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10,735 results for “dependability”
Summer litter decomposition is moderated by scale-dependent microenvironmental variation in tundra ecosystems
<p>Tundra soils are one of the world's largest organic carbon stores, yet this carbon is vulnerable to accelerated decomposition as climate warming progresses. The landscape-scale controls of litter decomposition are poorly understood in tundra ecosystems, which hinders our understanding of the global carbon cycle. We examined the extent to which the thermal sum of surface air temperature, soil moisture and permafrost thaw depth influenced litter mass loss and decomposition rates (<em>k</em>), and at which spatial thresholds an environmental variable becomes a reliable predictor of decomposition, using the Tea Bag Index protocol across a heterogeneous tundra landscape on Qikiqtaruk - Herschel Island, Yukon, Canada. We found greater green tea litter mass loss and faster decomposition rates (<em>k</em>) in wetter areas within the landscape, and to a lesser extent in areas with deeper permafrost active layer thickness and higher surface thermal sums. We also found higher decomposition rates (<em>k</em>) on north-facing relative to south-facing aspects at microsites that were wetter rather than warmer. Spatially heterogeneous belowground conditions (soil moisture and active layer depth) explained variation in decomposition metrics at local scales (< 50 m<sup>2</sup>) better than thermal sum. Surprisingly, there was no strong control of elevation or slope on litter decomposition. Our results reveal that there is considerable scale dependency in the environmental controls of tundra litter decomposition, with moisture playing a greater role than the thermal sum at < 50 m<sup>2</sup> scales. Our findings highlight the importance and complexity of microenvironmental controls on litter decomposition in estimates of carbon cycling in a rapidly warming tundra biome.</p>
Additive and dose-dependent mixture effects of Flumite 200 (flufenzin, acaricide) and Quadris (azoxystrobin, fungicide) on the reproduction and survival of Folsomia candida (Collembola)
<p> Our model organism was Folsomia candida (Collembola). We aimed to gain information on the toxicity of Quadris (azoxystrobin) and Flumite 200 (flufenzine aka. diflovidazine) on survival and reproduction and whether the animals can mitigate the toxicity with soil and/or food avoidance behaviour. Also, we aimed to test the effect of the mixture of these two pesticides. We used the OECD 232 reproduction test, a soil avoidance test, and a food choice test for both single pesticides and their mixture. We prepared the mixtures based on the concentration addition model, so the 50% effective concentrations (EC50) of the single materials were used as one toxic unit with a constant ratio of the two materials in the mixture. In the end, the measured mixture EC and LC (lethal concentration) values were compared to the estimate of the concentration addition model.</p>
Serial Dependence improves performance and biases confidence-based decisions
<p>We uploaded all the sessions in one file for each participant.<br> Each file contains a single matrix called “RESP1”.<br> The columns contain the following information:</p> <ul> <li>1<sup>st</sup>: Orientation of top stimulus.</li> <li>2<sup>nd</sup>: Orientation of bottom stimulus.</li> <li>3<sup>rd</sup>: 1 whether current top orientation was equal of previous top orientation; 2 whether current bottom orientation was equal of previous bottom orientation.</li> <li>4<sup>th</sup>: 0 whether top orientation was as right orientation. 1 whether top orientation was as left orientation.</li> <li>5<sup>th</sup>: orientation of left stimulus.</li> <li>6<sup>th</sup>: Stimulus chosen to judge (1 top; 2 bottom).</li> <li>7<sup>th</sup>: 1 whether chosen stimulus had same orientation of previous in the same position, otherwise 0.</li> <li>8<sup>th</sup>: Orientation response (1 left; 2 right).</li> <li>9<sup>th</sup>: 1 response correct, 0 response wrong.</li> <li>10<sup>th</sup>: Timestamp of start presentation of the stimulus.</li> <li>11<sup>th</sup>: Timestamp of end presentation of the stimulus.</li> <li>12<sup>th</sup>: Timestamp of chosen stimulus.</li> <li>13<sup>th</sup>: Timestamp of orientation judgment.</li> <li>14<sup>th</sup>: 1 whether variable stimulus was up or down (2).</li> <li>15<sup>th</sup>: Noise level of top stimulus.</li> <li>16<sup>th</sup>: Noise level of bottom stimulus.</li> <li>17<sup>th</sup>: 1 whether participant chosen the variable stimulus, otherwise 0.</li> <li>18<sup>th</sup>: 1 whether variable stimulus was a continuous stimulus, otherwise 0.</li> </ul>
[Supplementary material] IDLGen: Automated Code Generation for Inter-parameter Dependencies in Web APIs
<p>This is the supplementary material of the paper entitled IDLGen: Automated Code Generation for Inter-parameter Dependencies in Web APIs.</p>
Impact of forest disturbance on microarthropod communities depends on underlying ecological gradient and species traits
<p>Dataset and R scripts used in the publication "Impact of forest disturbance on microarthropod communities depends on underlying ecological gradient and species traits", PeerJ</p>
Dataset: Formulation and Implementation of Frequency-Dependent Linear Response Properties with Relativistic Coupled Cluster Theory for GPU-accelerated Computer Architectures
<p>This dataset collects the data (outputs, coordinate files) for the calculations presented in the manuscript "Formulation and Implementation of Frequency-Dependent Linear Response Properties with Relativistic Coupled<br> Cluster Theory for GPU-accelerated Computer Architectures".</p>
Data and scripts for the analysis of the influence of crop pollinator dependence and growth form on yield decline
<p>Marcelo A. Aizen, Gabriela R. Gleiser, Thomas Kitzberger, Ruben Milla. <strong>Being a tree crop increases the odds of experiencing yield declines irrespective of pollinator dependence </strong>(to be submitted to PCI)</p> <p> </p> <p>Data and R scripts to reproduce the analyses and the figures shown in the paper. All analyses were performed using R 4.0.2.</p> <p> </p> <p><strong>Data</strong></p> <p>1. FAOdata_21-12-2021.csv</p> <p>This file includes yearly data (1961-2020, column 8) on yield and cultivated area (columns 6 and 10) at the country, sub-regional, and regional levels (column 2) for each crop (column 4) drawn from the United Nations Food and Agriculture Organization database (data available at <a href="http://www.fao.org/faostat/en">http://www.fao.org/faostat/en</a>; accessed July 21-12-2021). [Used in Script 1 to generate the synthesis dataset]</p> <p>2. countries.csv</p> <p>This file provides information on the region (column 2) to which each country (column 1) belongs. [Used in Script 1 to generate the synthesis dataset]</p> <p>3. dependence.csv</p> <p>This file provides information on the pollinator dependence category (column 2) of each crop (column 1).</p> <p>4. traits.csv</p> <p>This file provides information on the traits of each crop other than pollinator dependence, including, besides the crop name (column1), the variables type of harvested organ (column 5) and growth form (column 6). [Used in Script 1 to generate the synthesis dataset]</p> <p>5. dataset.csv</p> <p>The synthesis dataset generated by Script 1.</p> <p>6. growth.csv</p> <p>The yield growth dataset generated by Script 1 and used as input by Scripts 2 and 3.</p> <p>7. phylonames.csv</p> <p>This file lists all the crops (column 1) and their equivalent tip names in the crop phylogeny (column 2). [Used in Script 2 for the phylogenetically-controlled analyses]</p> <p>8.phylo137.tre</p> <p>File containing the phylogenetic tree.</p> <p> </p> <p><strong>Scripts</strong></p> <p>1. dataset</p> <p>This R script curates and merges all the individual datasets mentioned above into a single dataset, estimating and adding to this single dataset the growth rate for each crop and country, and the (log) cumulative harvested area per crop and country over the period 1961-2020.</p> <p>2. analyses</p> <p>This R script includes all the analyses described in the article’s main text.</p> <p>3. figures</p> <p>This R script creates all the main and supplementary figures of this article.</p> <p>4. lme4_phylo_setup</p> <p>R function written by Li and Bolker (2019) to carry out phylogenetically-controlled generalized linear mixed-effects models as described in the main text of the article.</p> <p> </p> <p><strong>References</strong></p> <p>Li, M., and B. Bolker. 2019. wzmli/phyloglmm: First release of phylogenetic comparative analysis in lme4- verse. Zenodo. https://doi.org/10.5281/zenodo.2639887.</p>
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
<p>Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status. Gene expression changes were highly correlated with direct cohesin binding and gain of TAD boundaries than with the loss of boundaries. Moreover, cohesin was broadly enriched in active compartment A chromosomes, which were retained after CTCF depletion. Our results demonstrate context-specific roles of cohesin for gene expression and chromatin folding.</p>
Dataset of Commit Classification via Diff-Code GCN based on System Dependency Graph
<p>Commit Classification via Diff-Code GCN based on System Dependency Graph</p> <p>The dataset is based on Lobna Ghadhab et al. [1]. Levin et al.[2]'s dataset, and we extract all commits with pure java codes of two versions. </p> <p>In the dataset, evert commit folder have two sub-folder called before and after, they contains two version of codes. we extracted it by pydriller.</p> <p>The dataset have 1213 commits with two version java codes,and it contains three categories:</p> <p>(1) The first category is Corrective, which involves rectifying errors and faults identified during software usage.</p> <p>(2)The second category is Perfective, which entails enhancing software quality attributes, such as performance, maintainability, and usability.</p> <p>(3) Lastly, is Adaptive, which encompasses adapting the software to new environments (e.g., software or hardware) or introducing new functionalities.</p> <p>The dataset have 450 labels of Corrective. 441 for Perfective the rest for Adaptive.</p> <p> </p> <p>[1]L. Ghadhab, I. Jenhani, M. W. Mkaouer, and M.Ben Messaoud, ”Augmenting commit classification by using fine-grained source code changes and a pretrained deep neural language model,” Information and Software Technology, vol. 135, p. 106566, 2021/07/01/2021.</p> <p>[2]S. Levin and A. Yehudai, ”Using Temporal and Semantic Developer-Level Information to Predict Main</p> <p>tenance Activity Profiles,” in 2016 IEEE International Conference on Software Maintenance and Evolution (ICSME), 2016.</p> <p> </p>
Magnetic structure and field-dependent magnetic phase diagram of Ni2In-type PrCuSi
<p>Data sets for original figures in the article 'Magnetic structure and field-dependent magnetic phase diagram of Ni<sub>2</sub>In-type PrCuSi' published in <a href="https://iopscience.iop.org/article/10.1088/1361-648X/aae28d/meta">J. Phys.:Condens. Matter 30 (43) 2018</a>. The file name of each xls file corresponds to the figure number in the published article. The files can be opened using the Excel program. If there are sub-figures, or multiple frames in each figure, the data of each sub-figure is stored in separate sheets within one xls file. The files with the file extension 'vesta' can be opened using the freely available program <a href="https://jp-minerals.org/vesta/en/">VESTA</a>.</p>
Model output from "The chance of freezing – a conceptional study to parameterize temperature-dependent freezing by including randomness of ice-nucleating particle concentrations"
<p>Model output from "The chance of freezing – a conceptional study to parameterize temperature-dependent freezing by including randomness of ice-nucleating particle concentrations", accepted for publication in Atmospheric Chemistry and Physics, 2023, same authors.<br> The simulations were done using MIMICA version4 (Savre at el., 2014) and the data includes all model output presented in the publication.</p>
Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations
<p>Raw molecular dynamics simulations for the complexes simulated for 20 ns with the AMBER 12 software. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.5b01928">https://doi.org/10.1021/acscatal.5b01928</a>). Molecular topology in AMBER Parameter Topology format and Trajectories in NETCDF binary coordinate format.</p> <p>Two protonation states were simulated: non-charged state of catalytic Lys212/Asp275 (<strong>LYN626+ASH275+ASP666</strong>) and charged state of catalytic Lys212/Asp275 (<strong>LYS626+ASP275+ASP666</strong>)</p> <p>Production trajectories are included in the <strong>MM-MD</strong> folders. Input and restart coordinates files for reproducibility are located in folders <strong>inputs</strong> and <strong>rst</strong>.</p> <p>Instructions for the calculations are summarized in <em>amber_min-md.sh</em>.</p>
Data from: Sex-dependent integration of ornamentation, personality, morphology and life history
<p>Phenotypic integration can be defined as the patterns and strength of the covariance between traits in an organism. The pace of life syndrome (POLS) hypothesis provides a testable case of phenotypic integration as it predicts that traits that mediate the trade-off between current and future reproduction, should have coevolved with the slow-fast life-history continuum, and may thus covary across individuals of a population. Although the POLS hypothesis has received increasing attention over the last decade, there is still a need for investigating whether POLS are sex-specific or if ornamental traits can be included within the POLS framework. We used nine years of data to describe the integration patterns of ornamental coloration, personality, morphology and life history in blue tits (<em>Cyanistes caeruleus</em>) and whether they differed between males and females. With that aim, we fitted multivariate mixed models separating the among- from the within-individual covariances. We found that the overall integration between the studied traits was weak, but our results suggested some sex-specific covariances at the among- and within-individual levels. Besides, we found several covariances between the ornamental colors and personality in males but not in females. Finally, using structural equation models, we tested for the presence of trait modules (i.e. covariances between traits involved in the same biological function). Our results support the presence of a morphological module, not of ornamental or behavioral modules in males or females. Also, our results do not align with the POLS hypothesis, however they highlight the importance of considering sex when studying phenotypic integration.</p>
Aggregation of symbionts on hosts depends on interaction type and host traits
<p>Symbionts tend to be aggregated on their hosts, such that few hosts harbor the majority of symbionts. This ubiquitous pattern can result from stochastic processes, but aggregation patterns may also depend on the type of host-symbiont interaction, plus traits that affect host exposure and susceptibility to symbionts. Untangling how aggregation patterns both within and among populations depend on stochastic processes, interaction type and host traits remains an outstanding challenge. Here, we address this challenge by using null models to compare aggregation patterns in a neutral system of Balanomorpha barnacles attached to patellid limpets and a host-parasite system of Trinidadian guppies (Poecilia reticulata) and their Gyrodactylus spp. monogeneans. We first used a model to predict patterns of symbiont-host aggregation due to random partitioning of symbionts to hosts. This null model accurately predicted the aggregation of barnacles on limpets, but the degree of aggregation varied across 303 quadrats. Quadrats with larger limpets had less aggregated barnacles, whereas aggregation increased with variation in limpet size. Across 84 guppy populations, Gyrodactylus spp. parasites were significantly less aggregated than predicted by the null model. As in the neutral limpet-barnacle system, aggregation decreased with mean host size. Parasites were also significantly less aggregated on males than females because male guppies tended to have higher prevalence and lower parasite burdens than predicted by the null model. Together, these results suggest stochastic processes can explain aggregation patterns in neutral but not parasitic systems, though in both systems host traits affect aggregation patterns. Because the distribution of symbionts on hosts can affect symbiont evolution via intraspecific interactions, and reciprocally host behavior and evolution via host-symbiont interactions, identifying the drivers of aggregation enriches our understanding of host-symbiont interactions.</p>
Dataset: Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory
<p>This dataset comprises outputs and post-processing results related to the paper "Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory", by Xiang Yuan, Loic Halbert, Lucas Visscher and Andre Severo Pereira Gomes.</p>
Effects of local density dependence and temperature on the spatial synchrony of marine fish populations
<ol> <li><span>Disentangling empirically the many processes affecting spatial population synchrony is a challenge in population ecology. Two processes that could have major effects on the spatial synchrony of wild population dynamics are density dependence and variation in environmental conditions like temperature. Understanding these effects is crucial for predicting the effects of climate change on local and regional population dynamics.</span></li> <li><span>We quantified the direct contribution of local temperature and density dependence to spatial synchrony in the population dynamics of nine fish species inhabiting the Barents Sea. First, we estimated the degree to which the annual spatial autocorrelations in density are influenced by temperature. Second, we estimated and mapped the local effects of temperature and strength of density dependence on annual changes in density. Finally, we measured the relative effects of temperature and density dependence on the spatial synchrony in changes in density. </span></li> <li><span>Temperature influenced the annual spatial autocorrelation in density more in species with greater affinities to the benthos and to warmer waters. Temperature correlated positively with changes in density in the eastern Barents Sea for most species. Temperature had a weak synchronising effect on density dynamics, while increasing strength of density dependence consistently desynchronised the dynamics. </span></li> <li><span>Quantifying the relative effects of different processes affecting population synchrony is important to better predict how population dynamics might change when environmental conditions change. Here, high degrees of spatial synchrony in the population dynamics remained unexplained by local temperature and density dependence, confirming the presence of additional synchronizing drivers, such as trophic interactions or harvesting. </span></li> </ol>
Dataset for Task-dependent spatial processing in the visual cortex
<p>The dataset contains the mean ERPs values of each participant after the audiovidual stimulus (S2 for the spatial bisection and S for the spatial localization), divided as follows:</p> <p>- condition (i.e., 1sc: short distance between S1 and S2, 1sl: long distance between S1 and S2),</p> <p>- task (i.e., spatial bisection or spatial localization),</p> <p>- time window (i.e., 50-90 ms or 110-160 ms post stimulus), </p> <p>- roi (i.e., O1, O2, C1, C2, T7 or T8 electrodes). </p>
Dataset supporting: Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks
<p>This dataset supports the Figures in the preprint: 'Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks' by Anil et. al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.20.533396v1">2023</a>.</p> <p>The code used to genrate this data can be found on the github repository: <a href="https://github.com/swathianil">swathianil </a><a href="https://github.com/swathianil/homeostatic_structural_plasticity_rTMS"> /homeostatic_structural_plasticity_rTMS</a>.</p> <p>To interactively regenerate the figures, follow the Jupyter notebook, GraphPlotter, available in the repository.</p>
New Method for the Determination of Voltage Dependency of High- Voltage Capacitors
<p>For the measurement of high AC voltages mainly voltage transformers or capacitors are used. Capacitors are either set up as voltage dividers, in conjunction with a voltage transformer or other means in order to obtain a lower output voltage. In national metrology laboratories compressed gas capacitors are used as references for calibration purposes. The main influences on the capacitance therefore need to be clearly determined. The voltage dependency is the most significant and challenging uncertainty component up to now. This paper will discuss a new method for the direct voltage dependency determination of any capacitor design. Existing methods mainly depend on the tracking of electrodes in capacitors based on Schering-Vieweg setup. This new method considers all factors influencing the voltage dependency, not only the electrode shifting due to the electrical field.</p>
Naturalization of introduced plants is driven by life-form-dependent cultivation biases
<p><em>Aims: </em></p> <p>Most naturalized plants are escapees from cultivation. Inventories of cultivated introduced species thus offer unique, still underutilized, opportunities to assess naturalization drivers of introduced plants. We used a comprehensive inventory of 13,718 introduced species cultivated in China's botanical gardens to test which species characteristics distinguish the 739 species that have naturalized.</p> <p><em>Locations:</em> China.</p> <p><em>Methods: </em></p> <p>We used generalized linear models to test whether the naturalization of cultivated introduced plants in China is associated with functional traits, propagule pressure, environmental niche, and introduction history. To test direct and indirect effects of those variables and their relative importance in driving naturalization, we used structural equation models.</p> <p><em>Results: </em></p> <p>We showed that species were more likely to naturalize when they originate from the Americas, are more widely cultivated, and have a longer residence time. Moreover, species were more likely to naturalize if they have a good environmental match, are short-lived herbs, are predominantly propagated from seeds, and, in the case of herbs, are relatively tall compared to other herbs. Part of the latter effects are mediated by how these variables relate to propagule-pressure proxies, and this varies among short-lived herbs, long-lived herbs and woody plants. Main conclusions: Naturalization is partly driven by life-form-dependent cultivation biases.</p>
ScienceDex guides
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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.