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276 results for “Integrated assessment”
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
<p><span>Assessing biodiversity in marine nearshore ecosystems is crucial for effective management, especially in the context of climate change and overexploitation of marine resources. Conventional methods often fall short in providing comprehensive information for managing seagrass ecosystems. However, the emergence of environmental DNA (eDNA) techniques has transformed the field by enabling non-invasive surveys that are cost-effective and provide detailed information with high resolution. In this study, we utilized eDNA to assess fish diversity and compared its effectiveness to conventional techniques such as catch assessment surveys and underwater surveys. </span>We sampled three habitats (A: mangrove-seagrass, B: seagrass only, and C: coral-seagrass) with 4 replicates. Site A recorded 8 fish species, site B had 16 species, and site C, characterized by coral and seagrass habitats, exhibited the highest fish diversity with 45 species (mean H' index = 2.455), underscoring its ecological importance. To ensure accurate taxonomic identification, we utilized an updated MiFish reference database containing a larger number of fish species compared to the initial library. This expanded reference database with 9,569 fish species, facilitated more precise identification and enhanced the reliability of our findings. Notably, the eDNA technique outperformed conventional methods by detecting 23 additional fish species that went undetected using traditional surveys. Moreover, our study documented five fish species previously unknown to occur within the study region, further emphasizing the value of eDNA analysis in uncovering hidden biodiversity. These findings strongly advocate for integrating eDNA techniques into the monitoring and assessment of biodiversity in shallow tropical habitats of the Western Indian Ocean. By leveraging eDNA surveys, we can gain valuable insights into fish diversity, discover hidden species, and make informed decisions for the conservation and management of these ecologically significant areas.</p>
A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short and long-read 16S rRNA gene sequences
Open the record for dataset details and reuse information.
Integration of environmental DNA metabarcoding technique to reinforce fish biodiversity assessments in seagrass ecosystems: A case study of Gazi Bay Seagrass meadows
Open the record for dataset details and reuse information.
Data for: An integrated population model and population viability assessment for the southern population of a data-poor species
Open the record for dataset details and reuse information.
Data from: Assessing species boundaries in the open sea: an integrative taxonomic approach to the pteropod genus Diacavolinia
To track changes in pelagic biodiversity in response to climate change, it is essential to accurately define species boundaries. Shelled pteropods are a group of holoplanktonic gastropods that have been proposed as bio-indicators because of their vulnerability to ocean acidification. A particularly suitable, yet challenging group for integrative taxonomy is the pteropod genus Diacavolinia, which has a circumglobal distribution and is the most species-rich pteropod genus, with 24 described species. We assessed species boundaries in this genus, with inferences based on geometric morphometric analyses of shell-shape variation, genetic (cytochrome c oxidase subunit I, 28S rDNA sequences) and geographic data. We found support for a total of 13 species worldwide, with observations of 706 museum and 263 freshly collected specimens across a global collection of material, including holo‐ and paratype specimens for 14 species. In the Atlantic Ocean, two species are well supported, in contrast to the eight currently described, and in the Indo‐Pacific we found a maximum of 11 species, partially merging 13 of the described species. Distributions of these revised species are congruent with well-known biogeographic provinces. Combining varied datasets in an integrative framework may be suitable for many diverse taxa and is an important first step to predicting species-specific responses to global change.
Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales
<p>Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can be used to improve the assessment of cetacean populations. We combined three types of data that are typically available for cetaceans of conservation concern: population-level visual survey data, individual-level capture-recapture data, and data on anthropogenic mortality. We used this IPM to estimate the population dynamics of the Cook Inlet population of beluga whales (CIBW; <i>Delphinapterus leucas</i>) as a case study. Our state-space IPM included a population process model and three observational submodels: 1) a group detection model to describe group size estimates from aerial survey data; 2) a capture-recapture model to describe individual photographic capture-recapture data; and 3) a Poisson regression model to describe historical hunting data. The IPM produces biologically plausible estimates of population trajectories consistent with all three datasets. The estimated population growth rate since 2000 is less than expected for a recovering population. The estimated juvenile/adult survival rate is also low compared to other cetacean populations, indicating that low survival may be impeding recovery. This work demonstrates the value of integrating various data sources to assess cetacean populations and serves as an example of how multiple, imperfect datasets can be combined to improve our understanding of a population of interest. The model framework is applicable to other cetacean populations and to other taxa for which similar data types are available.</p>
Integrative assessment of climate change-related impacts and risks on urban land
<p>Shapefile data set estimating trends of mean annual terrestrial surface air temperature (°C) and mean annual total precipitation (mm) and several heat indicators for urban land, characterised by clusters of local spatial autocorrelation in regard to the age of urban area and the coefficient of variation of urban area extent over time.</p>
VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
<p><span>In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, m</span><span>ovement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with </span><span>genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level. </span></p>
Application of flow cytometry using advanced chromatin analyses for assessing changes in the sperm structure and DNA integrity in a porcine model
<p><span>Chromatin status is critical for sperm fertility. We tested a multivariate approach for studying pig sperm chromatin, aiming to capture the chromatin structure's complexity with a set of quick and simple techniques, not only DNA damage. Sperm doses from 36 boars (3 ejaculates/boar) were analyzed at days 0 and 11 (cooled storage). Analyses were: CASA (motility) and flow cytometry to assess sperm functionality and chromatin structure by SCSA (DNA fragmentation %DFI and chromatin maturity %HDS), monobromobimane (mBBr, tiol status/disulfide bridges between protamines), chromomycin A3 (CMA3, protamination) and 8-hydroxy-2'-deoxyguanosine (8-oxo-dG, DNA oxidative damage). Data were analyzed by linear models for effects of boar and storage, correlations, and multivariate analysis as hierarchical clustering and principal component analysis (PCA). Storage reduced sperm quality parameters, mainly motility, with no critical oxidative stress increases, while chromatin status worsened slightly (%DFI and 8-oxo-dG increased while mBBr MFI and disulfide bridges decreased). Boar significantly affected most chromatin variables except for CMA3, with storage affecting most except %HDS. At day 0, sperm chromatin variables clustered closely, except for CMA3, and %HDS and 8-oxo-dG correlated with many variables (notably, mBBr). After storage, the relation between %HDS and 8-oxo-dG remained, but correlations among other techniques disappeared, and mBBr variables clustered separately. The PCA suggested a considerable influence of mBBr on sample variance, especially regarding storage, with SCSA and 8-oxo-dG affecting between-sample variability. Overall, CMA3 was the least informative, in contrast with results in other species. The combination of DNA fragmentation, DNA oxidation, chromatin compaction, and tiol status seems a good candidate for obtaining a complete picture of the pig sperm nucleus status, raising many questions for future molecular studies and deserving further research to establish its usefulness as fertility predictors in multivariate models. The meaning of CMA3 should be clarified.</span></p>
Assessing Heavy Metal Contamination in Agricultural Soils: A Predictive Model Integrating GIS Tools and Probability-Risk Matrix – Case Study: Guarda Region, Portugal
<p>In these files we can find the final risk map of heavy metal contamination for the guarding area in Portugal obtained according to the methodology explained in the paper "Assessing Heavy Metal Contamination in Agricultural Soils: A Predictive Model Instegrating GIS Tools and Probability-Risk Matrix - Case Study: Guarda Region (Portugal)</p> <p>Final Risk Equal.tiff: GeoTiff with a pixel size of 30m. EPSG:3763 - ETRS89 / Portugal TM06</p> <p>Also attached is the symbolisation for the image in .qml (Quantum GIS Layer Style File) format.</p> <p>A file called RISK RECLASS is also available, where you can find the risk classification maps for each of the studied factors: </p> <ul> <li>Proximity to roads</li> <li>Proximity to industrial areas</li> <li>Ph</li> <li>Soil organic content</li> <li>Slope</li> <li>Soil texture</li> <li>Mining extraction areas </li> <li>Drainage</li> </ul> <p>finally a DATABASE file where the data of the 360 points for the calculation of the risk maps can be found. </p>
A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates
<p>Dataset and R script supporting the findings of the study "A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates". </p>
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
<p>Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.</p>
An integrative assessment of the plastic debris load in the Mediterranean Sea
<p>An integrative assessment of the plastic debris load in the Mediterranean Sea</p> <p>Maria Luiza Pedrotti, Fabien Lombard, Alberto Baudena, François Galgani, Amanda Elineau, Stephanie Petit, Maryvonne Henry, Romain Troublé, Gilles Reverdin, Enrico Ser-Giacomi, Mikaël Kedzierski, Emmanuel Boss, Gabriel Gorsky</p> <p>This manuscript contains the results of the Tara Mediterranean Expedition, which sampled surface plastics throughout the Mediterranean Sea. The advanced imaging methods (ZoosCan) and data processing (Zooprocess) used allowed us to undertake an integrative study of surface plastic pollution, analyzing and classifying more than 75,000 plastic debris. We also provided estimates of regional differences in floating plastic loads and plastic characteristics. Notably, a new Lagrangian diagnostic predicting the concentration of plastic debris allowed us to link observed plastic concentrations to terrestrial plastic sources encountered by the water parcel carrying them.</p> <p>The dataset presented here is related to the publication M.L. Pedrotti et al. 2022, <a href="https://doi.org/10.1016/j.scitotenv.2022.155958">https://doi.org/10.1016/j.scitotenv.2022.155958</a></p>
Assessing the Integrity of Older Archaeological Collections: An Example from La Ferrassie - supplemental material (data and R code)
<p>Supplemental data and R code for reproducing figures and table values in paper 'Assessing the Integrity of Older Archaeological Collections: An Example from La Ferrassie' by HL Dibble, SC Lin, DM Sandgathe, A Turq.</p>
Open dataset for the research of "Assessing accuracy improvement of integrating digital footprints into gridded population mapping: spatiotemporal variations and data bias"
<p>Result datasets for "Assessing accuracy improvement of integrating digital footprints into gridded populationmapping:spatiotemporal variations and data bias":</p> <ol> <li> S1 is the results for gridded population mapping using different methods.</li> <li> S2 is the aggregate results of population mapping at county level.</li> <li> S3 is the results for intraday variation of population disaggregation accuracy,</li> <li> S4 is the data bias of different digital footprints.</li> </ol>
Survey data of an integrative evaluation framework for assessing the sustainability of different types of urban agriculture
<p>In this dataset we present core data of an integrative evaluation framework for assessing the environmental, social, and economic sustainability of urban agriculture. The multi-criteria analysis is conducted by an Analytic Hierarchy Process and a participatory approach. The data integrate the selection and weighting of sub-criteria based on two online surveys:</p> <p>1) Survey 1: The selection of suitable sub-criteria for assessing the sustainability of urban agriculture was done by European scientific experts.</p> <p>2) Survey 2: The weighting of the selected sub-criteria was done on the example of vertical farming and community supported agriculture. Therefore, we involved stakeholders representing key actors for the implementation of urban agriculture: city administrations and non-governmental organizations (NGOs) of ten German case study cities, practitioners and technical-scientific experts.</p> <p> </p> <p><strong>List of data and content</strong></p> <p>1) Survey_1 (*.zip):</p> <ul> <li>Survey_1_Criteria_Selection_English: Online survey in English (*.pdf)</li> <li>Survey_1_Information_Sub-criteria_English: Information about the sub-criteria provided in the survey (in English) (*.pdf)</li> <li>Survey_1_Groups: Results of the statistical analyses (U-tests and Kruscal-Wallis) to detect group-specific differences (e.g. gender, different length or degree of experience with urban agriculture, scientific focus, target group, expertise); the tests were conducted with IBM SPSS Statistics 25 (*.xlsx)</li> </ul> <p>2) Survey_2 (*.zip):</p> <ul> <li>Survey_2_AHP_City_Administrations_German: Online survey for city administrations in German (*.pdf)</li> <li>Survey_2_AHP_Practitioners_German: Online survey for practitioners and technical-scientific experts in German (*.pdf)</li> <li>Survey_2_AHP_NGOs_German: Online survey for NGOs in German (*.pdf)</li> <li>Survey_2_Information_Sub-Criteria_German: Information about the sub-criteria provided in the survey (in German) (*.pdf)</li> <li>Survey_2_Groups: Results of the statistical analyses (U-tests and Kruscal-Wallis) to detect group-specific differences (e.g. gender, different length or degree of experience with urban agriculture, scientific focus, target group, expertise); the tests were conducted with IBM SPSS Statistics 25 (*.xlsx)</li> <li>rdata_CA_AHP_edible_Cities_2022-03-18_10-28: Results of the survey for city administrations (*.csv)</li> <li>rdata_NGO_AHP_edible_Cities_2022-03-18_10-40: Results of the survey for NGOs (*.csv)</li> <li>rdata_PE_AHP_edible_Cities_2022-03-18_10-41: Results of the survey for practitioners and technical-scientific experts (*.csv)</li> <li>rdata_all_AHP_edible_Cities_2022-03-18_09-53: Total results of the survey</li> </ul> <p> </p> <p><strong>Data acquisition and processing</strong></p> <p>The methods are described in this linked publication:</p> <p><span>John, H., & Artmann, M. (2024). Introducing an integrative evaluation framework for assessing the sustainability of different types of urban agriculture. </span><span>I<em>nternational Journal of Urban Sustainable Development, </em></span>16 (1), 35-52<em><span>. </span></em><span>doi:<em> </em>10.1080/19463138.2024.2317795</span></p> <p>The methodology of the performed analytic hierarchy process (AHP) is published in a separate repository on GitHub including a paper that systematically explains the AHP by means of code examples, starting with the raw data, through their adaptation to the software functions of the ahpsurvey R-package, and finally, execution of the AHP up to the visualization of the results.</p> <p> </p> <p><strong>Acknowledgments</strong></p> <p>The authors thank Mabel Killinger and Marie Herzig for their help in stakeholder identification as well as all experts and stakeholders for their participation in the two online surveys and their helpful comments. Data processing and analysis by means of an Analytic Hierarchy Process in R would not have been possible without the help of Björn Kasper.</p>
Brazilian Starter Data Kit Update to Support the Paper "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage"
<p>This dataset presents updates on the Brazilian starter data kit, considering current load profile data and specific renewable energy sources production, using public data from official Brazilian power system agents. The dataset contains the input data and respective files to run OSeMOSYS and Flextool, including the utility-scale storage model. Additionally, this dataset contains the results of the study "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage". This study evaluates the increase in variable renewable energy in Brazil and its integration with Storage systems. </p>
Data from: Integrating ecological niche and hydrological connectivity models to assess the impacts of hydropower plants on an endemic and imperiled freshwater turtle
<p>We built this dataset to assess the impacts of hydropower plants on the distribution of an endemic and imperiled freshwater turtle with very unique ecological requirements, the Williams' side-necked turtle (<em>Phrynops</em> <em>williamsi</em>). To prevent and mitigate impacts, we prioritized sites for species conservation by classifying planned HPP locations according to their predicted adverse effects on species distribution. The dataset has two files: i) species occurrence records and ii) hydropower plant data. The first dataset was fully built by the authors and the second was modified from the Brazilian Electricity Regulatory Agency (ANEEL) georeferenced data system.</p>
Assessing the Integration of Tobacco Cessation Treatment Into Lung Cancer Screening (LCS)
ClinicalTrials.gov study NCT03611881. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Assessment of Clinically Related Outcomes and Biomarker Analysis for Translational Integration in Colorectal Cancer
ClinicalTrials.gov study NCT01762813. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
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.