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466 results for “priority”
Dataset on Spatial Analysis and Clustering of Deforestation in the Amazon Biome: Spatio-Temporal Patterns and Priority Areas
<p>The dataset was developed with the aim of facilitating the development of a methodology to identify and evaluate deforestation patterns and trends in the Amazon. This innovative method combines deforestation alerts from the Real-Time Deforestation Detection System (DETER) with detailed information on various land categories, including environmental protection areas, settlements, rural properties, undesignated public forests, indigenous lands, and conservation units. The integration of this robust data allowed for the precise identification of areas at risk of deforestation, significantly strengthening monitoring and control activities aimed at combating deforestation in the Amazon region.</p> <p> </p> <p><strong>Spatial resolution</strong></p> <p>The data are available with a spatial resolution of 25 x 25 km (625 km²) and cover the Amazon biome.</p> <p> </p> <p><strong>Temporal resolution </strong></p> <p>Period of observed data: 2017 and 2021</p> <p> </p> <p><strong>Coordinate reference system</strong> </p> <p>Geographic Coordinate System with Datum SIRGAS 2000 (EPSG:5880)</p> <p> </p> <p><strong>Data format</strong></p> <p>Data is provided as Shapefile.</p> <p> </p> <p><strong>Dataset usage</strong> </p> <p>It is free to use, but please make sure to cite the repository and our paper properly if you use this dataset.</p> <p> </p> <p><strong>Publication & further information</strong></p> <p>For additional scenario information, please contact Francisco Gilney Silva Bezerra (franciscogilney@gmail.com).</p>
Expanding drug targets for 112 chronic diseases using a machine learning-assisted genetic priority score
<h2>ML-GPS: Machine Learning-Assisted Genetic Priority Score</h2> <p>This Zenodo repository contains data and code associated with the publication:</p> <p>Chen R, Duffy Á, Petrazzini BO, Vy HM, Stein D, Mort M, Park JK, Schlessinger A, Itan Y, Cooper DN, Jordan DM, Rocheleau G, Do R. Expanding drug targets for 112 chronic diseases using a machine learning-assisted genetic priority score. Nat Commun. 2024 Oct 15;15(1):8891. doi: <a href="https://doi.org/10.1038/s41467-024-53333-y">10.1038/s41467-024-53333-y</a>.</p> <h3>Important notes</h3> <ul> <li>You can interactively view the top 10% of ML-GPS predictions without download at <a href="https://rstudio-connect.hpc.mssm.edu/mlgps/">https://rstudio-connect.hpc.mssm.edu/mlgps/</a>.</li> <li>For running Jupyter notebooks, please follow the instructions in the README of the GitHub repository at <a href="https://github.com/robchiral/ML-GPS">https://github.com/robchiral/ML-GPS</a>.</li> </ul> <h3>Repository contents</h3> <p>Files needed to train ML-GPS and ML-GPS DOE:</p> <ul> <li><strong>Files needed for Jupyter notebooks.zip</strong>: Data files required for preprocessing and training.</li> <li><strong>Jupyter notebooks.zip</strong>: Notebooks for cleaning data, training models, and generating predictions.</li> </ul> <h3>Other files:</h3> <ul> <li><strong>Predictions for all gene-phecode pairs.zip</strong>: ML-GPS and ML-GPS DOE scores for all analyzed gene-phecode pairs.</li> <li><strong>Summary statistics.zip</strong>: Genetic association summary statistics for all tested gene-phecode pairs.</li> </ul> <h3>Updated performance metrics</h3> <table> <tbody> <tr> <td><strong>Model</strong></td> <td><strong>Open Targets AUPRC</strong></td> <td><strong>SIDER AUPRC</strong></td> </tr> <tr> <td>ML-GPS (non-DOE)</td> <td>0.074</td> <td>0.080</td> </tr> <tr> <td>ML-GPS DOE (activator predictions)</td> <td>0.029</td> <td>0.042</td> </tr> <tr> <td>ML-GPS DOE (inhibitor predictions)</td> <td>0.067</td> <td>0.064</td> </tr> </tbody> </table> <h3>Zenodo versions</h3> <ul> <li><strong>Version 4: </strong>Updated notebooks and external data to use Open Targets 2024.9; summary statistics are unchanged</li> <li><strong>Version 3: </strong>Corrected error where DOE for rare and ultrarare variants was incorrectly incorporated</li> <li><strong>Version 2: </strong>Original release accompanying the publication</li> </ul>
The quest for successful Atlantic salmon restoration: perspectives, priorities, and maxims
<p>Data supporting publication https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsab201/6425092?casa_token=nTwNIhkC314AAAAA:FBK2iqeXsVgELsFGUxQAMjyWoOU6p2uJMe9UZ5ynGrdWIH6JxDSqN16EanyKWvZdtf1F3KdN4RW9Vg</p>
Data from: Sequential use of niche and occupancy models identifies conservation and research priority areas for two data-poor endemic birds from the Colombian Andes
<p>The lack of high-quality information on data-poor species can hinder efforts to inform conservation actions via spatial distribution modeling. This is particularly true for tropical birds of conservation concern, for which ecological studies and assessments of their conservation status have received limited funding. Here we use a cost- and time-efficient protocol for assessing the distribution of range-restricted taxa and to identify priority areas for their conservation based on a sequential application of Environmental Niche Models (ENMs) and Occupancy-Detection Models. This approach first uses available geographical information and niche-theory to prioritize potential study sites, which can later be surveyed to obtain high-quality presence-absence data to accurately model distributional ranges with limited resources. We apply this protocol to identify priority areas for two Neotropical birds of conservation concern endemic to the Colombian Andes: Yellow-headed Brush-finch (<i>Atlapetes flaviceps</i>) and Tolima Dove (<i>Leptotila conoveri</i>). We first fitted ENMs using spatially-filtered datasets containing all available records up to 2018. We then conducted field surveys across climatically suitable areas identified for both species, carrying out a total of 1750 counts to generate input data for the occupancy models. Overall, our results suggested more extended and more continuous distribution ranges for both species than previously reported, but also identified population strongholds that are not currently represented within the national protected areas system. Both species occupied a narrow elevational belt (~1300–2600) of the Central Andes of Colombia primarily on the slopes of the Magdalena River valley, with isolated populations in the Western and Eastern Andes; these areas have undergone some of the most marked landscape transformations in Colombia. This straightforward protocol maximizes available information and minimizes costs, while allowing for estimation of occurrence probabilities for range-restricted, data-poor taxa.</p>
Data on plant health stakeholder priorities for tests and general prioritisation framework
<p>Data collected in the framework of work package 4 of the Valitest project. They correspond to a qualitative assessment of plant health stakeholder requirements, have been collected using online surveys supplemented by desk-based research, as well as impact assessments</p>
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation
<p>Core corridors: derived from Circuitscape modeling results -top 50% of wood frog, boreal chorus frog and tiger salamander results converted to binary value and summed to produce core corridors (probable movement for 2-3 amphibian species). <br> <br> To derive core corridors, we summed connectivity models for three amphibian species. For each species we derived focal nodes from high habitat value (based on HSI modelling), used three resistance scenarios and summed the three scenarios for each species to represent probable movement pathways between focal nodes. Species connectivity models were then classified to top 50% of the model, and converted to a binary value of 0 to 1. The three species were summed where by values 0-3 represent number of amphibian species the corridor probably supports movement. </p>
Not all regions with high pesticide risk deserve priority concern
<p>The datasets with 14 sheets contain basic data on pesticide use in China since 1991, parameters of four widely used pesticides (carbofuran, chlorpyrifos, atrazine and acetochlor), and related changing legacies, concentrations, and ecological risk in multimedia of each basin for 30 years. The detailed content can be found in the sheet 'Readme'.</p>
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation - Raw Data
<p>Call of the Wetland Program observation data reported by citizen scientists at wetlands in the City of Calgary during three amphibian seasons from 2017 to 2019. Wetlands were surveyed up to 11 times per season and participants reported observations to a smartphone application – where they documented species, and type of observation (eggs, adult, juvenile, tadpole or call). Participants also recorded when they participated in a survey and there were no observations. Observations associated without a site ID represent opportunistic observations at non-survey wetlands. This data was used to validate habitat suitability models derived from the occupancy modeling results. <br> <br> Survey wetland location shapefile (centroid point of wetland) also included. </p>
Fig. 2 in Seasonal Variation In A Small-Mammal Assemblage In A Priority Site For Conservation In South-Central Chile
Fig. 2. Rodent capture rate (plus standard deviations) in the study
Latitudinal cline in the foraging dichotomy of loggerhead sea turtles reveals the importance of East China Sea for priority conservation
<p><strong>Aim:</strong> Quantifying the importance of habitat areas for conservation of highly migratory marine species with complex life histories can be challenging. For example, loggerhead turtles (Caretta caretta) nesting in Japan forage both oceanically and neritically after their reproductive period. Here, we aimed to quantify the proportions of turtles using these two contrasting habitats (foraging dichotomy) to suggest priority conservation areas.</p> <p><strong>Methods:</strong> We examined the occurrence of foraging dichotomy at three nesting sites (Ishigaki, Okinoerabu Islands, and Ichinomiya) based on stable isotope analysis of the egg yolks for 82 turtles and satellite tracking of post-nesting migration for 12 turtles. Moreover, we used the data of three other sites from previous studies (Yakushima Island, Minabe, and Omaezaki).</p> <p><strong>Results:</strong> Two neritic foraging grounds (East China Sea and the coastal area of the Japanese archipelago), and an oceanic ground (North Pacific Ocean) were identified. We found a latitudinal cline with respect to the occurrence of foraging dichotomy; >84% of the females nesting at southern sites (Ishigaki and Okinoerabu Islands), 73% at middle sites (Yakushima Island and Minabe), and <46% at northern sites (Omaezaki and Ichinomiya) were neritic foragers; the proportion of oceanic foragers increased at northern sites. Based on the annual number of nests in the entire nesting region of Japan, satellite tracking, and the latitudinal cline of foraging dichotomy, we estimated that 70% and 9% of annual nesting females in Japan utilise the neritic foraging habitat in the East China Sea and the coastal area of the Japanese archipelago, respectively and that and 22% utilise the oceanic habitat of the North Pacific Ocean.</p> <p><strong>Main conclusions:</strong> The East China Sea represents a critical foraging habitat for the North Pacific populations of endangered loggerhead sea turtles. Our findings emphasise the need for international management to ensure their protection.</p>
Data from: Patch size drives colonization by aquatic insects, with minor priority effects of a cohabitant
<p>Patch size is one of the most important factors affecting the distribution and abundance of species, and recent research has shown that patch size is an important niche dimension affecting community structure in aquatic insects. Building on this result, we examined the impact of patch size in conjunction with presence of larval anurans on colonization by aquatic insects. Hyla chrysoscelis (Cope's gray treefrog) larvae are abundant and early colonists in fishless lentic habitats, and these larvae can fill multiple ecological roles. By establishing larvae in mesocosms prior to colonization, we were able to assess if H. chrysoscelis larvae have priority effects on aquatic insect assemblages. We conducted a series of three experiments in naturally-colonized experimental landscapes to test whether (1) H. chrysoscelis larval density affects insect colonization, (2) variation in patch size affects insect colonization, and (3) the presence and larval density of H. chrysoscelis shifts colonization of insects between patches of different size. Larval density independently had almost no effect on colonization, while patch size had species-specific effects consistent with prior work. When larvae and patch size were tested in conjunction, patch size had numerous, often strong, species-specific effects on colonization; larval density had effects largely limited to the assemblages of colonizing beetles and water bugs, with few effects on individual species. Higher larval densities in large mesocosms shifted some insect colonization to smaller patches, resulting in higher beta diversity among small patches in proximity to high density large mesocosms. This indicates establishing H. chrysoscelis larvae prior to insect colonization can likely create priority effects that slightly shape insect communities. Our results support the importance of patch size in studying species abundances and distributions, and also indicate that colonization order plays an important role in determining the communities found within habitat patches.</p>
Data from: Using functional traits to identify conservation priorities for the world's crocodylians
<p>Over half of all crocodylians are threatened with extinction, with many species considered to be functionally extinct throughout their historical ranges. How such losses impact crocodylian functional diversity (FD) and its conservation is poorly understood, but can be investigated using measurable traits. Where such information is unavailable, phylogenetic diversity (PD) has been proposed as an effective strategy to capture FD, but this assumption is not well tested.</p> <p>We constructed a global trait database for 28 extant crocodylians [uploaded here], and quantified their functional diversity, distinctiveness and groupings. Functionally distinctive crocodylians include the most and least evolutionarily distinct species, likely because unusual trait values and combinations can be produced by both evolutionary isolation and evolutionarily recent adaptive radiation. We identified four functional groups of crocodylians, within which species have similar ecological roles. Highly distinctive species, such as the gharial, fit less well into functional groups.</p> <p>We combined functional distinctiveness and threat ranking scores to prioritise species for conservation. The metric is termed EcoDGE (Ecologically Distinct and Globally Endangered), and we tested how well it operates to preserve crocodylian FD amongst extant Crocodylia. Under current extinction scenarios, 32-38% of crocodylian FD might be lost within 100 years. Losses increase to 48% if all threatened species go extinct, with Asia identified as a hotspot of threatened FD in crocodylians. Highly-threatened distinctive species lead this extinction scenario, exacerbated by clusters of species sharing traits linked to high extinction risk. These traits include habitat specialism and lower reproductive investment; in contrast, species that tolerate climate extremes are more resilient.</p> <p>Prioritising at-risk species based on functional distinctiveness and threat status appears to be an effective way to conserve present-day crocodylian diversity. Conservation prioritisation based on the EcoDGE metric performed well to minimize projected losses in FD. Among extant crocodylians, FD losses are projected when high diversity overlaps with high extrinsic threats.</p> <p>We then examined the utility of PD-based measures as surrogates for FD conservation, to better understand the advantages and drawbacks of such substitutions. A PD-based measure such as the EDGE metric, provided an effective tool to capture functional diversity in our tests.</p>
Assessing the conservation priority of freshwater lake sites based on taxonomic, functional and environmental uniqueness
<p><strong>Aim: </strong>We propose a novel approach that considers taxonomic uniqueness, functional uniqueness and environmental uniqueness, and show how it can be used in guiding conservation planning. We illustrate the approach using data for lake biota and environment.</p> <p><strong>Location: </strong>Lake Puruvesi, Finland.</p> <p><strong>Methods: </strong>We sampled macrophytes and macroinvertebrates from the same 18 littoral sites. By adapting the original 'ecological uniqueness' approach, we used distance‒based methods to calculate measures of taxonomic (LCBD‒t), functional (LCBD‒f) and environmental (LCEH) uniqueness for each site. We also considered the numbers and locations of the sites needed to protect up to 70% of total variation in taxonomic, functional or environmental features in the studied part of the lake.</p> <p><strong>Results: </strong>Relationships between taxonomic (LCBD‒t), functional (LCBD‒f) and environmental (LCEH) uniqueness were generally weak, and only the relationship between macrophyte LCBD‒t and LCBD‒f was statistically significant. Overall, however, if the whole biotic dataset was considered, macroinvertebrate LCBD‒f values showed a consistent positive relationship with macrophyte LCBD‒f. Depending on the measure of site uniqueness, between one third to one half of the sites could help protect up to 70% of the ecological uniqueness of the studied part of Lake Puruvesi.</p> <p><strong>Main conclusions: </strong>Although the dataset examined originated from a large lake system, the approach we proposed here can be applied in different ecosystems and at various spatial scales. An important consideration is that a set of sites has been sampled using the same methods, resulting in species and environmental matrices that can be analysed using the methodological approach proposed here. This framework can be easily applied to grid‒based data, sets of islands, or sets of forest fragments. We suggest that the approach based on taxonomic, functional and environmental uniqueness will be a useful tool in guiding nature conservation and ecosystem management, especially if associated with meta‒system ideas or network thinking.</p>
Data for 'Warming and predation risk only weakly shape size-mediated priority effects in a cannibalistic damselfly'
<p>In a laboratory experiment, we studied effects of warming (low and high temperature) and predation risk (presence and absence of predator cues of perch) on SMPE in life history and physiological traits in the cannibalistic damselfly <em>Ischnura elegans</em>. We induced SMPE by manipulating hatching dates, thereby creating four groups: non-mixed phenology early (E) and late (L) hatchlings, and mixed phenology early (E+L) and late (L+E) hatchlings.</p> <p>This data set includes:</p> <ul> <li>hatch date</li> <li>emergence date</li> <li>survival until emergence and emergence success data</li> <li>mass of adult insects</li> <li>development time (from hatching to emergence, in days)</li> <li>growth rate (mass of adult insect/development time in days)</li> <li>protein content (μg of protein/μl of prepared homogenate)</li> <li>fat content (μg of fat/μl of prepared homogenate)</li> <li>phenoloxidase activity (PO, value of activity curve slope)</li> <li>PO activity/protein (value of activity curve slope/(μg of protein/μl of prepared homogenate)</li> </ul>
Figure 2 in Reproduction phenology of a high conservation priority cracid - the Bare-faced Curassow (Crax fasciolata; Aves, Galliformes, Cracidae)
Figure 2. Sampling effort (y-axis) in SESC Baía das Pedras Park (northern Pantanal, Mato Grosso State, Brazil) expressed in days per month (x-axis) for different years (2015, 2016, and 2017) is represented by stacked bars. The presence of Bare-faced Curassow (Crax fasciolata) offspring is represented by the shapes on the x-axis. The triangle represents their presence during surveys in 2016, and the circle represents those in 2017.
Figure 1 in Reproduction phenology of a high conservation priority cracid - the Bare-faced Curassow (Crax fasciolata; Aves, Galliformes, Cracidae)
Figure 1. Orthophoto of SESC Baía das Pedras Park (northern Pantanal, Mato Grosso State, Brazil) and associated sampling locations in a 1 km square grid (numbers). Orange circles represent sampling locations where family groups (parent(s) with offspring) of the Bare-faced Curassow (Crax fasciolata) were captured with camera traps. Gold circles represent sampling locations where only adults were captured, while white circles represent those where no BFC was captured.
Database for the Priority Program 2322 SoilSystems – Soils and substrates used in the first phase (2021-2024)
<p><span>The presented data set represents a comprehensive characterization of soil samples that were used in the German joint research priority program 2322 ”SoilSystems: Systems ecology of soils – energy discharge modulated by microbiome and boundary conditions” funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). The joint research program <em><span>SoilSystems</span></em> aims to integrate a thermodynamic description of the soil system for the first time in order to gain a systemic view on energy and matter fluxes and their interactions with living and non-living soil components. </span><span>These include numerous aspects and parameters of soil (organic matter) chemistry, soil microbiology (including faunal trophic levels) and the new discipline of soil thermodynamics. In order to have a joint focus in the individual research activities, a ‘Common Experimental Platform’ has been set up. The provision of shared soil samples, substrates and incubation conditions should enable coherent and interlinked data to be obtained. </span><span>More information can be found here: <a href="https://soilsystems.net/">https://soilsystems.net/</a>. </span></p>
Prioritising GitHub Priority Labels - Data Set and Software
<p>This is the data set and software produced for the paper <em>Prioritising GitHub Priority Labels</em>, J. Caddy and C. Treude.</p> <p>The CSV file contains a manually categorised set of GitHub issue labels that are priority-related. They have been ranked and normalised into three values; "High", "Medium", and "Low" priorities. These labels have been gathered from the 5000 most-starred repositories on GitHub as of 2022-06-01.</p> <p>The Python script makes use of this data set as an example, and will retrieve the highest priority issues from all of the repositories contributed to by the author specified.</p> <p>Run the python script from the same directory as the CSV file, providing the username you wish to see the highest priority issues for as the first command line argument. Supply your GitHub Personal Access Token either at the prompt so it's not displayed, or as the second command line argument.</p>
Identifying priority survey sites for early-season milkweed conservation
<p>Monarch butterfly (<em>Danaus plexippus</em>) populations are experiencing decline due to habitat degradation and climate threats. In 2024, this iconic species became protected under the Endangered Species Act. Critical to the persistence of this species of cultural and ecological importance is milkweed (<em>Asclepias spp.</em>), which monarchs rely on as an essential resource for food and reproduction. Motivated by concerns over the loss of monarch habitat, the Santa Barbara Botanic Garden (SBBG) and local collaborators are working to identify potential restoration areas in the Los Padres National Forest (LPNF). However, the vast size and complex terrain of the LPNF pose a logistical challenge to surveying. Therefore, there is a need for a tool to aid in selecting sites to prioritize. Our team created a priority index for surveying milkweed within the LPNF by predicting the habitat suitability for four early-season milkweed species using Maximum Entropy (MaxEnt) species distribution modeling and creating a novel survey site accessibility index. We identified high priority sites for the team to survey based on high predicted suitability for each species of early-season milkweed and high physical accessibility. To communicate these results, we created an interactive web dashboard, which the SBBG team will use for field planning to support the ongoing monitoring of milkweed populations for monarch habitat restoration efforts within the LPNF.</p>
Plant diversity darkspots for global collection priorities: time-to-event datasets per botanical country as defined by the World Geographical Scheme for Recording Plant Distributions (WGSRPD).
<p>Datasets used to predict the number of plant species remaining to be described and/or geolocated within a botanical country, which represents the third level of subdivision (generally equating to a political country) used by WGSRPD for recording plant distributions. The folder is composed of two subfolders <em>has_coords</em> and <em>has_no_coords</em> containing the time-to-event data for species with valid and no (invalidated) occurrence records within a given botanical country respectively<em>.</em></p> <ul> <li>Each folder contains a<strong> </strong>list of 361 botanical countries with the following 16 fields:</li> </ul> <pre><strong>species:</strong> species name<br><strong>time_ofdescription:</strong> year of the (first) description<br><strong>time_ofcollection:</strong> year of the collection of the earliest record<br><strong>family:</strong> species family name<br><strong>lifeform_description: </strong>the life form categorised into 4 classes <br><strong>CHELSA_bio_1: </strong>annual mean temperature (°C)<br><strong>CHELSA_bio_12:</strong> annual precipiation (mm)<br><strong>CHELSA_bio_15</strong>: temperature seasonality (-)<br><strong>CHELSA_bio_4</strong>: precipitation seasonality (-)<br><strong>elevation</strong>: elevation (m)<br><strong>range_size_area:</strong> total area of the botanical countries encompassing the species' native range <br>according to the World Checklist of Vascular Plants (WCVP) (km^2) <br><strong>taxo_activity</strong>: taxonomic activity calculated as the number of named authors in the World Checklist of Vascular Plants<br>describing species from the same family during the year of description of the species,<br>divided by the number of species described within the given family that year. <br><strong>num_records_per_year:</strong> geographic activity calculated as the number of occurrence records<br>collected within the native range of the species, divided by the number of years between <br>the earliest and the lastest (first) record collected within this range.<br><strong>num_uses</strong>: number of human uses<br><strong>time_todescription:</strong> number of years between the (first) description and 1753<br><strong>time_tocollection:</strong> number of years between the (first) description and the collection of the first record of the species<br><br></pre> <p> </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.