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5,573 results for “optimality”
Juggling options: manipulation ease determines primate optimal fruit size choice
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Data for optimizing energetics of lateral undulatory locomotion unveiling morphological adaptations in different environments
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Data and code from: Deep reinforcement learning for pressure optimization in water distribution networks with multiple pumping stations: Case study
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A Comparative Study of Multi-objective Optimization Methodologies for Molecular and Process Design
<p>The files contain the set of solutions generated with various multi-objective optimization methods.</p>
SELECTION METHODS TO OPTIMIZE THE GAIN AND GENETIC DIVERSITY IN Pinus caribaea var. caribaea
The proposal of this work was to estimate the genetic variability in orchards of Pinus caribaea var. caribaea based on growth traits and to analyze the best selection method. This study was conducted in two areas of P. caribaea var. caribaea situated in Savannah biome. The first orchard was a randomized complete block design with 76 progenies and 4 controls (area 1), the second orchard, the lattice design was 10x10 with 99 progenies and one control (area 2), 28 and 27 years old, respectively. The software SELEGEN was used to estimate genetic parameters trough REML/BLUP method. Significant variation was observed between and with progeny all traits in area 2 and only between plants within plots for height in area 1. The highest estimates of genetic variation and heritability were obtained for area 1. Without the optimization of selection, the highest gain (4.8%) in the selection between and within with a selection intensity of 52%, for area 1. In area 2, the highest gain (2.86%) in individual selection. We conclude that there is low genetic variability in seedlings orchards of P. caribaea var. caribaea. However, area 1 presents higher genetic control than area 2, and should be better explored. For the next generations, it is recommended the infusion of new genetic material to proceed with a forest improvement program, since it was observed low variability and low gains in the selection of P. caribaea var. caribaea.
Fig. 7 in Optimal fishing samplers to reveal the morphological structure of a fish assemblage in a subtropical tidal flat
Fig. 7. Morphospaces obtained using the first and second relative warps for large gillnet, small gillnet and hook and line. Warm colours in the Kernel density plots indicate the shapes of major occurrence.
Fig. 6 in Optimal fishing samplers to reveal the morphological structure of a fish assemblage in a subtropical tidal flat
Fig. 6. Morphospaces obtained using the first and second relative warps for cast net, fish trap and marginal encircling gillnet. Warm colours in the Kernel density plots indicate the shapes of major occurrence.
Fig. 5 in Optimal fishing samplers to reveal the morphological structure of a fish assemblage in a subtropical tidal flat
Fig. 5. Morphospaces obtained using the first and second relative warps for otter trawl, beach seine and inner encircling gillnet. Warm colours in the Kernel density plots indicate the shapes of major occurrence.
Fig. 3 in Optimal fishing samplers to reveal the morphological structure of a fish assemblage in a subtropical tidal flat
Fig. 3. Morphological diversification and variance explained for the relative warps (RW) 1 to 3 using the thin-plate spline.
Fig. 1. a in Optimal fishing samplers to reveal the morphological structure of a fish assemblage in a subtropical tidal flat
Fig. 1. a. Araçá Bay location, bordering São Sebastião Channel, north shore of São Paulo State, Brazil; b. Araçá Bay (Photo: Gabriel Monteiro).
Demand data belonging to paper "A Practical Optimization Scheme for Real-Time Operation of Water Distribution Systems"
<p>The CSV file contains the demand data used in the paper "A Practical Optimization Scheme for Real-Time Operation of Water Distribution Systems" published in the Journal of Water Resources Planning and Management (2020)</p> <p><a href="https://doi.org/10.1061/(ASCE)WR.1943-5452.0001188">https://doi.org/10.1061/(ASCE)WR.1943-5452.0001188</a></p> <p>The demand data is for the test case and consists of one year of hourly demand values for the 8 demand nodes of the demo network. The data is in units of cubic meters per hour.</p>
Data associated with "Adjoint methods for stellarator shape optimization and sensitivity analysis"
<p>All data produced for this dissertation and the associated post-processing scripts have been archived. </p>
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>
Figure 4. Optimal maximum-likelihood tree resulting from the RAxML analysis. Bootstrap support values greater than 50 in Taxonomy of Micronesian monitors (Reptilia: Squamata: Varanus): endemic status of new species argues for caution in pursuing eradication plans
Figure 4. Optimal maximum-likelihood tree resulting from the RAxML analysis. Bootstrap support values greater than 50% are shown on the nodes. Scale bar corresponds to the mean number of nucleotide substitutions per site.
Supplemental materials for: Peri- and post-pubertal estrogen exposures of female mice optimize uterine responses later in life
<p>At birth, all female mice, including those that either lack estrogen receptor α (ERα-knockout) or that express mutated forms of ERα (AF2ERKI), have a hypoplastic uterus. However, uterine growth and development that normally accompanies pubertal maturation does not occur in ERα-knockout or AF2ERKI mice, indicating ERα mediated estrogen signaling is essential for this process. Mice that lack Cyp19 (aromatase, ArKO mice), an enzyme critical for estrogen (E2) synthesis, are unable to make E2, and lack pubertal uterine development. A single injection of E2 into ovariectomized adult (10 weeks old) females normally results in uterine epithelial cell proliferation, however, we observe that, although ERα is present in the ArKO uterine cells, no proliferative response is seen. We assessed the impact of exposing ArKO mice to E2 during pubertal and post-pubertal windows and observed that E2 exposed ArKO mice acquired growth responsiveness. Analysis of differential gene expression between unexposed ArKO samples and samples from animals exhibiting the ability to mount an E2-induced uterine growth response (WT or E2 exposed ArKO) revealed activation of EZH2 and HAND2 signaling and inhibition of GLI1 responses. EZH2 and HAND2 are known inhibit uterine growth, and GLI1 is involved in IHH signaling, which is a positive mediator of uterine response. Finally, we show that exposure of ArKO females to dietary phytoestrogens results in their acquisition of uterine growth competence. Altogether our findings suggest that pubertal levels of endogenous and exogenous estrogens impact biological function of uterine cells later in life via ERα-dependent mechanisms.</p>
Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI
<p>Repository of an anonymized sample patient dataset for paper "Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13C MRSI"</p> <p>https://doi.org/10.1002/mrm.28328.</p>
All figures and tables for "Optimized approximate inverse Laplace transform for geo-deformation computation in viscoelastic earth model"
<p>It is the data set of all figures and tables in the paper with title "Optimized approximate inverse Laplace transform for geo-deformation computation in viscoelastic earth model".</p>
A model of the optimal selection of crypto assets - simulation code
<p>In the modelling we assume that crypto assets differ by two essential features: security (technological) and stability (governance). Investors make choices over crypto assets similarly to how they make choices by using a recommender app: the app presents each investor with a pair of crypto assets with certain security-stability characteristics to be compared. Each investor submits its preference for adopting one of the two assets to the app. The app, in turn, provides a recommendation on whether the proposed adoption is sensible given the assets' essential features, information about the adoption choices of all other investors, and expected future economic benefits of adoption. Investors continue making their adoption choices over all pairs of crypto assets until their expected future economic benefits can no longer be improved upon. This constitutes an optimal selection decision. We simulate optimal selection decisions considering the behaviour of different types of investors, driven by their attitudes towards assets' features. We find a variety of possible emergent outcomes for the investments in the crypto-ecosystem and the future adoption of the crypto assets.</p>
Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates
<p>Telomere length dynamics are an established biomarker of health and aging in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real-time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization requires the development of genomic reference primers suitable for qPCR, which remains challenging in non-model organism with genomes that have not been sequenced. Here we report reference primers that can be used in qPCR to measure telomere lengths in any vertebrate species. We designed primer pairs to amplify genetic elements that are highly conserved between evolutionarily distant taxa and tested them in species that span the vertebrate tree of life. We report five primer pairs that meet the specificity and reproducibility standards of qPCR. In addition, we demonstrate an approach to choose the best primers for a given species by testing the primers on multiple individuals within a species and then applying an established computational tool. These reference primers can facilitate qPCR-based telomere length measurements in any vertebrate species of ecological or economic interest.</p>
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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.