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403 results for “occurrence data”
Occurrence data on Beauvericin and Enniatins in food
<p>Beauvericin and enniatins are mycotoxins produced by various <em>Fusarium</em> species that invade and grow on crops, and may produce them under moist and cool conditions. They are predominantly found in cereal grains and their products. The datasets contain occurrence data submitted to the European Food Safety Authority (EFSA) by two European countries (Italy and Finland) following a call for data and supplemented with data from some European research groups. The samples have been taken in years 2002 and 2012, with majority of data collected in 2012. The analytical method used is LC-MS. This data has been used to inform the preparation of the Scientific Opinion on the risks to human and animal health related to the presence of beauvericin and enniatins in food and feed adopted by EFSA in 2014.</p>
Data and code for "Competition contributes to quantitative mismatches between plant fitness and occurrence along environmental gradients"
<p>This repository contains data and code for the following manuscript: Hayashi, K. T., & Kraft, N. J. B. (2025). Competition contributes to quantitative mismatches between plant fitness and occurrence along environmental gradients. Journal of Ecology, 113, 2590–2602. <a href="https://doi.org/10.1111/1365-2745.70115">https://doi.org/10.1111/1365-2745.70115</a></p>
Data from: Fox control and fire influence the occurrence of invasive predators and threatened native prey
<p>It can be challenging to distinguish management impacts from other population drivers, including 'natural' processes and co-occurring threats. However, disentangling processes is important, particularly when management may have unintended consequences, such as mesopredator release. We explored the effects of long-term, broadscale poison-baiting programs on the distribution of red foxes <em>Vulpes vulpes</em> (targeted invasive predator), feral cats <em>Felis catus</em> (unmanaged invasive competitor) and two of their threatened native prey in two fire-affected regions of south-eastern Australia. We synthesised data from 3,667 camera-trap deployments at 1,232 sites (172,052 trap-nights), combining experimental manipulation of foxes and fire with space-for-time approaches. Fox control effectiveness––in terms of decreased probability of fox occurrence and increased probability of prey occurrence––depended on the duration and intensity of the poison-baiting program. The effects of fox control on prey occurrence also varied between the two native prey species: fox control was strongly beneficial to the long-nosed potoroo <em>Potorous tridactylus</em> but had no measurable effect on southern brown bandicoot <em>Isoodon obesulus</em> occurrence. Feral cat occupancy tended to be higher in landscapes with long-term fox control, although we found no effect of fox-bait density on fine-scale cat occurrence. Time since fire (0–80 years) was associated with the occurrence of each study species, but its association with invasive predators also differed among vegetation types. Invasive predators and altered fire regimes are key, often overlapping, biodiversity threats. Our work highlights the importance of fine-scale monitoring and consideration of multiple drivers in distribution models to develop effective, tailored conservation strategies.</p>
Occurrence data
Open the record for dataset details and reuse information.
Data from "Elevation affects both the occurrence of ungulate browsing and its effect on tree seedling growth for four major tree species in European mountain forests"
<p>This repository contains the field data used in the paper from Bernard et al. on the interactive effect of elevation and ungulate browsing on tree regeneration. This dataset is associated with a github repository containing the code to run the analyses of the paper, publicly available at https://github.com/jbarrere3/BaccaraPaper. </p><p> </p><p>Data were collected for the Baccara project, by Elena Granda, Raquel Benavides, Sonia Rabasa, Georges Kunstler, and Marco Heurich. </p>
Occurrence data of small rodent species from the Yamal peninsula (1958–2022)
<p>Range shifts and changes in dominance of species in communities are among the major predicted impacts of climate change on ecosystems, supported by numerous modeling studies. While climate is changing particularly rapidly in the Arctic, little observational data is available to document predicted changes in the composition of communities, in particular from the large Russian tundra areas. Small rodents are a key component of tundra ecosystems implementing important ecological functions both as herbivores and as main prey for a whole guild of predators. Here we document changes over 60 years in occurrence of nine species of small rodents along a latitudinal gradient spanning from the forest-tundra ecotone to the high Arctic tundra on the Yamal Peninsula. All data were obtained using a single method: snap-trapping. In general, the occurrence of lemmings, specialized arctic endemics, decreased in the southern parts of the peninsula, whereas the occurrence of voles, representing boreal or wide-spread species, increased and expanded northwards. The occurrence of Siberian lemmings (<em>Lemmus sibiricus</em>) in particular declined over the whole latitudinal gradient and possibly disappeared from the southernmost zones, whereas collared lemmings (<em>Dicrostonyx torquatus</em>) declined significantly only in the forest tundra. The strongest increase was observed in the tundra zones for narrow-headed voles (<em>Lasiopodomys gregalis</em>), a wide-spread species inhabiting meadows and riparian habitats, and Middendorff's voles (<em>Alexandromys middendorffii</em>), a primarily low Arctic species inhabiting waterlogged tundra. Both species also expanded their distribution range northwards during the last two decades. The observed changes might be due to the effect of several drivers of environmental change occurring in concert: climate warming both in winter and in summer, and increased human activity notably related to intensive reindeer herding and industrial development.</p>
The global distribution of plants used by humans datasets: list of utilised species, occurrence data and model outputs at 10 arc-minutes spatial resolution
<p>Datasets and model outputs used to map the global distribution of utilised plants by humans. The folder is composed of two subfolders <em>raw_data</em> and <em>processed_data</em> containing respectively the list of utilised plant species modelled -<em>utilised_plants_species_list.csv</em>-, and their occurrence data -<em>occurrence_data.zip-</em> and predicted distribution -<em>species_proba_per_cell.rds-.</em></p> <p> </p> <ul> <li>The file <em>utilised_plants_species_list.csv</em> in the <em>raw_data</em> folder contains a<strong> </strong>list of 35687 plant species (and hybrids) used by humans and 10 plant use categories with the following 14 fields:</li> </ul> <p><strong>plant_ID:<em> </em></strong>plant identifier number ranging from between 1-35687</p> <p><strong>binomial_acc_name:</strong> binomial accepted name of the plant species</p> <p><strong>author_acc_name</strong>: name of the author(s)</p> <p><strong>is_hybrid:</strong> logical TRUE or FALSE indicating whether the species is an hybrid or not.</p> <p><strong>AnimalFood:</strong> forage and fodder for vertebrate animals only.</p> <p><strong>EnvironmentalUses:</strong> examples include intercrops and nurse crops, ornamentals, barrier hedges, shade plants, windbreaks, soil improvers, plants for revegetation and erosion control, wastewater purifiers, indicators of the presence of metals, pollution, or underground water.</p> <p><strong>Fuels:</strong> charcoal, petroleum substitutes, fuel alcohols, etc. Given the importance of energy plants for people, those were distinguished from Materials.</p> <p><strong>GeneSources:</strong> wild relatives of major crops which may possess traits associated with biotic or abiotic resistance and may be valuable for breeding programs.</p> <p><strong>HumanFood:</strong> food for humans only, including beverages and food additives.</p> <p><strong>InvertebrateFood:</strong> plants consumed by invertebrates used by humans, such as bees, silkworms, lac insects and edible grubs.</p> <p><strong>Materials:</strong> woods, fibers, cork, cane, tannins, latex, resins, gums, waxes, oils, lipids, etc. and their derived products.</p> <p><strong>Medicines:</strong> both human and veterinary.</p> <p><strong>Poisons:</strong> plants which are poisonous to both vertebrates and invertebrates, both accidentally and intentionally, e.g., for hunting and fishing, molluscicides, herbicides, insecticides.</p> <p><strong>SocialsUses:</strong> plants used for social purposes, which cannot be defined as food or medicine, for instance, masticatories, smoking materials, narcotics, hallucinogens and psychoactive drugs, and plants with ritual or religious significance.</p> <p><strong>Totals:</strong> total number of uses recorded for a species</p> <p> </p> <ul> <li>The zipfile <em>occurrence_data.zip</em> in the <em>processed_data</em> folder contains 35687 Comma Separated Values (CSV) files, one for each species, containing curated geographic occurrence records used to build species distribution models with the following 14 fields:</li> </ul> <p><strong>Species:</strong> the binomial accepted name of the species</p> <p><strong>Fullname:</strong> same as species</p> <p><strong>decimalLongitude:</strong> the geographic longitude of the occurrence records of the species in decimal degrees</p> <p><strong>decimalLatitude:</strong> the geographic latitude of the occurrence records of the species in decimal degrees</p> <p><strong>countryCode:</strong> a three-letter standard abbreviation for the country of the occurrence locality</p> <p><strong>coordinateUncertaintyinMeters</strong>: indicator for the accuracy of the coordinate location, described as the radius of a circle around the stated point location</p> <p><strong>year:</strong> year of the observation of the occurrence record of the species</p> <p><strong>individualCount:</strong> the number of individuals present at the time of the observation</p> <p><strong>gbifID:</strong> unique identifier number for the occurrence from the original database</p> <p><strong>basisOfRecords:</strong> the type of the individual record, e.g. observation, physical specimen, fossil, living ex-situ, culture collection specimen</p> <p><strong>institutionCode</strong>: the name of the institution or organization listed as the data publisher on GBIF</p> <p><strong>establishmentMeans:</strong> statement about whether an organism has been introduced to a given place and time through the direct or indirect activity of modern humans</p> <p><strong>is_cultivated_observation:</strong> whether or not an organism is cultivated</p> <p><strong>sourceID:</strong> name of the source database</p> <p> </p> <ul> <li>The file <em>species_proba_per_cell.rds</em> in the <em>processed_data</em> folder is<em> a R Data Serialization </em>(RDS) file containing a data.table object with the following 3 fields:</li> </ul> <p><strong>plant_ID:</strong><em> </em>plant identifier number ranging from between 1-35687</p> <p><strong>proba:</strong> species occurrence probability</p> <p><strong>cell:</strong><em> </em>raster grid cell number between 1-2251762</p> <p>This object can be used in combination with a raster layer to reconstruct the modelled distribution of each species or retrieve species richness and endemism.</p>
Data from: Northern pikas experience reduced occupancy due to surrounding human land use despite the occurrence of suitable microclimates
<p>Aim: Despite warming temperatures, some species are found persisting at the trailing edge of their distribution. Microclimates provided by complex topography are considered a key factor in these cases of range stationarity, buffering stress from exposure to warming and enabling persistence. However, for species with trailing-edges located in human-modified landscapes, refugial conditions provided by microclimates could be disrupted by human activities. Here, we aimed to understand the determinants of trailing-edge occupancy for a small lagomorph found in rocky patches harboring cool microclimates.</p> <p>Location: Hokkaido Island, Japan</p> <p>Taxon: Northern pika (<em>Ochotona hyperborea</em>)</p> <p>Methods: We surveyed the occupancy of northern pikas across a wide elevational gradient (350–2200 m) for two consecutive summers. Ambient air and microhabitat (i.e., rock interstices) thermal conditions were measured to assess their relationship. We then analyzed their effects on occupancy at two nested spatial scales: (1) whole-distribution, and (2) at identified trailing-edge sites where we explored the effects of microclimates and surrounding human activities (i,e., distance to nearest road and area of human land use such as plantation forests or agricultural fields).</p> <p>Results: Overall, rock interstices exhibited cooler conditions than ambient air with temperature differences of 1–2 ºC. The overall distribution of northern pikas was affected by both mean ambient temperature and microhabitat availability, with warmer (lower elevation) sites with less microhabitats corresponding to the trailing edge of its distribution. Interestingly, trailing edge occupancy patterns were best explained by the negative effect of surrounding human land despite the existence of suitable microclimates in the rocky patches.</p> <p>Main conclusions: Our findings suggest that the local refugial conditions supported by cool microclimates are likely to be disrupted by the effects of human land at the larger landscape scale. This result highlights the importance of considering the effects of human activities and landscape alteration for effective microrefugia conservation. --</p>
Data from: Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot
<p>These datasets have the variables used in the paper "Land-use homogenization reduces the occurrence and diversity of frugivorous birds in a tropical biodiversity hotspot" as well as the script to perform the analysis.</p>
Data from: To lose is to win: long-term co-occurrence of two asexual populations realized by a dormant strategy of the inferior competitor
<p><span>Asexual organisms are ubiquitous. While they are the same single species with the same ecological requirements, multiple asexual genotypes within a species are often found in a single habitat. Niche partitioning in time and space among genotypes has been proposed to explain this phenomenon. However, it is not clear whether these different genotypes co-occur in the long term. </span><span>Therefore, we examined the population dynamics of two asexual <em>Daphnia</em> cf. <em>pulex</em> genotypes (JPN1 and JPN2) over nine years in a small mountain lake. These two genotypes consistently occurred in the same seasons and layers, suggesting that niche partitioning cannot explain their long-term co-occurrence. The abundance of JPN1 was typically higher in most years. However, the abundance of dormant eggs in lake sediments was at the same level between the genotypes. </span><span>The laboratory experiment showed that JPN1 excluded JPN2. However, many JPN2 individuals produced the dormant eggs before JPN1 competitively excluded them from the experiment. Furthermore, the competitively inferior JPN2 produced the dormant eggs abundantly in the medium containing a crowding cue from JPN1. However, no such trend was observed for JPN1. </span><span>These results showed that the competitively inferior asexual genotype could maintain the population with the competitively superior genotype for a long period of time because it had the ability to detect the increase in competitors and produce the dormant eggs each year before being competitively eliminated. </span><span>Based on these results, we suggest that the variation in the genotype-specific response in dormant egg production to environmental change plays a key role in t</span><span>he long-term co-occurrence of different asexual genotypes in single habitats.</span></p>
Annex B - Dietary surveys and occurrence data in feed and food submitted to EFSA
<p>Occurrence data on PCNs in food and feed and dietary surveys per country and age group available in the EFSA Comprehensive Database, considered in the exposure assessment</p>
Occurrence data on PCNs provided to EFSA
<p><span>The file contains the raw occurrence dataset on PCNs in food and feed as extracted from EFSA DWH on 25th October 2022 and presented in the EFSA scientific opinion on the risks for animal and human health related to the presence of polychlorinated naphthalenes (PCNs) in feed and food. This dataset is compliant with EFSA SSD2 data model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the outcome of the action taken (column: outcome) to address the issue (e.g., delete record or update values in specific fields). The link to the catalogues of controlled terminologies for the updated textual description of fields values can be found under "Related works, supplemented by”.</span></p>
Galaxias maculatus occurrence data in marine and freshwater environments in rivers of southern Chile
<p>In the present study, we assessed ecological and historical factors (Gondwanan vicariance, marine dispersion) and potential dispersion (niche-tracking) that explain distribution of <em>Galaxias maculatus</em> in the Southern Hemisphere based on occurrences available in the Global Biodiversity Information Facility (GBIF; period 1980 to 2022) and ichthyological sampling in five river systems in southern Chile between March and November 2019. Ocurrence data extracted from GBIF are available at <a href="http://www.gbif.org">http://www.gbif.org</a> and additional ichthyological sampling data that were used are provided here. Data provided here are based on sampling of <em>Galaxias maculatus</em> at 12 sites in five river systems in southern Chile during March, May, August, and November 2019. Sampling sites were selected to cover a continuous river gradient, including (whenever possible) the lower, middle, and upper sections of each river system. Fish were captured using beach seines (5 m long, 1.5 m high, and 10 mm stretched mesh) in shoreline habitats of each evaluated river system.</p>
The upper crustal deformation field of Greece inferred from GPS data and its correlation with earthquake occurrence
<p>These are Tables S1 and S2 which accompany the Article "The upper crustal deformation field of Greece inferred from GPS data and its correlation with earthquake occurrence" by Konstantinos Chousianitis, Sotirios Sboras, Vasiliki Mouslopoulou, Gerasimos Chouliaras, and Dionissios T. Hristopulos.</p>
Data on the occurrence of Anisakids in fishery products from aquaculture in European countries (Jan 2010 – Sept 2023)
<p><span>This file contains data on Anisakids in fishery products from aquaculture in European countries covering studies published between January 2010 and September 2023. </span><span>The systematic review protocol used to identify and extract the information is available<strong> at <a href="../records/10270810">https://zenodo.org/records/10270810</a>.</strong></span></p>
Age Dependence of the Occurrence and Architecture of Ultra-Short-Period Planet Systems (public data release)
<p>This file includes key data and column definitions for generating figures in the manuscript. The data were collected and processed from publicly available datasets, including Kepler DR25 and the planetary systems table (https://exoplanetarchive.ipac.caltech.edu/), LAMOST DR9 (https://www.lamost.org/), Gaia DR3 (https://gea.esac.esa.int/archive/), and The California-Kepler Survey (https://california-planet-search.github.io/cks-website/). Additional data required for the manuscript can also be obtained from these publicly available datasets.</p>
Tree census data associated to 'Large-scale informative priors to better predict the local occurrence rate of a rare tree-related microhabitat'
<p>This repository contains two excel spreadsheets providing data about the trees studied in Cottais et al. study (doi : 10.1101/2024.11.28.625900):</p> <ul> <li>df_TreM.xlsx has 1462 lines (headers not included); each line corresponds to one oak tree sampled in 2021 survey of Cottais et al. study. Fields are: <ul> <li>Plot_Id : the id of the sampling plot where the tree is located</li> <li>Tree_Id : a unique id of the tree used in the BloBiForM project</li> <li>Species_Latin_Name : the latin name of the tree species ('Quercus_sp' for all trees given than only oaks are reported here)</li> <li>DBH_cm : the diameter at breast height of the tree in cm</li> <li>TreM : whether the tree harbours a basal rot hole (1) or not (0)</li> <li>Life_Stage : whether the tree is a living tree or a snag</li> <li>Last_Logging_Year : the year of the last logging event in the stand where the tree is located</li> <li>conv : whether the last logging event occured less that 120 years before 2024 (conv=0; the stand is now classic high forest) or is more ancient (conv=1, the stand is being converted to high forest through sprout thinning)</li> </ul> </li> <li>DMH_2022.xlsx has 1190 lines (headers not included); each line corresponds to one tree sampled in 2022 survey of Cottais et al. study. Fields are: <ul> <li>Plot_Id: the id of the sampling plot where the tree is located</li> <li>Species_Latin_Name: the latin name of the tree species, obtained as a translation from french using the dictionnary in page 2; oaks are not the only species reported, but only oaks are used in Cottais et al. study;</li> <li>Species_French_Name : the french name of the tree species;</li> <li>DBH_cm: the diameter at breast height of the tree in cm</li> <li>TreM: whether the tree harbours a basal rot hole (1) or not (0)</li> <li>Tree_Id: when the tree belongs to the cohort of the BloBiForM project, the tree id is reported; left empty otherwise</li> <li>Nb_brin: number of stems on the tree stump;</li> <li>Commentaire: any comments during fieldwork</li> </ul> </li> </ul>
Data on the occurrence on anisakids and other parasites in fishery products from wild and farmed fish in all countries (Jan 2010 – Sept 2023)
<p><span>This file contains data on anisakids and other parasites in fishery products from wild and farmed fish in all countries, covering studies published between January 2010 and September 2023. The systematic review protocol used to identify and extract the information is available at <a href="https://zenodo.org/records/10270810"> https://zenodo.org/records/10270810</a>. For data on anisakids for the period 2010-2020, this file is complementary to the zenodo file https://zenodo.org/records/14047972, and includes publications that were not selected in published meta-analyses. </span></p>
Raw Data for the article: Functional Gastrointestinal Disorders in Patients With Epilepsy: Reciprocal Influence and Impact on Seizure Occurrence
<p><strong>Introduction:</strong> The complex relationship between the microbiota-gut-brain axis (MGBA) and epilepsy has been increasingly investigated in preclinical studies. Conversely, evidence from clinical studies is still scarce. In recent years, the pivotal role of MGBA dysregulation in the pathophysiology of functional gastrointestinal disorders (FGID) has been recognized. With this background, we aimed to investigate the prevalence of FGID in patients with epilepsy (PWE) and the possible impact of bowel movement abnormalities on seizure recurrence. <strong>Methods:</strong> A total of 120 PWE and 113 age-, sex-, and BMI-matched healthy subjects (HS) were consecutively enrolled. A questionnaire to evaluate the presence of FGID (according to Rome III diagnostic criteria) was administrated to all participants. In a subgroup of drug-resistant patients, we administered an <em>ad-hoc</em> questionnaire combining Bristol stool charts and seizure diaries to evaluate seizure trends and bowel movement changes. <strong>Results:</strong> A higher prevalence of FGID in PWE (62.5%) than in HS (39.8%) was found (<em>p</em> < 0.001). The most frequently observed disorder was constipation, which was significantly higher in PWE than in HS (43.3 vs. 21.2%, <em>p</em> < 0.001), and was not associated with anti-seizure medication intake according to multivariable analysis. In drug-resistant patients, most seizures occurred during periods of altered bowel movements, especially constipation. A significant weak negative correlation between the number of days with seizures and the number of days with normal bowel movements was observed (<em>p</em> = 0.04). According to multivariable logistic regression analysis, FGID was significantly associated with temporal lobe epilepsy as compared with other lobar localization (<em>p</em> = 0.03). <strong>Conclusions:</strong> Our clinical findings shed new light on the complex relationship between epilepsy and the MGBA, suggesting a bidirectional link between bowel movement abnormalities and seizure occurrence. However, larger studies are required to better address this important topic.</p>
Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest
<p>1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition).</p> <p>2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence.</p> <p>3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.</p> <p>4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.</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.