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21 results for “optimality theory”
Novel estimates of the leaf relative uptake rate of carbonyl sulfide from optimality theory
<p>Data and Matlab scripts for repeating the analysis presented in the paper. In addition, global monthly climatological LRUs are provided at 0.05° resolution for the period 2001-2010 as nc-files. </p>
Mapping the global distribution of C4 vegetation using observations and optimality theory
<p>This dataset includes annual C4 vegetation distribution and its uncertainty from 2001 to 2019. We also provide the distribution of C4 natural grasses and C4 crops during the same period, as well as the code and interim dataset to generate the main figures. Please refer to manuscript for more details:</p> <p>Luo, X., Zhou, H., Satriawan, T.W., Tian, J., Zhao, R., Keenan, T.F., Griffith, D. M., Sitch, S. Smith, N.G. & Still, C.J. (2024). Mapping the global distribution of C4 vegetation using observations and optimality theory. <em>Nature Communications.</em> https://doi.org/10.1038/s41467-024-45606-3.</p> <p><strong>Update (Nov 2023): </strong>we have updated the observational constraint from a linear model to a non-linear model - logistic curve, to better depict how C4 photosynthetic advantage translates into C4 grass coverage changes (C4_distribution_NUS_v2.2.nc).</p> <p><strong>Update (August 2023): </strong>we corrected the issue caused by a bias in the remote sensing grassland base map, and released the version 2 of the C4 vmap (C4_distribution_NUS_v2.nc).</p> <p><strong>Update (June 2023): </strong>we noticed there is a critical issue in the version 1 of our C4 map, due to the quality of remote sensing grassland base map used. We are now working on providing a new version (V2) in the next few months (Jun 2023).</p>
Figure 1.Flowchart of the CoDOA.-Realizing an Optimization Approach Inspired from Piaget's Theory on Cognitive Development
<p>The objective of this paper is to introduce an artificial intelligence based optimization<br> approach, which is inspired from Piaget’s theory on cognitive development. The approach has been<br> designed according to essential processes that an individual may experience while learning<br> something new or improving his / her knowledge. These processes are associated with the Piaget’s<br> ideas on an individual’s cognitive development. The approach expressed in this paper is a simple<br> algorithm employing swarm intelligence oriented tasks in order to overcome single-objective<br> optimization problems. For evaluating effectiveness of this early version of the algorithm, test<br> operations have been done via some benchmark functions. The obtained results show that the<br> approach / algorithm can be an alternative to the literature in terms of single-objective optimization.<br> The authors have suggested the name: Cognitive Development Optimization Algorithm (CoDOA)<br> for the related intelligent optimization approach.</p>
Global dataset for "Global leaf-trait mapping based on optimality theory "
<p>This repository contains Global data used for “<em>Global leaf-trait mapping based on optimality theory</em><strong>” </strong>published in GEB.</p> <ol> <li>Global_Maps_SLA represents climatology of published Global SLA used for comparison (details products see table 1 and figure 4).</li> <li>Global_Maps_Na represents climatology of published Global Narea used for comparison (details see table 1 and figure 4).</li> <li>Global_Maps_Nmass represents climatology of published Global Nmass used for comparison (details see table 1 and figure 4).</li> <li>TS_SLA is simulated time-series of <em>SLA</em> based on optimality theories from 1992 to 2015</li> <li>TS_Na is simulated time-series of <em>Narea </em>based on optimality theories from 1992 to 2015</li> <li>TS_Nmass is simulated time-series of <em>Nmass </em>based on optimality theories<em> </em> from 1992 to 2015</li> <li>TS_LMA_decidudous is simulated time-series of deciduous <em>LMA</em> based on optimality theories from 1982 to 2016</li> <li>TS_LMA_evergreen is simulated time-series of evergreen <em>LMA</em> based on optimality theories from 1982 to 2016</li> <li>TS_Vcmax25 is simulated time-series of Vcmax25 based on optimality theories from 1982 to 2016</li> </ol>
Dataset and source code for "Explanation and optimizing multi-model blending algorithm using random variables theory"
<p>this dataset contain: </p> <ol> <li>2m temperature de-biased model forecast data on station location, ECMWF, NCEP, JP and CMA</li> <li>2m temperature observaton data, obs_t2m</li> <li>24H QPF model forecast data on station location, ECMWF, NCEP, CMA-GFS, in raw_data_r24.zip</li> <li>24H precipitation data, in raw_data_r24.zip</li> <li>source code (in python)</li> </ol> <p> </p> <p>how to use it: </p> <p>1. prepare data and python environment<br> 1.1 if you want to run [Station_FCST_MMWB.py] or [Station_FCST_MMWB_r24.py] , please download the station forecast and observation data<br> 1.2 neet meteva package to read/write micaps-3 format data: https://github.com/nmcdev/meteva<br> 1.3 need cartopy to draw picture FigS01. </p> <p>2. try the 2m temperature blending methods <optional><br> 2.1 unzip the [CMA.zip, ECMWF.zip, jp.zip, NCEP.zip, obs_t2m.zip] file into ./raw_data/<br> 2.2 run the Station_FCST_MMWB.py in python environment </p> <p>3. try the 24h QPF multi blending methods <optional><br> 3.1 unzip the [raw_data_r24.zip] file into ./raw_data_r24/<br> 3.2 run the Station_FCST_MMWB_r24.py in python environment</p> <p>4. draw figures<br> 4.1 run Fig01.py in python environment <br> 4.2 run Fig02.py in python environment <br> 4.3 run Fig03.py in python environment <br> 4.4 run FigA01.py in python environment <br> 4.5 run FigS01.py in python environment </p>
Data for: Nest material preferences in wild hazel dormice Muscardinus avellanarius: Testing predictions from optimal foraging theory
<p class="MsoNormal">Obtaining nesting material presents an optimal foraging problem, collection of materials incurs a cost in terms of risk of predation and energy spent, and individuals must balance these costs with the benefits of using that material in the nest. The hazel dormouse, <em>Muscardinus avellanarius</em> is an endangered British mammal in which both sexes build nests. However, whether material used in their construction follows the predictions of optimal foraging theory is unknown. Here, we analyse the use of nesting materials in forty two breeding nests from six locations in Southwest England. Nests were characterised in terms of which plants were used, the relative amount of each plant, and how far away the nearest source was. We find that dormice exhibit a preference for plants closer to the nest, but that the distance they are prepared to travel depends on the plant species. Dormice travelled further to collect honeysuckle <em>Lonicera periclymenum</em>, oak <em>Quercus robur</em>, and beech <em>Fagus sylvatica</em> than any other plants. Distance did not affect the relative amount used, although the proportion of honeysuckle in nests was highest, and more effort was expended collecting honeysuckle, beech, bramble <em>Rubus fruticosus</em> and oak compared to other plants. Our results suggest that not all aspects of optimal foraging theory apply to nest material collection. However, optimal foraging theory is a useful model to examine nest material collection, providing testable predictions. As found previously honeysuckle is important as a nesting material, and should be taken account when assessing suitability of sites for dormice.</p>
Data from: Evaluating Sphagnum traits in the context of resource economics and optimal partitioning theories
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Data for: Nest material preferences in wild hazel dormice Muscardinus avellanarius: Testing predictions from optimal foraging theory
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Optimal Defense Theory in an ant‐plant mutualism: extrafloral nectar as an induced defense is maximized in the most valuable plant structures
<ol> <li class="Normal1">Optimal Defense Theory (ODT) predicts that to maximize the benefits of defense against herbivores while minimizing its costs, plants will <span><span>invest in defenses</span></span> to structures according to their value and to the likelihood that they will be attacked. Constitutive defenses are expected in structures of high value, whereas induced defenses are expected in structures of low value. Regarding the biotic defense mediated by extrafloral nectaries (EFNs) and based on ODT, we predicted that under control conditions EFNs on higher-value structures would produce more nectar than would EFNs on lower-value structures, attracting more ants; however, when damaged, EFNs on higher-value structures would not increase the production of extrafloral nectar (since constitutive defenses should be employed in this region), whereas EFNs on lower-value structures would so (since induced defenses should be employed in this region), at a level commensurate with the extent of damage. </li> <li class="Normal1">Here we test these predictions in a Brazilian ant-plant mutualism. <i>Qualea multiflora</i> (Vochysiaceae), a savanna tree, presents EFNs on both lower-value structures (leaves) and higher-value structures (inflorescences). We simulated herbivory by cutting 10% or 40% of the leaves, or 10% of the flowers, then monitoring extrafloral nectar production and ant attendance. </li> <li class="Normal1">Extrafloral nectar volume and calorie content, as well as ant abundance, were higher in EFNs of inflorescences compared to EFNs of leaves both before and after simulated herbivory, consistent with one of our predictions. However, EFNs on both leaves and inflorescences, not leaves only, were induced by simulated herbivory, a pattern opposite to our prediction. Plants subjected to higher levels of leaf damage (i.e., more damage to lower-value tissues) <span><span>produced more and higher-calorie extrafloral nectar, but showed similar ant abundance, partially consistent with our prediction</span></span>. </li> <li class="Normal1"><span><span><span><span><span><span><span><span><span><span><span>Our results show that extrafloral nectar production before and after simulated herbivory, as well as the ant recruitment, vary according to the plant structure on which EFNs are located. Our study is unique showing that ant recruitment via extrafloral nectar follows predictions from Optimal Defense Theory, and that the ant foraging patterns may be shaped by the level and region damaged in the plant.</span></span></span></span></span></span></span></span></span></span></span></li> </ol>
Data for PASP paper: Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation
<p>High-resolution figures for paper "Optimal photometry of point sources: Joint source flux and background determination on array detectors - from theory to practical implementation", accepted for publication in The Publications of the Astronomical Society of the Pacific (PASP).</p>
Research data for: "Band Structure Interpolation using Optimized Local Orbitals from Linear-Scaling Density-Functional Theory"
<p>This file was created by Laura E. Ratcliff on 23rd March 2018. It contains the input files employed for the ONETEP and CASTEP calculations in the above publication.</p> <p>Directory Listing:</p> <p>castep/</p> <p>Contains the input files used to generate the CASTEP reference data.</p> <p>onetep/</p> <p>Contains the input files used to generate all of the ONETEP data, where filenames are labelled with the number of repeat CNT units, val (cond) indicates a valence (conduction) calculation and the suffixes follow a similar labelling convention to that employed in the manuscript.</p>
Optimizing the Social Engagement System in Prader-Willi Syndrome: Insights From the Polyvagal Theory
ClinicalTrials.gov study NCT03101826. IPD Sharing: NO. Countries: 1. Publications: 6.
Optimal Defense Theory in an ant‐plant mutualism: extrafloral nectar as an induced defense is maximized in the most valuable plant structures
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Data for "An application of upscaled optimal foraging theory using hidden Markov modelling: year-round behavioural variation in a large arctic herbivore"
<p>Data for the article “An application of upscaled optimal foraging theory using hidden Markov modelling: year-round behavioural variation in a large arctic herbivore”</p> <p>By LT Beumer, J Pohle, NMS Schmidt, M Chimienti, JP Desforges, LH Hansen, R Langrock, SH Pedersen, M Stelvig, FM van Beest</p> <p> </p> <p>The data set includes three files: A readme file describing the data files and two data files accompanying the above publication.</p> <p>Combined, the two data files represent the dataset collected by GPS collars fitted on 19 female muskoxen in northeast Greenland (28 muskox-years with 153-1062 observation days/animal) and associated extracted covariates, divided into a summer and winter season dataset as modelled in the article. Data here are given as included in the models (for a description of cleaning procedures, see article). All continuous, non-cyclical covariates were standardised to have zero mean and unit standard deviation to improve numerical stability of parameter estimation. This is indicated by “_scaled” in the column name.</p> <p>For further queries please contact nms@bios.au.dk</p>
Project files provided as supporting information to the manuscript "An information theory-based approach for optimal model reduction of biomolecules"
<p>The dataset contains the following files:</p> <ul> <li>- adenylate.zip</li> <li>- antitrypsin.zip</li> <li>- tamapin.zip</li> <li>- analysis_notebooks.zip</li> </ul> <p>Each of these refers to one of three proteins. For each CG sites number N, each compressed folder contains the following files:</p> <ul> <li>random mappings (random_mappings_${N}.txt) </li> <li>random mapping entropies (random_smaps_${N}.txt) [fig1]</li> <li>optimal mappings (lowest_mappings_${N}.txt) [fig3, fig4, figS2]</li> <li>optimal mapping entropies (lowest_smaps_${N}.txt) [fig1]</li> <li>pdb files with conservations probabilities in the beta factor column (${N}_probs.pdb) [fig4, figs2]</li> <li>SASA values (${protein_name}_SASA_residues.xvg </li> <li>transition mapping entropies (${protein_name}_transition_smaps.txt) [fig2]</li> <li>additional transition mapping entropies (${protein_name}_transition_smaps*) [figs3]</li> </ul> <p>The file analysis_notebooks.zip contains the python3 notebooks employed to perform all the analysis present in the paper:</p> <ul> <li>paper_analysis_adenylate.ipynb</li> <li>paper_analysis_antitrypsin.ipynb</li> <li>paper_analysis_tamapin.ipynb</li> </ul> <p>Packages required for the usage of these python 3 scripts:</p> <p>- numpy<br> - pandas<br> - matplotlib<br> - seaborn<br> </p>
Data from: Locally and systemically induced glucosinolates follow optimal defence allocation theory upon root herbivory
1. Herbivore-induced defences in plants are considered a strategy to manage multiple interactions while saving resources. The optimal defence theory (ODT) is one of the most prominent theoretical frameworks to explain the defence allocation patterns within plants. It was recently shown that the ODT generally applies to constitutive glucosinolate (GSL) allocation in shoot and root organs. Previous studies showed that both root and shoot herbivore feeding may alter defence allocation over plant organs. For shoots, the effect depends on where the herbivores feed. It is as yet unknown whether similar principles apply to root-herbivore induced GSLs. 2. To analyse the effects of root localized herbivore feeding on GSL allocation, we conducted a pot experiment using Anomala cuprea grubs and four Brassicaceae; Brassica rapa, B. nigra, B. oleracea, and Sinapis alba. Individuals of these four plant species were grown in dedicated mesocosms. The grubs were confined either to the bottom soil, the middle section, or to the top soil. Plants grown in the same set-ups but without root herbivores served as controls. Glucosinolate levels of the leaf lamina, petiole, and stem as well as of the taproot, lateral roots, and fine roots were measured after eight days of herbivory. 3. Plant biomass reduction due to herbivory was the largest when herbivores were confined to the top soil. In the three Brassica species, taproot GSL levels increased upon herbivory independent of where the root herbivores were feeding. Glucosinolate levels in fine roots and shoots, on the other hand, hardly responded to root herbivory. Indole GSLs, which are more effective to pathogens than to herbivores, were more strongly induced than aliphatic and aromatic GSLs, especially in the taproots. Sinapis alba did not show remarkable increments in any GSL level upon herbivory. 4. These results show that locally and systemically induced defences in roots are consistent with the ODT: the taproot which is the most vulnerable and valuable to plant performance shows the highest increase in defence induction. The induced GSL profiles suggest that the response may not only target herbivores, but may also help to prevent secondary infection by microbial pathogens.
Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife
1. Better understanding human-wildlife interactions and their links with management can help improve the design of wildlife protection zones. One important example is the problem of wildlife collisions with vehicles or human-built structures (e.g. power lines, wind farms). In fact, collisions between marine wildlife and watercraft are among the major threats faced by several endangered species of marine mammals. Natural resource managers are therefore interested in finding cost-effective solutions to mitigate these threats. 2. We combined abundance estimators with encounter rate theory to estimate relative lethal collision risk of the Florida manatee (Trichechus manatus latirostris) from watercraft. We first modeled seasonal abundance of watercraft and manatees using a Bayesian analysis of aerial survey count data. We then modeled relative lethal collision risk in space and across seasons. Finally, we applied decision analysis and Linear Integer Programming to determine the optimal design of speed zones in terms of relative risk to manatees and costs to waterway users. We used a Pareto efficient frontier approach to evaluate the performance of alternative zones, which included additional practical considerations (e.g. spatial aggregation of speed zones) in relation to the optimal zone configurations. 3. Under the various relationships for probability of death given strike speed that we considered, the current speed zones reduced the relative lethal collision risk by an average of 51.5% to 70% compared to the scenario in which all speed regulations were removed (i.e. the no-protection scenario). We identified optimal zones and near-optimal zones with additional management considerations that improved upon the current zones in terms of cost or relative risk. 4. Policy Implications: Our analytical framework combines encounter rate theory and decision analysis to quantify the effectiveness of speed zones protecting manatees while accounting for uncertainty. Our approach can be used to optimize the design of protection zones intended to reduce conflicts between human waterborne activity and marine mammals. This framework could be extended to address many other problems of human-wildlife interactions, such as the optimal placement of wind farms to minimize collisions with wildlife or the optimal allocation of ranger effort to mitigate poaching threats.
Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife
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Data from: Root and shoot glucosinolate allocation patterns follow optimal defence allocation theory
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Data from: Locally and systemically induced glucosinolates follow optimal defence allocation theory upon root herbivory
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ScienceDex guides
Understand access before you commit
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.