterns. The median AKDE<sub>95 </sub>range in the dry season was 0.54km<sup>2</sup> and in the wet season was 0.31km<sup>2</sup>, while the median AKDE<sub>core </sub>range in the dry season was 0.08km<sup>2</sup> and in the wet season was 0.04km<sup>2</sup>. Seasonal variation was, in part, related to owner activities. Dogs from hunting households had ranges that were five times larger in the dry season. At least 70% of individuals were more predictably 'at home' (<50m from the household) throughout the day in the dry season. 80% of dogs demonstrated periodicity in activity levels (speed) and just over half the dogs exhibited periodicity in location (repeated space use). In the wet season, dogs mostly exhibited 24-hour cycles in activity and location, with peaks at midday. In the dry season, dogs exhibited both 12 and 24-hour cycles, with either a single peak at midday, or one peak between 6am and 12 noon and a second between 6 and 10pm. Strategies to control canine-mediated zoonoses can be improved by tailoring operations to the local spatial ecology of free-ranging dogs. Interventions using a door-to-door strategy in rural Chad would best conduct operations during the dry season, when access to dogs around their household more reliably exceeds 70% throughout the day. Given the importance of use in hunting for explaining variation in dog space-use, targeting approaches to disease control at the household level on the basis of owner activities offers potential to improve access to dogs.</p>
Understanding complex spatial dynamics from mechanistic models through spatio-temporal point processes
<p>Landscape heterogeneity affects population dynamics, which determine species persistence, diversity and interactions. These relationships can be accurately represented by advanced spatially-explicit models (SEMs) allowing for high levels of detail and precision. However, such approaches are characterised by high computational complexity, high amount of data and memory requirements, and spatio-temporal outputs may be difficult to analyse. A possibility to deal with this complexity is to aggregate outputs over time or space, but then interesting information may be masked and lost, such as local spatio-temporal relationships or patterns. An alternative solution is given by meta-models and meta-analysis, where simplified mathematical relationships are used to structure and summarise the complex transformations from inputs to outputs. Here, we propose an original approach to analyse SEM outputs. By developing a meta-modelling approach based on spatio-temporal point processes (STPPs), we characterise spatio-temporal population dynamics and landscape heterogeneity relationships in agricultural contexts. A landscape generator and a spatially-explicit population model simulate hierarchically the pest-predator dynamics of codling moth and ground beetles in apple orchards over heterogeneous agricultural landscapes. Spatio-temporally explicit outputs are simplified to marked point patterns of key events, such as local proliferation or introduction events. Then, we construct and estimate regression equations for multi-type STPPs composed of event occurrence intensity and magnitudes. Results provide local insights into spatio-temporal dynamics of pest-predator systems. We are able to differentiate the contributions of different driver categories ( i.e., spatio-temporal, spatial, population dynamics). We highlight changes in the effects on occurrence intensity and magnitude when considering drivers at global or local scale. This approach leads to novel findings in agroecology where, for example, we show that the organisation of cultivated patches and semi-natural elements play different roles for pest regulation depending on the scale considered. It aids to formulate guidelines for biological control strategies at global and local scale.</p>
Data from: Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress
<p>Data and codes associated with the manuscript '<span>Hyperspectral imaging reveals differential carotenoid and chlorophyll temporal dynamics and spatial patterns in Scots pine under water stress</span>'. </p>
Contrasting intra-annual population dynamics of two codominant species are consistent across spatial and temporal scales
<p>1. Despite asymmetric competition and a wide array of functional similarities, two ecologically important C4 perennial grasses, Andropogon gerardii and Sorghastrum nutans, frequently codominate areas of the mesic tallgrass prairie of the US Great Plains. A subtle difference in their vegetative reproduction strategies may play a role in preventing exclusion of S. nutans, the presumed weaker competitor in this region.</p> <p>2. While A. gerardii vegetative tiller densities peak in the early growing season and decline thereafter (determinate recruitment), those of S. nutans may continue to increase throughout the growing season (indeterminate recruitment), providing a potential avenue for recovery from more intensive early season competition. However, until now these patterns have only been informally observed in the field.</p> <p>3. We examined the year-to-year consistency of growing season vegetative tiller dynamics (measured as seasonal change in tiller densities) of each grass species from at an intact tallgrass prairie in Kansas - a site within the core of both species' distributions - over a period of 8 years. Then, to investigate environmental effects on these dynamics, we examined whether they differ across a Kansas landscape varying in topography, fire management regimes and the abundances of the study species. Finally, we expanded the investigation of environmental effects on growing season tiller dynamics by observing them at the periphery of the species' distributions in central Colorado, where climatic conditions are dryer and the study species' abundances are reduced.</p> <p>4. Synthesis: We found that the tiller densities of A. gerardii decline within seasons with striking consistency regardless of spatio-temporal scale or environmental factors (topography and fire regimes). In contrast, we found the seasonal dynamics of S. nutans tiller densities were dependent on environmental factors, with seasonal tiller density increases occurring only within the Kansas populations but not consistently between years. These observations lay the groundwork for establishing differences in tiller recruitment determinacy as a potentially important yet underappreciated mechanism for promoting coexistence and codominance among perennial plant species.</p>
Supplementary Tables and Datasets for publication: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream
<p>This is a data dump of the tables, genomes, and .faa files that were too large to submit as part of the publication titled: Spatial and finely tuned temporal metagenomics of river compartments reveals viral community dynamics in an urban stream</p> <p> </p> <p>Files here include:</p> <p>-Fasta file containing 1230 vMAGs.</p> <p>-Zip file containing individual fasta files for 125 MAGs</p> <p>-Annotations output for DRAM and DRAM-v for all MAGs and vMAGs</p> <p>-.faa proteins file for the full Freshwater / Wastewater / TARA Oceans dataset that was used for vContact2 biogeography analyses</p>
DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics
<p>Datasets associated with https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009797</p>
Contrasting intra-annual population dynamics of two codominant species are consistent across spatial and temporal scales
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Data from: Temporal and spatial dynamics of competitive parapatry in chewing lice
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Spatial and temporal dynamics of space use by free-ranging domestic dogs Canis familiaris in rural Africa
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Understanding complex spatial dynamics from mechanistic models through spatio-temporal point processes
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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.