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1,855 results for “Framework”
Productivity simulation framework in software engineering - Bibliometric data
<p>Bibliographic data from the Web of Science and SCOPUS relate to this search string: <em>framework AND simulation AND productivity AND (software development OR software engineering)</em>. The authors also include the Bibliometrix application report.</p>
Data from: The roles of non-production vegetation in agroecosystems: a research framework for filling process knowledge gaps in a social-ecological context
<p>1. An ever-expanding human population, climatic changes, and the spread of intensive farming practices is putting increasing pressure on agroecosystems and their inherent biodiversity. Non-production vegetation elements, such as woody patches, riparian margins, and restoration plantings, are vital for conserving agroecosystem biodiversity. Further, such elements are key building blocks that are manipulated via land management, thereby influencing the biotic and abiotic processes that underpin functioning agroecosystems.</p> <p>2. Despite this critical role, there has been a lack of synthesis on which types of vegetation elements drive and/or support ecological processes, and the mechanisms by which this occurs. Using a systematic, quantitative literature review of 342 articles, we asked: what are the effects of non-production vegetation on agroecosystem processes and how are these processes measured within global agroecosystems?</p> <p>3. Woody patches, hedgerows and borders, riparian margins, and shelterbelts were the most studied types of non-production vegetation. The majority (61%) of studies showed positive effects of non-production vegetation on ecological processes, where the presence, level or rate of the studied process was increased or enhanced.</p> <p>4. However, four key research gaps were revealed: (1) most studies (83%) used proxies for, instead of direct measurements of, ecosystem processes related to non-production vegetation; (2) study designs used to investigate non-production vegetation effects on ecosystem processes directly were largely limited to observational comparisons of non-production vegetation types, farm-scale vegetation configurations, and different proximities to vegetation in terms of the effect on ecological processes; relatively few studies used manipulative experiments (3) the relatively few studies directly measuring ecosystem processes were dominated by four process categories: invertebrate biocontrol, predator and natural enemy spillover, animal movement, and ecosystem cycling, and (4) the methods used to directly measure non-production vegetation effects comprised a surprisingly limited set of approaches.</p> <p>5. To fill key research gaps that will inform the use of non-production vegetation to enhance agroecosystem processes, we present a framework for future research that emphasises the need to combine an understanding of human decision making with carefully-designed and targeted investigations into the roles of taxa, ecosystem processes, and landscape heterogeneity related to non-production vegetation, at multiple spatial scales within agroecosystems.</p>
Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"
<p>Supporting Dataset for "Comparing GGA, GGA+U, and Meta-GGA Functionals for Redox-Dependent Binding at Open Metal Sites in Metal−Organic Frameworks"</p>
Molten Salt Templated Synthesis of Covalent Isocyanurate Frameworks with Tunable Morphology and High CO2 Uptake Capacity
<p>The use of reactive molten salts, i.e., ZnCl2, as a soft template and a catalyst has been actively investigated in the preparation of covalent triazine frameworks (CTFs). Although the soft templating effect of the salt melt is more prominent at low<br> temperatures, close to the melting point of ZnCl2, leading to the formation of abundant micropores, a significant mesopore<br> formation is observed that is due to the partial carbonization and other side reactions at higher temperatures (>400 °C).<br> Evidently, high-temperature synthesis of CTFs in various eutectic salt mixtures of ZnCl2 with alkali metal chloride salts also leads to mesopore formation. We reasoned that using the isocyanate moieties instead of cyano groups in the monomer, 1,4-phenylene isocyanate, could enable efficient interactions between carbonyl moieties and alkali metal ions to realize efficient salt templating to form covalent isocyanurate frameworks (CICFs). In this direction, the trimerization of 1,4-phenylene diisocyanate was carried out under ionothermal conditions at different reaction temperatures using ZnCl2 (CICF) and the eutectic salt mixture of KCl/NaCl/ZnCl2 (CICF-KCl/NaCl) as the reactive solvents. We observed notable differences in the morphologies of the two polymers, whereas CICF showed irregular-shaped micrometer-sized particles, the CICF-KCl/NaCl exhibited a filmlike morphology. Moreover, favorable ion-dipole interactions between alkali metal cations and oxygen atoms of the monomer facilitated two-dimensional growth and the formation of a purely microporous framework in the case of CICF-KCl/NaCl along with a near theoretical retention of the nitrogen content at 500 °C. The CICF-KCl/NaCl showed a BET surface area of 590 m2 g−1 along with a CO2 uptake capacity of 5.9 mmol g−1 at 273 K and 1.1 bar because of its high microporosity and nitrogen content. On the contrary, in the absence of alkali metal ions, CICF showed high mesopore content and a moderate CO2 uptake capacity. This study underscores the importance of the strength of the interactions between the salts and the monomer in the ionothermal synthesis to control the morphology,<br> porosity, and gas uptake properties of the porous organic polymers</p>
Sei framework resources (hg19 and hg38 FASTA files)
<p>This is the `resources` directory that should be downloaded in order to run the Sei framework code. It contains the hg19 and hg38 genome FASTA files downloaded from UCSC, as well as the index files generated by `pyfaidx` Python package for fast indexing and querying of genome coordinate sequences. </p>
Training data for the Sei framework sequence model
<p>Training data for the Sei framework deep learning model. The data contains chromatin profiles from the Cistrome Project: <strong>please agree to the terms of usage at the Cistrome Project (http://cistrome.org/db/#/bdown) before downloading. </strong></p>
Multiple-model stock assessment frameworks for precautionary management and conservation on fishery-targeted coastal dolphin populations off Japan
<p>1. Stock assessment approaches are often oversimplified due to lack of biological knowledge and insufficient data. In spite of worldwide attention, fishery-targeted coastal dolphin species in Japan have lacked in-depth quantitative stock assessments because of limited time-series of population size and an absence of associated biological information. We consequently developed integrated population models that analyzed multiple sources of data simultaneously with published biological information within a Bayesian framework.<br> 2. We estimate population status and trends for three main species targeted by fisheries, bottlenose dolphins <em>Tursiops truncatus</em>, Risso's dolphins <em>Grampus griseus</em>, and short-finned pilot whales <em>Globicephala macrorhynchus</em>, using single-species age-aggregated and age-structured population dynamics models. Models were fit to absolute abundance estimates from systematic line-transect surveys, four series of abundance indices calculated from fisher's logbooks, and historical catch records. Published biological information was used to develop prior distributions for the biological parameters. We assessed the possible effects of ecological disturbance and competition using state-space and multispecies models.<br> 3. The multispecies model was selected by the model selection both for the age-aggregated and the age-structured approaches.<br> 4. Single-species assessments found that population size declined 4.2% (Risso's dolphin) to 8.0% (bottlenose dolphin) for three species since the late 1800s based on median posterior values, while the state-space and multispecies models found that environmental disturbance and an interaction among species could have reduced population size more substantially.<br> 5. '<em>Policy implications</em>' Simple single-species models are often used to provide conservation and management advice for wild animals but, in this case, results from such models are overly optimistic because they overlook important ecological process. In contrast, current population status could be less favorable if environmental disturbance and interspecific competition actually control population dynamics. Even if that is not the case, considering ecological process in the model will provide more precautionary ways. Our approach of combining multiple modelling frameworks is applicable to many other management systems, and offers increased confidence in estimated status and trends over assessments that consider only a single model.</p>
A trait-based framework for predicting foodborne pathogen risk from wild birds
<p>Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (<i>e.g</i>., habitat associations, movement, and foraging strategy) and pace-of-life (clutch size and generation length) mediated foodborne pathogen prevalence and proclivities to enter farm fields and defecate on crops. <i>Campylobacter </i>spp. were the most prevalent enteric pathogen (8.0%), while <i>Salmonella</i> and Shiga-toxin producing <i>E. coli </i>(STEC) were rare (0.46% and 0.22% prevalence, respectively). We found that several traits related to pathogen exposure predicted pathogen prevalence. Specifically, <i>Campylobacter </i>and STEC-associated virulence genes were more often detected in species associated with cattle feedlots and bird feeders, respectively. <i>Campylobacter </i>was also more prevalent in species that consumed plants and had longer generation lengths. We found that species associated with feedlots were more likely to enter fields and defecate on crops. Our results indicated that canopy-foraging insectivores were less likely to deposit foodborne pathogens on crops, suggesting growers may be able to promote pest-eating birds and birds of conservation concern (<i>e.g.</i>, via nest boxes) without necessarily compromising food safety. As such, promoting insectivorous birds may represent a win-win-win for bird conservation, crop production, and food safety. Collectively, our results suggest that separating crop production from livestock farming may be the best way to lower food safety risks from birds. More broadly, our trait-based framework suggests a path forward for co-managing wildlife conservation and food safety risks in farmland by providing a strategy for holistically evaluating the food safety risks of wild animals, including under-studied species.</p>
Data from: Trophic strategies of two sympatric endemic pigeons in insular ecosystems: a framework for understanding spatiotemporal frugivory interactions
<p><span><span><span><span>Pigeons are considered to play key ecological roles in frugivory and seed dispersal. They have colonised numerous oceanic islands and diversified into several species in sympatry. How these species coexist in similar niches is </span></span><span>poorly understood, although dietary separation is among the mechanisms suggested to avoid trophic </span><span><span>overlap. </span></span><span>We investigated the trophic ecology of the two endemic </span><i><span>Columba </span></i><span>species co-occurring in the laurel forest and thermosclerophyllous relicts of two of the Canary Islands. This study includes diet description in spatiotemporal terms, its relationship with fruit availability, and seed treatment in ten study areas established on La Palma and La Gomera. We used non-invasive DNA analysis to identify the faeces of the two congeneric species and microhistological methods to examine their diets. The degree of trophic overlap was evaluated by niche similarity and breadth indices. Molecular faecal sampling determined the spatiotemporal distribution of both pigeons to identify their areas of coexistence. These frugivorous pigeons' diets did not differ concerning the main plant species, but they diverged quantitatively in the proportions and parts of plants consumed. Lauraceae fruits were their staple foods, although Rhamnaceae and some Fabaceae and Solanaceae were also important. Both pigeons showed selective preferences for some fruits. Significant spatiotemporal variations in their diets were observed along with a general tendency to increase fruit intake at its ripening times. Our results suggest that different trophic strategies facilitate the coexistence of these frugivorous columbids. These pigeons act as seed dispersers and/or predators depending on seed features (size and hardness), and this may have valuable implications for their conservation.</span></span></span></p>
FIG. 2 in The position of Akkașdağı mammal locality in the neo-tectonic framework of Çankırı basin, Turkey
FIG. 2. — Geological map of the Akkasdağı area, modified from 1/100.000 scale MTA map.
FIG. 3 in The position of Akkașdağı mammal locality in the neo-tectonic framework of Çankırı basin, Turkey
FIG. 3. — Geological cross sections, see Figure 2 for locations.
Digital publishing of Indic manuscripts and inscriptions using the READ Workbench corpus development, research and publishing framework
<p>Paper presented on Friday 11 June 2021 at the Digital Medievalist Global Symposium <em>The past, present, and future of Digital Medieval Studies</em> for the Asia & Oceania Panel, in the session Reading Indic and Japanese scripts.</p> <p> </p>
An interpolated biogeographic framework for tropical Africa using plant species distributions and the physical environment
<p><strong>Aim:</strong> Existing phytogeographic frameworks for tropical Africa lack either spatial completeness, unit definitions smaller than the regional scale, or a quantitative approach. We investigate whether physical environmental variables can be used to interpolate floristically defined vegetation units, presenting an interpolated, hierarchical, quantitative phytogeographic framework for tropical Africa, which is compared to previously defined regions.</p> <p><strong>Location: </strong>Tropical mainland Africa 24°N to 24°S.</p> <p><strong>Taxon: </strong>31,046 vascular plant species and infraspecific taxa.</p> <p><strong>Methods: </strong>We calculate a betasim dissimilarity matrix from a comprehensive whole-flora database of plant species distributions. We investigate environmental correlates of floristic turnover with local non-metric multidimensional scaling. We derive a hierarchical biogeographic framework by clustering the dissimilarity matrix. The framework is modelled using a classification decision tree method and 12 physical environmental variables to interpolate and downscale the framework across the study region.</p> <p><strong>Results: </strong>Floristic turnover is related strongly to water availability and temperature, with smaller contributions from land cover, topographic ruggedness and lithology. Region can be predicted with 90% accuracy by the model. We define 19 regions and 99 districts. We find a novel arrangement of the arid regions. Regional subdivision within the savanna biome is supported with minor variation to borders. Within the forests of west and central Africa, our whole-flora gridded regionalisation supports the divisions identified by a previous analysis of trees only.</p> <p><strong>Main conclusions:</strong> Physical environmental variables can be used to predict floristically defined vegetation units with very high accuracy, and the approach could be pursued for other inc ompletely sampled taxa and areas outside of tropical Africa. Geographic coherence is higher than in previous quantitative phytoregional definitions. For most tropical African vascular plant species, we provide predictions of which species will occur within each mapped district and region of tropical Africa. The framework should be useful for future studies in ecology, evolution and conservation.</p>
Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory
<p></p><p>In the context of a timberline tree species (Betula ermanii) as "virtual island", we surveyed ectomycorrhizal (EcM) fungal diversity along a 430-m vertical gradient on the top of Changbai Mountain, China, sampling fine roots and neighboring soils of B. ermanii. Besides elevation, soil properties and plant functional traits, endophytic and saprotrophic fungal diversity were assessed as candidate predictors to construct integrative models. EcM fungal diversity decreased with increasing elevation, and exhibited positive diversity to diameter at breast height and negative diversity to distance from forest edge relationships in both roots and soils. Integrative models further showed that saprotrophic fungal diversity was the strongest predictor of EcM fungal diversity, directly enhancing EcM fungal diversity in roots and soils. All the metadata were stored here for use.</p><p></p>
A novel big data mining framework for reconstructing large-scale daily MAIAC AOD across China from 2000 to 2020
<p>This dataset contains the mean reconstructed MAIAC AOD and mean percentage of coverage of reconstructed MAIAC AOD across China from 2000 to 2020. </p>
Storm-scale and fine-scale boundary layer structures of tropical cyclones simulated with the WRF-LES framework
<p>The numerical simulations were carried out on the Tianhe Supercomputer, China. The TCBL data used in this study are uploaded here. Due to the large number, the original simulation data are available on request (liuqy@cma.gov.cn or liguangwu@fudan.edu.cn).</p>
Data from: Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches
<p><span>Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non-invasive, cost-efficient, and rapid surveys, the approach struggles to outperform traditional morphological approaches in providing reliable quantitative estimates for surveyed species (e.g., abundance and biomass).</span></p> <p><span>We present an integrated methodology for improving biodiversity surveys that pairs eDNA metabarcoding with morphological data, following a series of taxonomic and geographic filters. We demonstrate its power by applying it to a new spatiotemporal dataset generated on an Iberian-wide distributed aquatic mesocosm infrastructure that spans a wide biogeographic gradient.</span></p> <p><span>By building upon the strengths that these two approaches offer, our framework improved taxonomic resolution for 30% of the taxa and enabled species' traits (e.g., body-size) and abundance to be assigned to 85% of the taxa in hybrid datasets.</span></p> <p><span>These results indicate that eDNA-based assessments can complement, but not always replace, conventional approaches. Integrating conventional and modern eDNA metabarcoding approaches, already available in the ecologist's toolbox, will greatly enhance biodiversity assessments.</span></p>
Data of "Interaction-based material network: a general framework for (porous) microstructured materials"
<pre>Data related to the publication (we would be grateful if you could cite the paper in the case in which you are using the data) title = "Interaction-based material network: a general framework for (porous) microstructured materials", journal = "Computer Methods in Applied Mechanics and Engineering", pages = " ", year = "202?", issn = "0045-7825", doi = "https://doi.org/10.1016/j.cma.", author = "Nguyen, Van Dung and Noels, Ludovic"</pre>
Data for "Using an Uncertainty Quantification Framework to Calibrate the Runoff Generation Scheme in E3SM Land Model V1"
<p>The domain file and surface data file that used to run ELMv1, and processed ISIMP2a runoff data that used in <a href="https://gmd.copernicus.org/preprints/gmd-2021-401/">https://gmd.copernicus.org/preprints/gmd-2021-401/</a></p> <p>ELM_runoff_parameter_post.nc contains the ELM runoff generation relevant parameter posteriors at a global half degree spatial resolution.</p>
Database of the educational role of Citizen Science in the framework of Open Science from the paradigm of complex thinking
<p>Database for the analysis of the educational role of Citizen Science projects in the framework of Open Science from the paradigm of complex thinking</p>
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.