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5,573 results for “optimality”
Data from: Marginal likelihood estimate comparisons to obtain optimal species delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)
Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii.
Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?
For decades, biologists have debated why many parasites have obligate multi-host life cycles. Here, we use comparative phylogenetic analyses of aphids to evaluate the roles of ecological optimization and historical constraint in the evolution of life cycle complexity. If life cycle complexity is adaptive, it should be evolutionarily labile, i.e., change in response to selection. We provide evidence that this is true in some aphids (aphidines), but not others (non-aphidines) – groups that differ in the intensity of their relationships with primary hosts. Next, we test specific mechanisms by which life cycle complexity could be adaptive or a constraint. We find that among aphidines there is a strong association between complex life cycles and polyphagy but only a weak correlation between life cycle complexity and reproductive mode. In contrast, among non-aphidines the relationship between life cycle complexity and host breadth is weak but the association between complex life cycles and sexual reproduction is strong. Thus, although the adaptiveness of life cycle complexity appears to be lineage specific, across aphids, life cycle evolution appears to be tightly linked with the evolution of other important natural history traits.
Data from: Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn
Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark–recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1–7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1–10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples >7 days old and estimate that a sampling interval of 4–7 days in summer conditions (i.e. extreme heat and exposure to UV light) will achieve desired sample sizes for mark–recapture analysis while also maximizing efficiency.
Data from: Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes
Females choose specific mates in order to produce fitter offspring. However, several factors interfere with females' control over fertilization of their eggs, including sneaker males and phenotypically unpredictable allele segregation during meiosis. Mate choice at the individual level thus provides only a poor approximation for obtaining the best genetic match. Consequently, post-copulatory sperm selection by female oocytes has been proposed as a mechanism to achieve complementary combinations of parental haplotypes. Here, using controlled in vitro fertilization of three-spined stickleback eggs, we find haplotype-specific fertilization bias towards gametes with complementary major histocompatibility complex (MHC) immunogenes. The resulting zygote (and thus offspring) genotypes exhibit an intermediate level of individual MHC diversity that was previously shown to confer highest pathogen resistance. Our finding of haplotype-specific gamete selection thus represents an intriguing mechanism for fine-tuned optimization of the offspring's immune gene composition and an evolutionary advantage in the Red Queen dynamics of host-parasite coevolution.
Data from: Offspring fitness and the optimal propagule size in a fluctuating environment
Propagule size is an important maternal effect on offspring fitness and phenotype in birds and other oviparous animals. The performance of propagules often increases with size, but a fluctuating environment may introduce temporal variation in the optimal phenotype. Understanding these mechanisms will provide novel insights into the eco-evolutionary dynamics of life history strategies in parental reproductive investment. We investigated the interaction between propagule size (measured as egg volume) and environmental conditions on offspring mortality and phenotype in a Norwegian house sparrow population. Increased propagule size reduced offspring mortality in early life, with more pronounced effects under heavy precipitation. However, the optimal propagule size for low offspring mortality until recruitment shifted from large to small as temperature increased. Propagule size had no significant effect on fledgling body mass and tarsus length. These results reveal a potential for eco-evolutionary dynamics in propagule size, as populations adapt to fluctuating environmental conditions. The ultimate outcome of this dynamic process will also depend on variation in parental fitness and trade-offs with other life-history traits, particularly clutch size.
Bi-objective optimization for last-train coordination planning with dwell time adjustment strategy
<p><span><span><span><span>In the design of last-train coordination plan, adjusting (extending/reducing) dwell time can balance economic and service goals for operation company and late-night passengers, especially when transfer-passenger flow is uncertain. For this purpose, we first develop</span></span><span><span> a </span></span><span><span>bi-objective</span></span> <span><span>scenario-based</span></span> <span><span>stochastic programming model for</span></span> <span><span>last-train coordination planning problem combined with</span></span><span><span> the </span></span><span><span>dwell time adjustment strategy. Then, we</span></span> <span><span>develop a two-phase approach, wherein the first phase we adopt the varepsilon-constraint method to reformulate the original model to a modified single-objective one. This is followed by the second phase using the branch-and-bound algorithm implemented by</span></span><span><span> the </span></span><span><span>CPLEX solver to obtain</span></span> <span><span>Pareto-optimal solutions (frontier). Finally, we demonstrate the advantage of the proposed model through comparison with the corresponding model without dwell time strategy and the max-min robust model over a randomly generated small-scale network. Moreover, we also illustrate the application of the proposed model by a real-world case study on the large-scale Beijing subway network.</span></span></span></span></p>
Data from: A toolkit for optimizing fish passage barrier mitigation actions
The presence of dams, stream–road crossings and other infrastructure often compromises the connectivity of rivers, leading to reduced fish abundance and diversity. The assessment and mitigation of river barriers is critical to the success of restoration efforts aimed at restoring river integrity. In this study, we present a combined modelling approach involving statistical regression methods and mixed integer linear programming to maximize resident fish species richness within a catchment through targeted barrier mitigation. Compared to existing approaches, our proposed method provides enhanced biological realism while avoiding the use of complex and computationally intensive population/ecosystem models. To estimate barrier passability quickly and at low cost, we further outline a rapid barrier assessment methodology. The methodology is used to characterize potential passage barriers for various fish species common to the UK but can be readily adapted to different planning areas and other species of interest. We demonstrate the applicability of our barrier assessment and prioritization approach based on a case study of the River Wey, located in south-east England. We find that significant increases in species richness can be achieved for modest investment in barrier mitigation. In particular, dams and weirs with low passability located on mid- to high-order streams are identified as top priorities for mitigation. Synthesis and applications. Our study shows the benefits of combining a coarse resolution barrier assessment methodology with state-of-the-art optimization modelling to cost-effectively plan fish passage barrier mitigation actions. The modelling approach can help inform on-the-ground river restoration decision-making by providing a recommended course of action that best allocates limited resources in order to restore longitudinal connectivity and maximize ecological gains.
Data from: Scale-dependent home range optimality for a solitary omnivore
Spatial and temporal heterogeneity are fundamental mechanisms structuring home ranges. Under optimality, an individual should structure their space use economically to maximize fitness. We evaluated support for three hypotheses related to range optimality in American black bears (Ursus americanus), predicting (1) range location on a landscape will correspond with high vegetation productivity, (2) increasing forest fragmentation will result in larger ranges, and (3) increasing proportion of forest and/or mean vegetation productivity will result in smaller ranges. We used black bear radio telemetry data from Michigan (2009-2015), Missouri (2010-2016) and Mississippi (2008-2017), USA. Annual space use excluded winter, and we separated seasonal space use into spring, summer, and fall. We collected data from 143 bears (80 females, 63 males), resulting in 97 annual and 538 seasonal ranges. We used generalized linear mixed models to evaluate productivity (estimated through Normalized Difference Vegetation Index, NDVI) selection, and range size (km2) variation between individuals. At the annual scale, black bears consistently selected areas with greater vegetation productivity than the surrounding landscape; yet selection weakened and was more variable seasonally. Opposite to our prediction, we found that increasing fragmentation consistently resulted in smaller ranges; non-forested land covers and forest edges might provide greater abundance or more diverse foods for bears. Ranges with a greater proportion of forest were smaller, likely reflecting an increase in food and cover which could reduce movements, yet there was no support for more productive ranges also being smaller as expected from an area minimizing strategy. Black bears displayed a scale-dependent space use strategy: at larger spatial and temporal scales, productivity acted as the strongest limiting factor and energy maximizing was the dominant strategy, while an area minimizing strategy was exhibited seasonally. We revealed consistent, scale-dependent responses by black bears to environmental conditions, demonstrating the intrinsic plasticity of this adaptable omnivore.
Bronze Goat Sculpture, Evora - Optimized
Small bronze sculpture representing a goat. It could be an ex-vote or offering related to the Roman or pre-Roman culture of the Lusitania. It is currently preserved in the Frei Manuel do Cenáculo National Museum (Évora, Portugal). Catalog No. ME3297. PEREIRA, Gabriel - Estudos Eborenses, I, 2ª ed. Évora: Edições Nazareth, 1947, p. 130. VASCONCELOS, J. Leite de - "Cabrinhas ou bodes de bronze" in O Archeologo Português, vol. I. Lisboa: Museu Ethnografhico Português, 1895, pp. 296–301. 736 photos from Canon 5D Mk IV. Completely processed (aligned, scaled, meshed, cleaned, simplified, unwrapped, textured) in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Sharpening Stone, Sharjah - Optimized
Sharpening Stone, Sharjah. Unknown Provenience. 294 photos. Completely processed (aligned, scaled, modeled, cleaned, simplified, unwrapped, textured, meshed) in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Stone Bowl, Sharjah - Optimized
Stone bowl from Sharjah, unknown provenience. 523 photos. Completely processed (aligned, scaled, modeled, cleaned, simplified, unwrapped, textured, meshed) in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Glazed Mesopotamian Jar, Mleiha - Optimized
Green glazed vessels such as this vase with ornamental handles were imported from Southern Mesopotamia. Found at the site of Mleiha, Sharjah, UAE. 2nd Century BCE. Pre-Islamic Period. 781 photos processed and modeled in Reality Capture. Source: Objaverse 1.0 / Sketchfab
Calcite Vase No. 46 Mleiha, - Optimized
Calcite Vase No. 46 of 47, from cache, Mleiha, Sharjah, UAE. The find was made by the Sharjah Archaeology Authority. 2nd-3rd Century CE. 259 photos. Completely processed (aligned, scaled, modeled, cleaned, simplified, unwrapped, textured, meshed) in Reality Capture. J. Mª Córdoba 2016. La era de Mleiha: navegantes y caravanas antes del Islam. Pp 83-130 (Figure p. 92). In EN LOS CONFINES DE ORIENTE PRÓXIMO: El hallazgo moderno del país de Magán. Museo Arqueológico Nacional Catálogo de la Exposición Temporal Celebrada entre el 18 de abril y el 29 de mayo de 2016. Comisario: J. Mª Córdoba Zoilo. Comisarias adjuntas: C. del Cerro Linares, Mª C. Pérez Díe, E. Pons Mellado Source: Objaverse 1.0 / Sketchfab
Data used for ECAL 2015 paper "Optimal Mutation Rate Control under Selection in Hamming Spaces"
<p>This dataset contains the evolved mutation rate control functions, obtained by following the methods described in the following paper, from which the means and standard deviations shown in the paper were calculated.</p> <p>Paper: Optimal Mutation Rate Control under Selection in Hamming Spaces, accepted for publication in Advances in Artificial Life, ECAL 2015: Proceedings of the Thirteenth European Conference on the Synthesis and Simulation of Living Systems.</p>
Dataset of some transition state problems solved with a deterministic global optimization method.
<p>Data of all solutions found for each problem and data for each (iterations vs open nodes) graph.<br /> </p>
FIGURE 1. Optimal tree inferred using the Neighbor-Joining method inferred from 550 in Paracoccus leucadendri Mazzeo & Franco in Mazzeo, Franco & Russo, 2009, a junior synonym of Paracoccus hakeae (Williams, 1985) comb. nov. (Coccomorpha: Pseudococcidae)
FIGURE 1. Optimal tree inferred using the Neighbor-Joining method inferred from 550 replicates. Shown next to the branches is the percentage of replicate trees in which the associated taxa clustered together in the bootstrap test. The tree is drawn to scale, with branch lengths in the same units as those of the genetic distances used to infer the tree. Genetic distances were computed using the p-distance method and are in the units of the number of base differences per site.
Optimizing agents with genetic programming - An evaluation of hyper-heuristics in dynamic real-time logistics - datasets and results
<p>This directory contains the data and results that we used and obtained during the realization of the following paper:</p> <blockquote> <p>Optimizing agents with genetic programming - An evaluation of hyper-heuristics in dynamic real-time logistics. Rinde R.S. van Lon, Juergen Branke, and Tom Holvoet. Genetic Programming and Evolvable Machines (2017).</p> </blockquote> <p>The code that has been used can be found on GitHub (https://github.com/rinde/vanLon17-GPEM-code), an archive is available at https://doi.org/10.5281/zenodo.260130.</p> <p>This repository contains the following files:</p> <ul> <li>evo.zip (expands to 21.2 GB) A zip file containing all results of the training experiment and tuning experiment.</li> <li>JAAMAS.zip (expands to 227.6 MB) A zip file containing the main results of the JAAMAS experiment, also available at https://doi.org/10.5281/zenodo.209760</li> <li>realtime.zip (expands to 913.5 MB) A zip file containing the main results</li> <li>dataset10k.zip (expands to 4.9 GB) Contains the scenarios used for the training and tuning experiments.</li> <li>overview.zip (expands to 42 MB) Contains the following files: <ul> <li>overview/experiment-overview.csv - table containing basic overview of the 40 main evolutionary runs that were performed for this paper.</li> <li>overview/heuristics/ - folder with a tree visualization for every evolved heuristic.</li> <li>overview/makefile - executes the analysis scripts that were used in the paper (requires the R programming language, https://www.r-project.org/). All tables and figures will be placed in results/generated/.</li> <li>readme.txt - this file.</li> <li>overview/results/ - contains the scripts</li> <li>overview/results/data/ - empty directory in which evo.zip, JAAMAS.zip, and realtime.zip have to be unpacked for the analysis scripts to work.</li> </ul> </li> </ul>
Scalable Co-Optimization of Morphology and control in Embodied Machines
<p>Raw Data for: Scalable Co-Optimization of Morphology and control in Embodied Machines</p> <p>Trials from Nov 2, 2015 represent phase offset controllers for resolution 1000 (10^3), trails from Nov 9, 2015 represent phase offset controllers of resolution 125 (5^3), and trails from 2016 represent neural network controllers with resolutions 1000 (10^3). </p> <p>This data was produced by the code found at: https://github.com/ncheney/morphological-innovation-protection</p>
Baseline models and optimized CNN models for 8 datasets
<p>Datasets:</p> <ul> <li>Asirra</li> <li>CIFAR-10</li> <li>CIFAR-100</li> <li>GTSRB</li> <li>HASYv2</li> <li>MNIST</li> <li>STL-10</li> <li>SVHN</li> </ul>
Dataset for the manuscript 'Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction'
<p>Dataset for the manuscript 'Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction'</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.