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231 results for “Decoupling”
Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
<p>Data and analysis code repository for: </p> <p>Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation</p> <p>https://doi.org/10.1101/255380</p>
Code and Data for "Green Growth in the Mirror of History: Long-Term Evidence on Decoupling Emissions from GDP"
<p><span>The code and files contained in this repository allow for the reproduction of the results and figures from the paper <em>“Green Growth in the Mirror of History: Long-Term Evidence on Decoupling Emissions from GDP”</em> (submitted to <em>Nature Communications</em>). In particular, it generates the historical database of gross domestic product (GDP), population, and greenhouse gas emissions (GHGe) at the national, regional, and global levels from 1820 to 2022. It also includes the code required for data processing and allows reproduction of all figures and analyses in the manuscript.</span></p> <p><span>The repository is organized into a set of folders functioning as an R project. </span><span>These folders are as follows:</span></p> <p><span><span>·<span> </span></span></span><strong><span><span>data_input:</span></span></strong><span><span> Contains the databases and files necessary to run our code that have been preprocessed by ourselves. The databases which we have not preprocessed are downloaded directly from their original sources using the links provided in the R scripts. These databases were created by other researchers. Please cite the original databases if you use them directly.</span></span></p> <p><span><span><span>·<span> </span></span></span></span><strong><span><span>code:</span></span></strong><span><span> Contains R scripts used to process the datasets from data_input and to produce the figures. These scripts are:</span></span></p> <p><span><span>o<span> </span></span></span><strong><span><span>common.</span></span><span><strong>R</strong> </span></strong><span>contains code that is sourced in the other scripts and does not need to be run by the user.</span></p> <p><span><span>o<span> </span></span></span><strong><span>input_processing.R</span></strong><span> processes the data input to generate the main dataset saved in the folder data_output and used to make the figures.</span></p> <p><span><span>o<span> </span></span></span><strong><span>figures.R</span></strong><span> contains the code that processes the main dataset to produce each figure.</span></p> <p><span><span>·<span> </span></span></span><strong><span><span>data_output:</span></span></strong><span><span> Contains datasets generated by the scripts contained in<strong> </strong>input_processing.R that are used to produce the figures.</span></span></p> <ul> <li><strong><span>figures:</span></strong><span> This folder contains all the figures produced by figures.R. Note that some figures also underwent purely aesthetic edits in external software (Adobe Illustrator) for clarity purposes.</span></li> </ul>
Enhanced isohydric behavior decoupled the whole-tree sap flux response to leaf transpiration under nitrogen addition in a subtropical forest
<p><span>Anthropogenic nitrogen deposition has the potential to change the leaf water-use strategy in the subtropical region of China. Nevertheless, the whole-tree level response crucial for ecosystem functions has not been well addressed over the past decades. In this study, the stem sap flux density (J<sub>S</sub>) was monitored for the whole-tree water transport capacity in two dominant species (<em>Schima</em> <em>superba</em> and <em>Castanopsis</em> <em>chinensis</em>) in a subtropical forest. To simulate the increased nitrogen deposition, the NH<sub>4</sub>NO<sub>3</sub> solutions were sprayed onto the forest canopy at 25 kg </span><span>ha<sup>-1</sup> year<sup>-1</sup></span><span> (CAN25) and 50 kg ha<sup>-1</sup> year<sup>-1</sup> (CAN50), respectively, since April 2013. The </span><span>J<sub>S</sub></span><span> and microclimate (monitored since January 2014) derived from the whole-tree level </span><span>stomatal conductance </span><span>(G<sub>S</sub>) were used to quantify the stomatal behavior </span><span>(G<sub>S</sub> sensitive to</span><span> vapor pressure deficit</span><span>, G<sub>S-VPD</sub>)</span><span> in response to the added nitrogen. </span><span>The maximum shoot hydraulic conductance (Kshoot-max) was also measured for both species. After one year of monitoring</span><span> in January 2015, the </span><span>mid-day (J<sub>S-mid</sub>) and daily mean (J<sub>S-mean</sub>) sap flux rates did not change under all the nitrogen addition treatments (p > 0.05). A consistent</span><span> decline in the </span><span>G<sub>S-VPD</sub></span><span> indicated an enhanced isohydric behavior for both species. In addition, the G<sub>S-VPD</sub></span><span> in the wet season was much lower than that in the dry season. </span><span><em>S</em>. <em>superba</em> </span><span>had a lower </span><span>G<sub>S-VPD</sub></span><span> and decreased J<sub>S-mid</sub>/J<sub>S-mean</sub>, implying a stronger stomatal control under the fertilization, which might be attributed to the low efficient diffuse-porous conduits and a higher JS. In addition, the G<sub>S</sub> for </span><span><em>S</em>. <em>superba</em></span><span> decreased and the </span><span>G<sub>S-VPD</sub></span><span> increased more under CAN50 than that under CAN25, indicating that the high nitrogen dose restrains the extra nitrogen benefits. Our results indicate</span><span>d</span><span> that the J<sub>S</sub> for both species was decoupled from the leaf transpiration for both species due to an enhanced isohydric behavior, and a xylem anatomy difference and fertilization dose would affect the extent of this decoupling relation.</span></p>
Data from: Microbial population dynamics decouple growth response from environmental nutrient concentration
<p>To explore the diversity of microbial growth responses, we have compiled 247 measurements of half-saturation concentrations<strong> </strong>K and maximum growth rates gmax from previously-published studies (see Methods). The data includes a wide range of resources, including sources of carbon, nitrogen, phosphorus, metals, and vitamins, with phosphate, glucose, and nitrate having the largest number of measurements due to their emphasis in marine and laboratory systems. Organisms include prokaryotes and eukaryotes as well as autotrophs and heterotrophs.</p> <p>This data has been analyzed in a <strong>companion research article</strong>. For data plots and a discussion of results, please refer to:</p> <div class="csl-bib-body"> <div class="csl-entry">Fink, Justus Wilhelm, Noelle A. Held, and Michael Manhart. "Microbial Population Dynamics Decouple Growth Response from Environmental Nutrient Concentration." <em>Proceedings of the National Academy of Sciences</em> 120, no. 2 (January 10, 2023). <a href="https://doi.org/10.1073/pnas.2207295120">https://doi.org/10.1073/pnas.2207295120</a>.</div> </div>
Decoupling pioneering traits from latitudinal patterns in a North American bird experiencing a southward range shift
<ol> <li>Eco-geographic rules describe spatial patterns in biological trait variation and shed light on the drivers of such variation. In animals, a consensus is emerging that 'pioneering' traits may facilitate range shifts via a set of bold, aggressive, and stress-resilient traits. Many of these same traits are associated with more northern latitudes, and most range shifts in the northern hemisphere indicate northward movement. As a consequence, it is unclear whether pioneering traits are simply corollaries of existing latitudinal variation, or whether they override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> <li>The tree swallow (<em>Tachycineta</em> <em>bicolor</em>) is a songbird undergoing a <em>southward</em> range shift in the eastern United States, in direct opposition of the poleward movement seen in most other native species' range shifts. Because this organic range shift countervails the typical direction of movement, this case study provides for unique ecological insights on organisms and their ability to thrive in our changing world.</li> <li>We sampled female birds across seven populations, quantifying behavioral, physiological, and morphological traits. We also used GIS and field data to quantify a core set of ecological factors with strong ties to these traits as well as female performance.</li> <li>Females at more southern expansion sites displayed higher maternal aggression, higher baseline corticosterone, and more pronounced elevation of corticosterone following a standardized stressor, contrary to otherwise largely conserved latitudinal patterning in these traits. Microhabitat variation explained some quantitative phenotypic variation, but the expansion and historic ranges did not differ in openness, distance to water, or breeding density.</li> <li>This countervailing range shift therefore suggests that pioneering traits are not simply corollaries of existing latitudinal variation, but rather, they may override other well-trodden latitudinal patterning as a unique eco-geographic rule of phenotypic variation.</li> </ol>
Heteronuclear decoupling with rotorsynchronized phase-alternated cycles
<p>Raw NMR data used in Figures 4 to 10.</p>
Decoupling of functional traits from intraspecific patterns of growth and drought stress resistance
<p>Intraspecific variation in functional traits may mediate tree species' drought resistance, yet it remains unknown if trait variation is due to genotype (G), environment (E), or GxE interactions. Understanding the drivers of intraspecific trait variation and whether variation mediates drought response can improve predictions of species' response to future drought.</p> <p>Using populations of quaking aspen spanning a climate gradient, we investigated intraspecific variation in functional traits in the field as well as the influence of G and E among propagules in a common garden. We also tested for trait-mediated trade-offs in growth and drought stress tolerance.</p> <p>We observed intraspecific trait variation among the populations, yet this variation did not necessarily translate to higher drought stress tolerance in hotter/drier populations. Additionally, plasticity in the common garden was low, especially in propagules derived from the hottest/driest population. We found no growth-drought stress tolerance trade-offs and few traits exhibited significant relationships with mortality in the natural populations, suggesting that intraspecific trait variation among the traits measured did not strongly mediate responses to drought stress.</p> <p>Our results highlight the limits of trait-mediated responses to drought stress and the complex GxE interactions that may underly drought stress tolerance variation in forests in dry environments.</p>
Anthropogenic change decouples a freshwater predator's density feedback
<p>The datasets here were used to determine annual changes in anthropogenic environmental stressors, the prey-fish community, and the walleye population in Lake Erie and its western basin during 1969–2018. Here, we provide three datasets, which are used in the paper by Sinclair et al. titled: "Anthropogenic change decouples a freshwater predator's density feedback". Each dataset is provided as a separate tab in a single Excel worksheet. The first dataset ("Environmental stressors") provides the annual values for nutrient inputs, water transparency, temperature, and commercial walleye harvest. The second dataset ("Prey-fish community") provides the annual catch-per-unit-effort (CPUE; individuals per trawl minute) for all fish species that tend to be found in walleye diets caught in Lake Erie's western basin during 1969–2018 in fall (September-October) trawl surveys conducted by the Ohio Department of Natural Resources - Division of Wildlife. The third dataset ("Walleye") provides the annual estimated size of the age-3+ walleye population, the number of walleye growing degree days, and the average lengths of age-1 and age-2 walleye caught in gill net surveys conducted in the western basin by the Ohio Department of Natural Resources - Division of Wildlife. A summary and explanation of each variable are also provided in the "Info" tab. Further information on how values were calculated is provided in the methods and supporting information of the associated article.</p>
BioKG with attributes and decoupled benchmarks
<p>BioKG is a biomedical knowledge graph containing relationships between proteins, molecules, diseases, and others. It was originally proposed by Walsh et al. (2020) in <a href="https://dl.acm.org/doi/10.1145/3340531.3412776">"BioKG: A Knowledge Graph for Relational Learning On Biological Data"</a>.</p> <p>We enrich this dataset with the aim of incorporating multimodal data associated with biomedical entities:</p> <ul> <li>Proteins: Protein embeddings computed with <a href="https://github.com/agemagician/ProtTrans">ProtTrans</a> from aminoacid sequences</li> <li>Molecules: Molecule embeddings computed with <a href="https://github.com/kexinhuang12345/MolTrans">MolTrans</a> from SMILES representations</li> <li>Diseases: Textual descriptions retrieved from <a href="https://www.nlm.nih.gov/mesh/meshhome.html">MeSH</a></li> </ul> <p>Furthermore, we decouple the benchmarks provided by Walsh et al. from the edges in the knowledge graph, which ensures that there is no direct data leakage between the benchmarks and the triples used to train link prediction models.</p>
Data for: A size-based perspective on the decoupling between compositional and functional changes in planktonic communities
<p><span>Recent studies have shown a decoupling in the way community composition and functions respond to environmental changes</span><span>. A common pattern observed is that aggregated functions at the community level are more stable than community composition, which is likely the result of functional compensatory dynamics driven by interspecific differences in response to environmental change. However, the mechanisms by which these patterns emerge remain largely unexplored. Here, we investigated in a mesocosm experiment for four weeks the compositional and functional responses of edible phytoplankton (<64µm) and cladoceran zooplankton communities to climate warming (</span><span>a constant increase of +3.5°C plus heat wave</span><span>) and eutrophication (nutrient additions) from a size-based perspective. Our results show that warming increases small-sized taxa and decreases large-sized taxa within both phytoplankton and zooplankton community composition. We found that such opposite responses of different-sized taxa contributed to the stability of planktonic community functions and thereby resulted in a decoupling between compositional and functional changes. We also found that nutrient additions increased the abundance of all-sized algal taxa, while phytoplankton community function remained stable. Nutrient additions did not alter the zooplankton community, neither compositionally nor functionally. Under the combined stress of warming and nutrient additions, the compositional and functional responses of planktonic communities were mainly driven by warming. In a broader perspective, our findings reveal a size-dependent compensation mechanism and suggest that functional stability relies on compensatory effects among different-sized taxa, and it is therefore important that communities host a large range of taxa differing in size to withstand an increasingly more variable environment in the future.</span></p>
Data from: Remotely sensed environmental measurements detect decoupled processes driving population dynamics at contrasting scales
<p class="MsoNormal">The increasing availability of satellite imagery has supported a rapid expansion in forward-looking studies seeking to track and predict how climate change will influence wild population dynamics. However, these data can also be used in retrospect to provide additional context for historical data in the absence of contemporaneous environmental measurements. We used 167 Landsat-5 Thematic Mapper (TM) images spanning 13 years to identify environmental drivers of fitness and population size in a well-characterized population of banner-tailed kangaroo rats (<em>Dipodomys spectabilis</em>) in the southwestern United States. We found evidence of two decoupled processes that may be driving population dynamics in opposing directions over distinct time frames. Specifically, increasing mean surface temperature corresponded to increased individual fitness, where fitness is defined as the number of offspring produced by a single individual. This result contrasts with our findings for population size, where increasing surface temperature led to decreased numbers of active mounds. These relationships between surface temperature and (i) individual fitness and (ii) population size would not have been identified in the absence of remotely sensed data, indicating that such information can be used to test existing hypotheses and generate new ecological predictions regarding fitness at multiple spatial scales and degrees of sampling effort. To our knowledge, this study is the first to directly link remotely sensed environmental data to individual fitness in a nearly exhaustively sampled population, opening a new avenue for incorporating remote sensing data into eco-evolutionary studies.</p>
Data: Multilayer integration in silicon nitride: decoupling linear and nonlinear functionalities for ultralow loss photonic integrated systems
<p>This folder contains the data relative to the paper with title:<br> Multilayer integration in silicon nitride: decoupling linear and nonlinear functionalities for ultralow loss photonic integrated systems<br> by<br> Marcello Girardi, Óskar Helgason, Alexander Caut, Magnus Karlsson, Anders Larsson, Victor Torres Company</p> <p>Chalmers University of Technology</p>
An elevational phylogeographic diversity gradient in Neotropical birds is decoupled from speciation rates
<p>A key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared to the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.</p>
Data associated with Vandeleest, Beisner et al. (PeerJ, 2016) "Decoupling Social Status and Status Certainty Effects on Health in Macaques: A Network Approach"
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Data associated with Vandeleest, Beisner et al. (PeerJ, 2016) "Decoupling Social Status and Status Certainty Effects on Health in Macaques: A Network Approach"
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Supplementary Movies: High-rate very-long-period seismicity at Yasur volcano, Vanuatu: Source mechanism and decoupling from surficial explosions and infrasound
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Barriers decouple population dynamics of riverine fish, and asynchrony of subpopulations promotes stability within fragments
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Decoupling pioneering traits from latitudinal patterns in a North American bird experiencing a southward range shift
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Data from: A trait-based approach elucidates the synergies and vulnerabilities of ecosystem services in drylands, as well as their decoupling from biodiversity
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Decoupling of uptake and transport-related traits in absorptive roots across coexisting herbaceous species in alpine meadows
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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.