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519 results for “Optimisation”
FIGURE 50. Preferred topology with ACCTRAN character optimisations. Strict consensus tree from 7 trees using implied weights K in The new Southeast Asian goblin spider genus Aposphragisma (Araneae, Oonopidae): diversity and phylogeny
FIGURE 50. Preferred topology with ACCTRAN character optimisations. Strict consensus tree from 7 trees using implied weights K=1–5 (L=149, CI=0.63, RI=0.77). Squares show synapomorphic (black) and homoplastic (white) character state changes. Numbers above the squares correspond to the character numbers, those below to character state changes. The ingroup Aposphragisma gen. nov. is marked in shades of grey: species showing completely ornamented sterna in light grey and those possessing sterna with a glabrous middle stripe ('stripe-clade') in dark grey.
Data from: Compact cities or sprawling suburbs? optimising the distribution of people in cities to maximise species diversity
1. Conservation of biodiversity in urban environments depends on the responses of species to the intensity of urban development. 'Land sharing' and 'land sparing' represent alternate ends of a gradient that conceptualises a trade-off between the human population and biodiversity. We used a linear optimisation procedure to 1) identify the optimal allocation of land for people and nature, 2) assess whether the optimal allocation is more similar to land sparing or land sharing, and 3) examine how this might change under scenarios of human population growth. 2. We surveyed birds in 28 landscapes, each 25 ha in size, along a gradient of human population density (zero to ~1600 persons/25 ha) in the Greater Melbourne region, Australia. Species' responses to population density were estimated using generalised additive models (GAMs). These relationships were then used to determine the optimal allocation of land among different categories of population density based on maximising a community index, the geometric mean of relative abundance (G) of bird species. 3. Human population density was an important driver of the reporting rate for 28 species. Response curves differed among 'urban avoider', 'urban adapter' and 'urban exploiter' species. For the current human population in the study area, optimal allocation of land included elements of both land sharing and land sparing. However, for scenarios of increased population size, optimal allocation converged upon a land sparing design. 5. Synthesis and applications. Urban areas represent a mosaic of land uses that offer habitats of differing quality. Land sharing, based on sustaining biota amongst residential areas, performed poorly under all scenarios due to its inability to support species that depend on natural or semi-natural habitat. To sustain more than a homogenised avifauna in urban regions, large tracts of natural vegetation are needed within, or adjacent to, the urban environment. Protecting natural areas on urban fringes will be critical to the safeguarding of nature in the future as urban populations and land-use inevitably expand.
Optimising nature conservation outcomes for a given region-wide level of food production
<ol> <li>The land sharing-sparing framework aims to quantify the trade-off between food production and biodiversity conservation, but it has been criticised for offering, for reasons of simplicity, an unrealistically limited set of different land uses.</li> <li>Here, we develop the framework to evaluate a much larger suite of land-use strategies in which the areas and yields of three land-use compartments, natural habitat, high-yield farmland, and lower-yield farmland, are varied simultaneously. For two regions of England, we use functions that relate the local population density of breeding bird species to farm yield to simulate species-specific region-wide population sizes under each strategy.</li> <li>We find that geometric mean population size, averaged across all species, is maximised when farmland yields are higher than the current average yield, and when spared land combines both natural habitat and low-yield farmland. This conclusion is relatively insensitive to the maximum yield considered feasible under extreme land sparing, and holds across a range of region-wide food production targets. </li> <li>To some extent, our conclusion depends on which species groups were included in the assessment. Considered alone, farmland birds preferred a strategy with little or no natural habitat. Nonetheless, the optimal strategy was broadly consistent across all widely-recognised listings of species of conservation concern.</li> <li>Synthesis and applications. Our study looks at landscapes with a long history of agricultural use, and which have little remaining natural habitat, such as those found in lowland England. In these landscapes, conservation outcomes are likely to be maximised by mixed strategies in which high-yield production enables an increase in area of both natural habitat and low-yield farmland elsewhere in the region. </li> </ol>
Data from: Optimising sampling of flying insects using a modified window trap
Insect populations are globally declining but standardized long‐term data to evaluate trends and consequences are largely missing. One difficulty among many is the rather narrow taxonomic cover of most conventional trap types, which makes the use of several complementary collection methods necessary to achieve comprehensive coverage. To avoid the effort associated with operating multiple traps, we demonstrate how to modify window traps in a simple and standardizable way to capture a wider range of flying insect taxa. While a typical window trap only has a collection unit below the windows, we added an additional collection unit on top of the windows. We tested this modified trap design in 135 study plots in a temperate forest over 5 months and compared trap catches between top and bottom collection units. The top collection unit captured considerably more individuals of Hymenoptera, Diptera, Lepidoptera, Neuroptera, Auchenorrhyncha and Thysanoptera than the bottom collection unit. In contrast, there were more individuals of Coleoptera, Heteroptera, Sternorrhyncha and Psocoptera in the bottom collection unit. Both collection units captured a highly distinct insect community and patterns were consistent throughout the season. These modified traps are suitable for collecting a broader range of flying insects compared to conventional window traps. The additional top unit is fast and easy to build and the traps require little maintenance while operating in the field. These characteristics make modified window traps with top and bottom collection units a promising tool for standardized and replicable biodiversity studies covering a broad range of insect taxa.
Data from: Optimising trait and source selection for explaining occurrence and abundance changes: a case study using British Butterflies
Functional traits that define the ecological role of an organism are increasingly being used to determine and predict responses to environmental change. Functional trait analyses of butterflies remain underexplored compared with other taxa, such as plants. Previous works using butterfly functional traits have not comprehensively addressed issues about the quality of trait data sets used and the relative predictive power of different trait types. We compare the consistency of trait descriptions between six widely used trait sources for the British butterfly fauna. We analysed consistency of trait sources using Fleiss's kappa and ICC. PCA was used to produce species ordinations, comparing outputs to examine which trait sets were better at explaining recent species range and abundance changes within the UK. There was a large range in congruence values for specific traits between sources. No single source can be relied upon to produce accurate trait information for British butterflies. Most trait sets are poor predictors of abundance and occurrence changes but are better at predicting current occurrence. An extensive trait set, supplementing biotope-related traits with explicit resource-based information recovers more informative ecological classifications and models than those primarily based on life-history traits or biotope descriptors. Smaller trait sets do, however, recover the specialist-generalist continuum. We conclude that analyses of distribution and abundance changes that rely on traits are highly dependent on trait source and trait type. For butterflies, traits that are based on measures of biotope occupancy should be avoided in explaining changes of abundance and distribution. Including trait information that describes their resource requirements is essential for such analyses.
Dataset for the paper "A catalyst layer optimisation approach using electrochemical impedance spectroscopy for PEM fuel cells operated with pyrolysed transition metal-N-C catalysts", J Power Sources, 2016, DOI: 10.1016/j.jpowsour.2016.05.035
<p>Data file for paper:"A catalyst layer optimisation approach using electrochemical impedance spectroscopy for PEM fuel cells operated with pyrolysed transition metal-N-C catalysts"</p> <p>Daniel Malko, Thiago Lopes, Edson A. Ticianelli, Anthony Kucernak</p> <p>Journal of Power Sources, 2016</p> <p>DOI: 10.1016/j.jpowsour.2016.05.035</p> <p>Please cite the above paper if you use this data</p>
Blended Learning: How can we optimise undergraduate student engagement?
<p>3 focus groups transcripts of focus groups that were carried out as part of a qualitative study exploring students' perceptions and experience of a new blended learning course in pharmacology taken as part of their BSc </p>
Expression and purification of full length huntingtin Q46 and optimisation of Grafix procedure (2016/09/11)
<p>Open lab notebook huntingtin structure function project.<br> </p>
Optimisation of huntingtin domain protein sample buffer conditions 2017/02/01
<p>Open lab notebook huntingtin structure function project.<br> </p>
Optimised geometries of a number of protonation models.
<p>Optimised geometries in pdb format presented in Fig.S12 of "A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion" paper (https://doi.org/10.1101/2023.10.11.561842).</p>
Supplementary data: Optimising centralisation and decentralisation in distribution networks for perishable products through mathematical modelling, parametric analysis, and machine learning
<p><span>The success of distribution companies for perishable products is enabled by optimally configuring distribution networks, which allows for reducing total logistic costs while ensuring reduced product spoilage and high service levels. Since customer demand for perishable products varies over time, the network configuration should not be optimised once, but periodically reviewed. Among the decisions to be reviewed, determining whether to centralise or decentralise inventory (i.e., stock allocation in distribution centres) is crucial. However, the literature overlooks stock allocation decisions, and existing methodologies to compare the economic performance of centralised, decentralised, and hybrid policies neglect important cost items, also requiring advanced computational technologies and skills to be applied. This paper addresses these gaps by providing two contributions. In this dataset, a comparison has been made between the cost performance of centralized, decentralized, and hybrid stock allocation policies in distribution networks for perishable products. The dataset comprises 100,000 realistic case studies generated through a Sobol quasi-random low discrepancy series.</span></p>
Optimisation of size and operation of stand-alone renewable-based systems with diesel and hybrid PHS-battery storage considering uncertainties
<p>Results of the optimal system found by the stochastic optimisation</p>
Dataset: Chromatographic data for publication Exploration and optimisation of structure-activity relationships of newtriazole-based C-terminal Hsp90 inhibitors towards in vivoanticancer potency
<p>Bio-chromoatographic data caming from publication Exploration and optimisation of structure-activity relationships of new triazole-based C-terminal Hsp90 inhibitors towards in vivo anticancer potency</p>
Supplementary data and code to: One site with multiple tags versus multiple sites with single tags: optimising the determination of localisation spaces by pseudocontact shifts
<p>Supplementary data and code to the publication:</p> <p>One site with multiple tags versus multiple sites with single tags: optimising the determination of localisation spaces by pseudocontact shifts</p> <p>Includes:</p> <p>Python scripts for use with paramagpy to calculate localisation spaces.</p> <p>Experimental NMR data and calculation scripts for Ubiquitin</p>
Data Bundle for PyPSA-Eur-Sec: A Sector-Coupled Open Optimisation Model of the European Energy System
<p>While small data files used in PyPSA-Eur-Sec are included directly in the git repository, larger ones are collected in this data bundle. The data bundle’s size is around 680 MB.</p> <p><strong>Licenses</strong></p> <p>Different licenses apply to the various components of this data bundle (mostly attribution).</p> <p>For details see <a href="https://pypsa-eur-sec.readthedocs.io/en/latest/installation.html#data-requirements">https://pypsa-eur-sec.readthedocs.io/en/latest/installation.html#data-requirements</a></p> <p><strong>Changelog 0.3.1</strong></p> <ul> <li>Fix IRENASTAT encoding</li> </ul> <p><strong>Changelog 0.3.0</strong></p> <ul> <li>Add <a href="https://pxweb.irena.org/pxweb/en/IRENASTAT">IRENASTAT</a> country-level power generation capacities.</li> </ul> <p><strong>Changelog 0.2.0</strong></p> <ul> <li>add hydrogen salt cavern storage potential (h2_salt_caverns_GWh_per_sqkm.geojson)</li> </ul> <p> </p>
Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies_Dataset_Rscript
<p>Datasets and Rscript associated with paper draft titled: "<span>Optimising recovery of DNA from minimally-invasive sampling methods: efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies".</span></p> <p> </p> <p>Abstract: <span>Studies in evolution, ecology and conservation are increasingly based on genetic and genomic inferences. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians.<span> </span>However, DNA yield and purity from swabs is often low, limiting its use. In this study we compare different types of swabs, preservation method and storage, and DNA extraction technique in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swab that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields than ethanol-fixed samples if kept cool. DNA extraction via a Qiagen</span><span>™</span><span> DNeasy Blood and Tissue Kit and McHale’s salting out extraction method resulted in similar DNA yields but the Qiagen</span><span>™</span><span> kit extracts contained less contamination. We also found that samples produce better DNA recovery if frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual sampled, access to cold storage facilities, and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.</span></p>
Dataset from: Electron root optimisation for stellarator reactor designs
<p>In this work, we propose a method of optimising stellarator devices to favour the presence of an electron root solution of the radial electric field. Such a solution can help avoid heavy impurity accumulation, improve neoclassical thermal ion confinement and helium ash exhaust, and possibly reduce turbulence. This study shows that an optimisation for such a root is possible in quasi-isodynamic stellarators. Examples are shown for both vacuum and finite plasma pressure configurations.</p>
Synthetic Datasets for "Binary Classification Optimisation with AI-Generated Data"
<p>Images of melanomas and Basal Cell Carcinoma generated with a stylegan2. Dataset corresponding to the article "Binary Classification Optimisation with AI-Generated Data"</p>
Associated data for "Optimisation strategies for directed evolution without sequencing"
<p>Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).</p>
Optimising Grid-Connected PV-Battery Systems for Energy Arbitrage and Frequency Containment Reserve
<p>Data and results of paper "Optimising Grid-Connected PV-Battery Systems for Energy Arbitrage and Frequency Containment Reserve"</p>
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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.