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5,573 results for “optimality”
Code for multidrug combination optimizations
<p>Matlab code and matrices to perform drug combination optimizations. For the full description and results please consult <em>Zoetemelk et al.</em> <strong>Optimized high-order low-dose drug mixtures boost selectivity and efficacy of colorectal carcinoma treatment </strong></p>
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>
Optimization of Convolution Reverberation (sound samples)
<p>Sound samples of the paper "Optimization of Convolution Reverberation" by Sadjad Siddiq. To be published in the proceedings of DAFx20.</p>
SUBINTERNM: Optimizing Internetwork Matching ofOntologies
<p>The dataset containing the experiment used in the article.</p> <p>- File .xlsx contains the results (times and metrics)</p> <p>- Files *.sh containing the script used to call LogMap</p> <p>- Subfolders contain the output generated by LogMap</p> <p>- RDF files - reference alignments</p> <p>- OWL files - ontologies and partial ontologies generated by the SubInterNM app</p> <p> </p> <p> </p> <p> </p>
Juggling options: manipulation ease determines primate optimal fruit size choice
<p>Optimal foraging theory predicts that animals will seek simultaneously to minimize food processing time and maximize energetic gain. To test this hypothesis, we evaluated whether a specialist seed-predator primate forages optimally when choosing among variable-sized thick-husked fruits. Our objects of study were the golden-backed-uacari (<em>Cacajao ouakary</em>, Pitheciidae) and single seeded pods of the macucu tree (<em>Aldina latifolia</em>, Fabaceae). We predicted that golden-backed-uacari will consume fruits of the size class that requires the least time to obtain, handle, and ingest. We used scan-sampling, ad libitum to record feeding observations, and measured fruits, their penetrability and the size of taxidermised <em>C. ouakary</em> hands. To test if uacaris selected for optimal characteristics, we compared 8 metrics from 75 eaten and 105 uneaten seeds/fruits collected. Uacaris selected fruits of medium size and weight disproportionately to their abundance. Processing large fruits took six times longer than did medium-sized fruits, but seeds were only four times as large, that is, for energetic yield per unit time, thus choosing medium-sized pods was optimal. Disproportionate selection by <em>C. ouakary</em> of fruits of medium size and mass in relation to their abundance suggests active sub-sampling of the available weight-size continuum. This selectivity probably maximizes trade-offs between the energy derived from a seed, and time and energy expended in processing fruit to access this, so following optimal foraging theory predictions. The greater time spent processing large pods is attributed to difficulties manipulating objects five to seven times the size of the animal's palm and one-sixth its own body weight.</p>
Designing and Comparing Optimized Pseudo-Continuous Arterial Spin Labeling Protocols for Measurement of Cerebral Blood Flow
<p>This repository contains the the simulation data, preprocessed in vivo data, and analysis code used in the NeuroImage article titled 'Designing and Comparing Optimized Pseudo-Continuous Arterial Spin Labeling Protocols for Measurement of Cerebral Blood Flow' (<a href="https://doi.org/10.1016/j.neuroimage.2020.117246">https://doi.org/10.1016/j.neuroimage.2020.117246</a>). Please cite this article if you use this code or data in your work.</p>
Data and Code for: Performance Evaluation of the Particle Swarm Optimization Algorithm to Unambiguously Estimate Plasma Parameters from Incoherent Scatter Radar Signals
<p>This repository contains the datasets and scripts used to obtain the figures of the paper "Performance Evaluation of the Particle Swarm Optimization Algorithm to Unambiguously Estimate Plasma Parameters from Incoherent Scatter Radar Signals".</p> <p>The repository is organized as follows:<br> - Part I) Monte Carlo simulation codes</p> <p>- Part II) Monte Carlo simulations using the parameter configuration "Param. 1" of Shi et al. (1999)</p> <p>- Part III) Monte Carlo simulation using the parameter configuration "Param. 1" of Shi et al. (1999) and a limited ion composition search space</p> <p>- Part IV) Monte Carlo simulations using the parameter configuration "Param. 2" of Wang et al. (2012)</p> <p>- Part V) Monte Carlo simulation using the parameter configuration "Param. 2" of Wang et al. (2012) and a limited ion composition search space</p> <p>- Part VI) Monte Carlo simulations using the parameter configuration "Param. 2" of Wang et al. (2012) with uncertainty on the a priori plasma parameters obtained from the Plasma Line</p> <p>- Part VII) Codes to generate all figures of the manuscript</p> <p>All datasets and scripts were generated and tested using Matlab 2017. Simulations have been executed in parallel on a SLURM cluster, compilation and running scripts are provided.</p>
Crafted optimization instances in OPB format
<p>Crafted optimization instances in OPB format, inspired by (Elffers et al. 2018; Vinyals et al. 2018), but generated with larger parameters so as to be more challenging, allowing to “stress-test” combinatorial solvers by exposing them to problems that provably require sophisticated reasoning.</p> <p>- Elffers, J.; Giráldez-Cru, J.; Nordström, J.; and Vinyals, M. 2018. Using Combinatorial Benchmarks to Probe the Reasoning Power of Pseudo-Boolean Solvers.<br> - Vinyals, M.; Elffers, J.; Giráldez-Cru, J.; Gocht, S.; and Nordström, J. 2018. In Between Resolution and Cutting Planes: A Study of Proof Systems for Pseudo-Boolean SAT Solving.</p>
Experimental Repository for "Cutting to the Core of Pseudo-Boolean Optimization: Combining Core-Guided Search with Cutting Planes Reasoning"
<p>Code and Data supplement to "Cutting to the Core of Pseudo-Boolean Optimization: Combining Core-Guided Search with Cutting Planes Reasoning"</p>
Figure 4 in Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society
Figure 4. Graphical representation of original and recently modified pathways for feedback regarding Primary Biodiversity Data, showing information transfer among users, providers, and aggregators. Such feedback consists of suggested improvements or additions to data fields, for example a change in species identification or a newly determined georeference. The diagrams contrast two complementary mechanisms: (a) the original feedback loop (currently dominant); and (b) the emerging feedback pendulum (proposed for expansion). In a: (1) the user sends feedback to the provider (e.g., a given natural history museum); (2) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (3) that information becomes available for query by all users. In practice, because many providers do not consistently make such changes (denoted by an X), users do have access to updated information (dashed line). In b: (1) the user sends feedback to the aggregator; (2) the aggregator simultaneously both annotates the record (visible to all users) and sends the suggested information to the provider; (3) if the provider makes a corresponding change to its database, the updated information is sent to the aggregator; and (4) the aggregator makes the updated information available for query by all users. Note that even if a provider takes no action regarding the suggested information, the annotations placed by the aggregator are nevertheless available to users. Additionally, because the quantifications of data quality and use described in the text allow for benchmarks that can be tracked over time, we anticipate that the feedback pendulum will help providers become more successful in justifying and securing funding to make data improvements based on feedback from users.
Near-optimal robust bilevel linear instances
<p>This repository contains the bilevel instances used in the paper Near-Optimal Robust Bilevel Optimization (https://arxiv.org/abs/1908.04040). They come in four groups, small, medium, large and mips instances, with different numbers of variables and constraints as described in the paper.</p> <p>The MIPS instances are constructed from the MIPS/RANDOM instances from https://coral.ise.lehigh.edu/data-sets/bilevel-instances/</p> <p>The /data folder contains instances in JLD format, the DataReader folder contains a Julia project for reading the data.</p>
Improved hybrid particle swarm optimizer with sine-cosine acceleration coefficients for transient electromagnetic inversion
<p>The Xishan Landslide Research area is located in Sichuan Lixian County, Southwest China. </p> <p>The N.O. 1 profile from Li et al., (2020), containing 15 measuring points, was chosen to test data fitting of IH-PSO-SCAC and to determine the hydrogeological structure of landslides.</p> <p> </p>
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
<p>Matlab output files and raw data used for the evaluation presented in "DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks" <a href="https://github.com/MetExplore/dexom">https://github.com/MetExplore/dexom</a></p>
Dataset related to article "Optimization of a Luciferase-Expressing Non-Invasive Intrapleural Model of Malignant Mesothelioma in Immunocompetent Mice"
<p>This record contains data related to article "Optimization of a Luciferase-Expressing Non-Invasive Intrapleural Model of Malignant Mesothelioma in Immunocompetent Mice"</p> <p>Malignant Pleural Mesothelioma (MPM) is an aggressive tumor of the pleural lining that is usually identified at advanced stages and resistant to current therapies. Appropriate pre-clinical mouse tumor models are of pivotal importance to study its biology. Usually, tumor cells have been injected intraperitoneally or subcutaneously. Using three available murine mesothelioma cell lines with different histotypes (sarcomatoid, biphasic, epithelioid), we have set up a simplified model of in vivo growth orthotopically by inoculating tumor cells directly in the thorax with a minimally invasive procedure. Mesothelioma tumors grew along the pleura and spread on the superficial areas of the lungs, but no masses were found outside the thoracic cavity. As observed in human MPM, tumors were highly infiltrated by macrophages and T cells. The luciferase-expressing cells can be visualized in vivo by bioluminescent optical imaging to precisely quantify tumor growth over time. Notably, the bioluminescence signal detected in vivo correctly matched the tumor burden quantified with classical histology. In contrast, the subcutaneous or intraperitoneal growth of these mesothelioma cells was considered either non-representative of the human disease or unreliable to precisely quantify tumor load. Our non-invasive in vivo model of mesothelioma is simple and reproducible, and it reliably recapitulates the human disease.</p>
Optimized composite microspheres containing spinosad and an attractant for control of a fruit fly pest
<p>These original data and analysis graph are for the manuscript titled "<strong>Optimized composite microspheres containing spinosad and an attractant for control of a fruit fly pest</strong>". If readers are interested in this paper, you can email to me and discuss the result. Also, we wecolme the coopertion on the fruit fly control program and techniques. </p>
Optimal allocation of law enforcement patrol effort to mitigate poaching activities
<p>Poaching is a global problem causing the decline of species worldwide. Optimizing the efficiency of ranger patrols to deter poaching activity at the lowest possible cost is crucial for protecting species with limited resources. We applied decision analysis and spatial optimization algorithms to allocate efforts of ranger patrols throughout a national park. Our objective was to mitigate poaching activity at or below management risk targets for the lowest monetary cost. We examined this tradeoff by constructing a Pareto efficiency frontier using integer linear programing. We used data from a ranger-based monitoring program in Nyungwe National Park, Rwanda. Our measure of poaching risk is based on dynamic occupancy models which account for imperfect detection of poaching activities. We found that in order to achieve a 5% reduction in poaching risk, 622 ranger patrol events (each corresponding to patrolling 1 km2 sites) were needed within a year at a cost of $49,760 USD. In order to attain a 60% reduction in poaching risk, 15,560 patrol events were needed at a cost of $1,244,800 USD. We evaluated the tradeoff between patrol cost and poaching risk based on our model by constructing a Pareto efficiency frontier and park managers found the solution for a 50% risk reduction to be a practical tradeoff based on funding constraints (comparable to recent years) and the diminishing returns between risk mitigation and cost. This expected reduction in risk required 8,558 patrol events per year at a cost of $684,640 USD. Our results suggest that optimal solutions could increase efficiency compared to the actual effort allocations from 2006 – 2016 in Nyungwe National Park (e.g., risk reductions of ~30% under recent budgets compared to ~50% reduction in risk under the optimal strategy). The modeling framework in this study took into account imperfect detection of poaching risk as well as the directional and conditional nature of ranger patrol events given the spatial adjacency relationships of neighboring sites and access points. Our analyses can help to improve the efficiency of ranger patrols, and the modeling framework can be broadly applied to other spatial conservation planning problems with conditional, multi-level, site selection.</p>
Data from: In search of an optimal DNA diagnosis for taxonomic descriptions with MOLD, a novel tool to identify diagnostic nucleotide characters
<p>While DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa remains scarce and inconsistent. The major impediments until recently was a lack of a suitable algorithm to identify signature DNA characters. The 2019-2020 however were marked by an almost simultaneous release of three softwares, simple to run and designed specifically for taxonomists. There is, nevertheless, a major concern, whether taxonomy will benefit from wide application of these, or any of the previously available tools. The reluctance of using DNA data in taxonomy is partly due to concerns of insufficient reliability of DNA characters, as robustness of DNA based diagnoses, depending on the sampled fraction of the species diversity has not thus far been assessed.</p> <p>We propose a novel program, named MOLD that recovers diagnostic nucleotide combinations (DNCs) for selected taxa with DNA sequences available. We carried our random iterated haplotype subsampling on species in six published DNA data sets of varying complexity, providing a diagnosis to each subsample to evaluate how the robustness of DNA based diagnosis changes depending on the sampled fraction of the taxon's diversity. We demonstrate that the currently used diagnostic DNA characters, or combinations thereof (DNCs) often do not exist for a particular species in a particular data set, or are not sufficiently reliable. We propose a new type of DNA diagnosis, termed herein rDNCs, which is compiled to suit pre-defined criteria of reliability, and is implemented in MOLD. We demonstrate that rDNCs can be successfully identified even in data sets comprising hundreds of species, and allow for notably more reliable diagnoses, than the currently used diagnostic DNA characters. MOLD recovers reliable and reproducible diagnoses in traditionally problematic cases, such as cryptic species or species with pronounced genetic structure, and shows unparalleled efficiency in large DNA data sets, making a valuable complement to the currently existing toolkit.</p>
Data set for study '"Optimal intervention strategies to mitigate the COVID-19 pandemic effects"
<p>Data associated with the findings presented in the study '"Optimal intervention strategies to mitigate the COVID-19 pandemic effects"</p>
Time-Plan Optimization with Genetic Algorithm for Regain of Energy from Train Tracks
<p>Dataset using for Time-Plan Optimization with Genetic Algorithm for Regain of Energy from Train Tracks</p>
Images of loop-mediated isothermal amplification (LAMP) for SARS-CoV-2 testing and optimized 'Cap-iLAMP'
<p>Here we present images of loop-mediated isothermal amplification (LAMP) and optimized Cap-iLAMP (capture and improved loop-mediated isothermal amplification). Cap-iLAMP combines a hybridization capture-based RNA extraction of gargle lavage samples with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. The sensitivity is 97% and the specificity is 99%.</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.