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1,855 results for “Framework”
Data from: A unifying comparative phylogenetic framework including traits coevolving across interacting lineages
Models of phenotypic evolution fit to phylogenetic comparative data are widely used to make inferences regarding the tempo and mode of trait evolution. A wide range of models is already available for this type of analysis, and the field is still under active development. One of the most needed development concerns models that better account for the effect of within- and between-clade interspecific interactions on trait evolution, which can result from processes as diverse as competition, predation, parasitism, or mutualism. Here, we begin by developing a very general comparative phylogenetic framework for (multi)-trait evolution that can be applied to both ultrametric and nonultrametric trees. This framework not only encapsulates many previous models of continuous univariate and multivariate phenotypic evolution, but also paves the way for the consideration of a much broader series of models in which lineages coevolve, meaning that trait changes in one lineage are influenced by the value of traits in other, interacting lineages. Next, we provide a standard way for deriving the probabilistic distribution of traits at tip branches under our framework. We show that a multivariate normal distribution remains the expected distribution for a broad class of models accounting for interspecific interactions. Our derivations allow us to fit various models efficiently, and in particular greatly reduce the computation time needed to fit the recently proposed phenotype matching model. Finally, we illustrate the utility of our framework by developing a toy model for mutualistic coevolution. Our framework should foster a new era in the study of coevolution from comparative data.
Data from: Biodiversity as a multidimensional construct: a review, framework and case study of herbivory's impact on plant biodiversity
Biodiversity is inherently multidimensional, encompassing taxonomic, functional, phylogenetic, genetic, landscape and many other elements of variability of life on the Earth. However, this fundamental principle of multidimensionality is rarely applied in research aimed at understanding biodiversity's value to ecosystem functions and the services they provide. This oversight means that our current understanding of the ecological and environmental consequences of biodiversity loss is limited primarily to what unidimensional studies have revealed. To address this issue, we review the literature, develop a conceptual framework for multidimensional biodiversity research based on this review and provide a case study to explore the framework. Our case study specifically examines how herbivory by whitetail deer (Odocoileus virginianus) alters the multidimensional influence of biodiversity on understory plant cover at Black Rock Forest, New York. Using three biodiversity dimensions (taxonomic, functional and phylogenetic diversity) to explore our framework, we found that herbivory alters biodiversity's multidimensional influence on plant cover; an effect not observable through a unidimensional approach. Although our review, framework and case study illustrate the advantages of multidimensional over unidimensional approaches, they also illustrate the statistical and empirical challenges such work entails. Meeting these challenges, however, where data and resources permit, will be important if we are to better understand and manage the consequences we face as biodiversity continues to decline in the foreseeable future.
Data from: Lexicon-enhanced sentiment analysis framework using rule-based classification scheme
With the rapid increase in social networks and blogs, the social media services are increasingly being used by online communities to share their views and experiences about a particular product, policy and event. Due to economic importance of these reviews, there is growing trend of writing user reviews to promote a product. Nowadays, users prefer online blogs and review sites to purchase products. Therefore, user reviews are considered as an important source of information in Sentiment Analysis (SA) applications for decision making. In this work, we exploit the wealth of user reviews, available through the online forums, to analyze the semantic orientation of words by categorizing them into +ive and -ive classes to identify and classify emoticons, modifiers, general-purpose and domain-specific words expressed in the public's feedback about the products. However, the un-supervised learning approach employed in previous studies is becoming less efficient due to data sparseness, low accuracy due to non-consideration of emoticons, modifiers, and presence of domain specific words, as they may result in inaccurate classification of users' reviews. Lexicon-enhanced sentiment analysis based on Rule-based classification scheme is an alternative approach for improving sentiment classification of users' reviews in online communities. In addition to the sentiment terms used in general purpose sentiment analysis, we integrate emoticons, modifiers and domain specific terms to analyze the reviews posted in online communities. To test the effectiveness of the proposed method, we considered users reviews in three domains. The results obtained from different experiments demonstrate that the proposed method overcomes limitations of previous methods and the performance of the sentiment analysis is improved after considering emoticons, modifiers, negations, and domain specific terms when compared to baseline methods.
Data from: The EGA+GNM framework: an integrative approach to modelling behavioural syndromes
1. Behavioural syndromes refer to correlated suites of behavioural traits exhibiting consistent among-individual variation, i.e. personality. Factor analysis (FA) is currently the dominant method for modelling behavioural syndromes in humans and animals. Although FA is useful for inferring the latent causes underlying trait correlations, it does not account for pairwise behavioural interactions that also contribute to syndrome structure. Given that latent factors and pairwise interactions are likely ubiquitous causes of trait covariation, both should be modelled simultaneously. Currently, however, behavioural ecologists lack an integrative framework for describing and inferring such behavioural syndromes. 2. Generalized network modelling (GNM), representing an integration of FA and Gaussian graphical modelling (GGM), meets this challenge. We provide a theoretical introduction to GNM as well as a method for detecting latent factors in GGMs called exploratory graph analysis (EGA). We then propose the novel EGA+GNM framework for modelling multiple sources of trait correlations and ensuring more robust causal inferences. To empirically demonstrate the utility of this framework, we compare models derived from EGA+GNM and FA using observational measures of social and arousal behaviour in common marmosets (Callithrix jacchus). 3. Using information-theoretic model comparison, we find support for the EGA+GNM models compared to models generated by FA. Two EGA+GNM models suggest that while latent factors contribute to the emergence of clustered sociability and arousal behaviours, correlations among these traits may also be partially explained by pairwise interactions. Additionally, these behavioural clusters are hypothesized to be causally linked by a positive pairwise interaction between allogrooming and activity level. 4. These results support our claim that EGA+GNM provides a superior and integrative framework for describing behavioural syndromes. Consequently, by simultaneously modelling both latent factors and pairwise interactions, behavioural ecologists can better understand the evolutionary causes and consequences of animal personality. A formal overview of the EGA+GNM framework and a R tutorial demonstrating its application are provided in the electronic supplementary material.
Data from: Genome-wide prediction of bacterial effector candidates across six secretion system types using a feature-based statistical framework
Gram-negative bacteria are responsible for hundreds of millions infections worldwide, including the emerging hospital-acquired infections and neglected tropical diseases in the third-world countries. Finding a fast and cheap way to understand the molecular mechanisms behind the bacterial infections is critical for efficient diagnostics and treatment. An important step towards understanding these mechanisms is the discovery of bacterial effectors, the proteins secreted into the host through one of the six common secretion system types. Unfortunately, current prediction methods are designed to specifically target one of three secretion systems, and no accurate "secretion system-agnostic" method is available. Here, we present PREFFECTOR, a computational feature-based approach to discover effector candidates in Gram-negative bacteria, without prior knowledge on bacterial secretion system(s) or cryptic secretion signals. Our approach was first evaluated using several assessment protocols on a manually curated, balanced dataset of experimentally determined effectors across all six secretion systems, as well as non-effector proteins. The evaluation revealed high accuracy of the top performing classifiers in PREFFECTOR, with the small false positive discovery rate across all six secretion systems. Our method was also applied to six bacteria that had limited knowledge on virulence factors or secreted effectors. PREFFECTOR web-server is freely available at: http://korkinlab.org/preffector.
Data from: Translocation tactics: a framework to support the IUCN Guidelines for wildlife translocations and improve the quality of applied methods
1. Translocation is a popular conservation tool, but the outcomes are variable. Many tactics can be used to improve the probability of success, but a comprehensive summary of these does not exist. This increases the risk that valuable tactics will be overlooked, and inhibits effective communication. 2. We assess the diversity of 'translocation tactics' used in mammal and bird translocations, by reviewing the IUCN/SSC Guidelines for Reintroduction and other Conservation Translocations, 195 peer-reviewed articles and 73 case studies from the IUCN/SSC Global Reintroduction Perspectives Series.3. We recorded descriptions of every technique used to influence the post-release performance of translocated wildlife. We developed the Translocation Tactics Classification System (TTCS) which defines a collection of 30 tactics and organize them into an ecologically relevant framework. We also assess the occurrence of tactics within the Guidelines, the primary literature and the case studies to evaluate how tactics are communicated within these mediums. 4. Our results indicate that the Guidelines are a valuable resource, but do not exhaustively cover tactics, and that detailed methodological accounts are rarely made publicly accessible. This highlights the need to develop context-specific resources to support the Guidelines, and to develop and exploit mediums that facilitate recording of methodological detail, the tactical rationale behind the design and evaluations of effectiveness. Although some forms of grey literature address this issue, the general lack of information limits the ability to investigate the relationship between tactics and translocation success. 5. Synthesis and applications. The Translocation Tactics Classification System (TTCS) provides a checklist which ensures that the full diversity of tactics is considered when developing translocation processes. Standardizing the communication of tactics, and encouraging detailed accounts of applied methodologies to be recorded, along with the tactical reasoning behind the design, will provide operational models and the data required to conduct broad-scale meta-analyses.
Rattus population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management
<p><a name="_Hlk13067419"></a><a name="_Hlk16009716">Invasive species have led to precipitous declines in biodiversity, especially in island systems. Brown (<i>Rattus norvegicus</i>) and black rats (<i>R. rattus</i>) are among the most invasive animals on the planet, with eradication being the primary tool for established island populations. The need for increased research for defining eradication units and monitoring outcomes has been highlighted as a means to maximize success. Haida Gwaii is an archipelago ~100 km off the northern coast of British Columbia, Canada that hosts globally significant breeding populations of seabirds that are at risk due to invasive rats. Here, we paired sampling of brown (n=287) and black (n=291) rats across the Haida Gwaii archipelago (British Columbia, Canada) with genotyping-by-sequencing (10,770-27,686 SNPs) to investigate patterns of population connectivity and infer levels/direction of gene flow among invasive rat populations in Haida Gwaii. We reconstructed three regional clusters for both species (north, central, south), with proximate populations within regions being largely more related than those that were more distant, consistent with predictions from island biogeography theory. Population assignment of recently detected individuals post-eradication on Faraday, Murchison, and the Bischof Islands revealed all were re-invaders from Lyell Island, rather than being on-island survivors. Based on these results, we identified six eradication units constituting single or clusters of islands that would limit the potential for re-invasion, some of which will need to be combined with biosecurity measures. Overall, our results highlight the importance of targeted research prior to conducting eradications and demonstrates a framework for applying population genomics for guiding invasive species management in island systems.</a></p>
Withdrawing Performance Indicators: Retrospective Analysis of General Practice Performance Under the UKs Quality and Outcomes Framework
<p>No description provided.</p>
Schönberg, J., Böhm-Beck, M., Trdan, Š., Grego, M., Knoblauch, D., Hinzmann, M., Dittmann, S., Knickmeier, K., Robič, U., Thiel, M., Kiessling, T., 2025. Public participation in EU legislation? Recommendations for involving citizen scientists in anthropogenic litter research within the Water Framework Directive.
<p>Research data and figures to the manuscript "Public participation in EU legislation? Recommendations for involving citizen scientists in anthropogenic litter research within the Water Framework Directive" by Schönberg et al. 2025</p>
Data from: Geographic Object-Based Image Analysis Framework for Mapping Vegetation Physiognomic Types at Fine Scales in Neotropical Savannas
<p>Spatially-explicit information featuring a wide range of detailed vegetation structural types are necessary to support conservation and ecological analyses. A systematic approach that accurately maps such detailed categories at regional scales is currently lacking for neotropical savannas. We developed a systematic Geographic Object-Based Image Analysis (GEOBIA) framework that accounts for spectral and spatial properties to map Cerrado vegetation structural types at 5-m resolution. This framework counts with a two-step mapping approach: (1) image segmentation and a Random Forest land cover classification based on spectral information (Level 1 classification), followed by (2) a GEOBIA knowledge-based classification that follows contextual and topological spatial rules developed in a systematic manner for mapping Cerrado ecological classes (Level 2 classification).</p><p>The framework was tested for two large study sites covering most major Cerrado physiognomic types: a control site in central Brazil (Taquara watershed site, located in Brasilia, Federal District, and embraces the IBGE Ecological Reserve) and another larger site that is located in an agricultural landscape in the western portion of Bahia State (encompasses parts of the municipalities of: Sao Desiderio, Luis Eduardo Magalhaes, Barreiras, and Riachao das Neves), which brings additional mapping challenges related to intra-class spectral similarity. </p><p>Results demonstrate that our GEOBIA approach is effective for mapping 13 land cover classes with 87.6% overall accuracy, of which all 11 major vegetation classes were identified. For additional details, please check the associated publication with these datasets (Ribeiro et al. 2020).</p><p>The datasets developed in this study are available in shapefile format with attributed metadata following ISO 19115 standards: </p><ul><li><strong>wba_lcmap_geobiaL2_2011lucmask:</strong> final land cover map (Level 2 -- physiognomic types) for a section of the western bahia region in the Cerrado. This product uses a land use mask of 2011 derived from ancillary data</li><li><strong>wba_lcmap_geobiaL2_2013lucmask:</strong> final land cover map (Level 2 -- physiognomic types) for a section of the western bahia region in the Cerrado. This product accounts for the land use mask of 2011 as well as an updated land use mask of 2013 derived from ancillary data</li><li><strong>ibge_taquara_luc_L1_L2_2013_original:</strong> land cover maps (Levels 1 and 2) developed for the Taquara/IBGE site</li><li><strong>ibge_taquara_detailed_luc_2013:</strong> final land cover map (Level 2 -- physiognomic types) developed for the Taquara/IBGE site with additional detailed land use categories</li></ul><p> </p><p><strong>Data</strong></p><p>Mapped land cover classes: 1) cerrado woodland, 2) savanna, 3) open savanna, 4) shrubby grassland, 5) grassland (only present in the Taquara site), 6) cerrado scrub (only present in the western bahia site), 7) marsh, 8) shrub swamp, 9) palm swamp, 10) riparian forest, 11) semi-deciduous forest, 12) seasonally dry tropical forest (only present in the western bahia site), 13) invasive forbes (only present in the Taquara site), 14) non-natural/barren, 15) water, 16) shade, 17) clouds</p><p>The land-use mask incorporated into our maps feature the following classes: main roads, farming/crops, silviculture, and urban areas. </p><p> </p><p><strong>Coordinate Reference System</strong></p><p>Datasets were projected to <strong>South America Albers Equal Area</strong> <strong>Conic</strong>, with all areal calculations based on this projection.</p><p> </p><p><strong>Data Usage</strong> </p><p>The datasets are publicly available and should be cited appropriately (main publication: Ribeiro et al. 2020).</p><p> </p><p><strong>Additional information</strong></p><p>For any other data requests or questions, please contact Fernanda Ribeiro (fernanda.ffr@gmail.com).</p>
COVINFORM Risk Model Framework
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Supplementary material 1 from: Probert AF, Vimercati G, Kumschick S, Volery L, Bacher S (2023) Clarification and guidance on the use of the Socio-Economic Impact Classification for Alien Taxa (SEICAT) framework. NeoBiota 89: 45-70. https://doi.org/10.3897/neobiota.89.109911
SEICAT assessment supplementary material
A data-and-knowledge driven structure-based molecular generative framework
<p>Dataset for pretraining and finetuning of PocketFlow.</p>
Active learning molecular dynamics-assisted insights into ultralow thermal conductivity of two-dimensional covalent organic frameworks
<p>This is a training sets for monolayer COF-5, which could be used for NEP trainging.</p>
Proteo Dataset (2023) for article "Proteo: A Framework for the Generation and Evaluation of Malleable MPI Applications"
<p>This dataset is the one used by the publication "Proteo: A Framework for the Generation and Evaluation of Malleable MPI Applications". The data are the data processed after the experiments to obtain the graphs and perform the analysis of the two applications shown.</p><p>On the one hand, there are data from the conjugate gradient (CG) execution and on the other hand, data from the Proteo framework, configured to emulate the CG.</p><p>The set is divided into 4 sections, each representing the results obtained for each result section of the article:</p><ul><li><strong>5.3</strong>: Similarity results between CG and Proteo configured to emulate CG. These results were obtained from the previous paper "Configurable synthetic application for studying malleability in HPC" at the PDP2023 conference. It consists of 4 datasheets:<ul><li><i>Nasp CG-VS-Proteo.xlsx</i>: Datasheet showing the total execution, iteration and computation times of Nasp (System_1) with the CG and Proteo. Used to create Figures 7 and 8.</li><li><i>JupiterThor CG-VS-Proteo.xlsx: </i>Datasheet showing the total execution, iteration and computation times of Jupiter (System_2) and Thor (System_3) with the CG and Proteus. Used to create Figures 7 and 8.</li><li><i>Comparison Comms CG Only.xlsx</i>: Datasheet showing MPI_Allgatherv communication times for different sizes on Nasp, Jupiter and Thor systems (System_1, System_2 and System_3). Used to create Table 1.</li><li><i>Comms CV_VS_Proteo.xlsx</i>: Datasheet showing MPI_Allgatherv communication times between the CG and Proteo for different sizes in Nasp, Jupiter and Thor systems (System_1, System_2 and System_3). Used to create Table 2.</li></ul></li><li><strong>5.4.1</strong>: Evaluation of the reconfiguration techniques in isolation of Proteo for synchronous methods. Used to create Figure 9. It is divided into three files:<ul><li><i>dataG.pkl</i>: Contains data on the complete runtimes in Proteo. The description can be found in the file <i>Proteo_dataG_description.txt</i></li><li><i>dataM.pkl</i>: Contains data on reconfiguration times in Proteo. The description can be found in the file <i>Proteo_dataM_description.txt</i></li><li><i>dataL.pkl</i>: Contains data on iteration times in Proteo. The description can be found in the file <i>Proteo_dataL_description.txt</i></li></ul></li><li><strong>5.4.2</strong>: Evaluation of the reconfiguration in a malleable application, CG against Proteo. Used to create Figure 10 and 11. It is divided into two directories, differentiating between CG and Proteus. In total there are the following 5 files:<ul><li><i>dataG.pkl</i>: Contains data on the complete runtimes in Proteo. The description can be found in the file <i>Proteo_dataG_description.txt</i></li><li><i>dataM.pkl</i>: Contains data on reconfiguration times in Proteo. The description can be found in the file <i>Proteo_dataM_description.txt</i></li><li><i>dataL.pkl</i>: Contains data on iteration times in Proteo. The description can be found in the file <i>Proteo_dataL_description.txt</i></li><li><i>dataCG_G.pkl</i>: Contains data on the complete execution times in the CG. The description can be found in the CG<i>_dataG_description.txt</i></li><li><i>dataCG_M.pkl</i>: Contains data on reconfiguration times in the CG. The description can be found in the CG<i>_dataM_description.txt</i></li></ul></li><li><strong>5.4.3</strong>: Evaluation of a malleable emulated application, CG against Proteo. Used to create Figure 12, 13 and 14. It is divided into two directories, differentiating between CG and Proteus. In total there are the following 5 files:<ul><li><i>dataG.pkl</i>: Contains data on the complete runtimes in Proteo. The description can be found in the file <i>Proteo_dataG_description.txt</i></li><li><i>dataM.pkl</i>: Contains data on reconfiguration times in Proteo. The description can be found in the file <i>Proteo_dataM_description.txt</i></li><li><i>dataL.pkl</i>: Contains data on iteration times in Proteo. The description can be found in the file <i>Proteo_dataL_description.txt</i></li><li><i>dataCG_G.pkl</i>: Contains data on the complete execution times in the CG. The description can be found in the CG<i>_dataG_description.txt</i></li><li><i>dataCG_M.pkl</i>: Contains data on reconfiguration times in the CG. The description can be found in the CG<i>_dataM_description.txt</i></li></ul></li></ul>
CONCEPTUAL FRAMEWORK OF FACTORS AFFECTING THE INCOME AND QUALITY OF LIFE OF THE POPULATION.
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CellDeathPred: a deep learning framework for ferroptosis and apoptosis prediction based on cell painting
<p><strong>Data Description:</strong></p> <ul> <li>Two cell death modalities are considered in this study: apoptosis and ferroptosis. The treatments and their cell death types used in these experiments are shown in Figure 1 in the paper. In total we have seven apoptosis and seven ferroptosis inducers. They target specific cell organelles and components. Besides, active treatments there are negative controls DMSO and untreated wells.</li> <li>Every image has a resolution of 1360 x 1024. These four channels were imaged in the experiments. For every well multiple images (fields) are taken typically ten fields.</li> <li>Three plates with four different settings were imaged. 20x non-confocal (very fast [1.5h]), 20x confocal (fast [2.5h]), 40x non-confocal (slow [5h]), 40x confocal (very slow [8h]). All for one time point 28h (incubation time).</li> </ul>
Data from 'Modeling and Solving Framework for Tactical Maintenance Planning Problems with Health Index considerations'
<p>Datasets used in the manuscript 'Modeling and Solving Framework for Tactical Maintenance Planning Problems with Health Index considerations'</p> <p>Format: CPLEX .dat data files</p>
Metadata - Tuning the electrochemical performance of covalent organic framework cathodes for Li- and Mg-based batteries: the influence of electrolyte and binder
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Supplementary material 1 from: Lymer G, Leliaert F, Mergen P, Pijls S (2023) Pre-Commercial Procurement framework and European funding sources for European Research Infrastructure Consortiums: Insights from the DiSSCo ERIC development. Research Ideas and Outcomes 9: e113294. https://doi.org/10.3897/rio.9.e113294
Glossary
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.