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3,015 results for “occurrences”
Intraguild interactions and abiotic conditions mediate occupancy of mammalian carnivores: co-occurrence of coyotes-fishers-martens
<p>The widespread eradication of large carnivores and subsequent expansion of top mesopredators have the potential to impact species and community interactions with ecosystem-wide implications. An example of these trophic dynamics is the widespread establishment of coyotes following the extirpation of wolves and mountain lions in eastern North America. Here, we examined the occupancy of three carnivores in northern New York considering both environmental/habitat factors and interspecific interactions. We estimated the co-occurrence of coyotes, fishers, and martens from a landscape-scale winter camera trap survey repeatedly annually for three years. Martens occurred independently of both coyotes and fishers, while fishers and coyotes displayed positive intraguild interactions that were constant across the landscape. Both marten and fisher first-order occupancy was driven by a combination of biotic and abiotic factors, with both species displaying positive associations with forest cover but antithetical responses to average snow depth. The integral and antithetical role of snow depth in driving the occurrence of martens (positive) and fishers (negative) in the landscape indicates that future climatic warming could reduce the availability of current spatial refuges for martens created by severe winter conditions. Climate-driven alterations to established competitive interactions and co-existence patterns between marten and fishers have critical implications for the species' survival and conservation. We provide correlational evidence consistent with the potential for positive top-down effects of dominant mesocarnivores on subordinate species, with fisher occupancy increasing conditional on the presence of coyotes across the landscape. These findings align with the hypothesis that under certain conditions, coyotes may facilitate certain subordinate carnivores. The evidence produced here is consistent with hypotheses on the dynamic nature of trophic niches. We demonstrate the need to consider the interplay between climate, habitat, and interspecific interactions to understand wildlife occupancy patterns and inform wildlife management in a rapidly changing world.</p>
Fig. 1 in Distribution and Occurrence of Vairimorpha plodiae (Opisthokonta: Microspora) in the Indian Meal Moth, Plodia interpunctella (Lepidoptera: Pyralidae) Populations: An Extensive Field Study
Fig. 1. The microsporidian pathogen, Vairimorpha plodiae infections in Plodia interpunctella populations in Turkey. Infected populations (note that the pathogen naturally disperses in all populations). (AYD: Aydın, BOL: Bolu, DNZ: Denizli, GZP: Gaziantep, ISP: Isparta, İST: İstanbul, İZM: İzmir, MLT: Malatya, ORD: Ordu, SAM: Samsun, ST: Siirt, TRB: Trabzon)
Resource Description Framework (RDF) Modeling of Named Entity Co-occurrences in Biomedical Literature and Its Integration with PubChemRDF
<p>This Zenodo record contains the co-occurrence RDF data generated in the work described in the paper “<strong>A resource description framework (RDF) model of named entity co-occurrences in biomedical literature and its integration with PubChemRDF</strong>” by Li et al., published in the Journal of Cheminformatics (<a href="https://doi.org/10.1186/s13321-025-01017-0" target="_blank" rel="noopener">https://doi.org/10.1186/s13321-025-01017-0</a>). It also contains the SPARQL query examples, the RDF schema in SHACL and ShEx, and the validation scripts.</p> <p>All content in this Zenodo record is for archival purposes. The latest version of the co-occurrence RDF data and other PubChemRDF data can be accessed via the PubChem FTP site (<a href="https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/" target="_blank" rel="noopener">https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/</a>). The up-to-date RDF schema in various formats is available on the PubChemRDF Schema page (<a href="https://pubchem.ncbi.nlm.nih.gov/docs/rdf-schema" target="_blank" rel="noopener">https://pubchem.ncbi.nlm.nih.gov/docs/rdf-schema</a>). A set of SPARQL query examples can be found on the PubChemRDF use case pages (<a href="https://pubchem.ncbi.nlm.nih.gov/docs/rdf-use-cases" target="_blank" rel="noopener">https://pubchem.ncbi.nlm.nih.gov/docs/rdf-use-cases</a>).</p>
Lesser Yellowlegs location data describing the occurrence of birds within harvest zones in the Caribbean and South America
<p>Shorebirds have experienced a precipitous reduction in abundance over the past four decades. While some threats to shorebirds are widespread (e.g. habitat alteration), others are regional and may affect specific populations. Lesser Yellowlegs (<i>Tringa flavipes</i>) are long-distance migrants that breed across the North American boreal biome and have declined in abundance by 60-80% since the 1970s. The documented harvest of Lesser Yellowlegs in the Caribbean and northeastern South America during southward migration is a possible limiting factor for the species, but it is unknown to what extent birds from different breeding origins may be affected. To address the question of differential occurrence in harvest zones during southward migration, we used PinPoint GPS Argos transmitters to track the southward migrations of 85 adult Lesser Yellowlegs from across the species' breeding range and 80° of longitude from Anchorage, Alaska, USA to the Mingan Archipelago, Quebec, Canada. We classified migratory locations as inside or outside three zones with high levels of harvest (Caribbean, coastal Guianas, and coastal Brazil) and then fit generalized additive mixed models to estimate the probability of occurrence of Lesser Yellowlegs in harvest zones according to their breeding origin. Individuals from the Eastern Canada population had a higher probability of occurrence within one or more harvest zones and remained in those zones longer than individuals breeding in Alaska and western Canada. Linear regressions also suggested that longitude of the breeding origin is an important predictor of occurrence in harvest zones during southward migration. Lastly, our findings, combined with other sources of evidence, suggest that current estimated harvest rates may exceed sustainable limits for Lesser Yellowlegs, which warrants further investigation.</p>
Fig. 1 in Occurrence and Molecular Barcode of the Freshwater Heteronemertean Apatronemertes albimaculosa (Nemertea: Pilidiophora) from Japan
Fig. 1. Apatronemertes albimaculosa Wilfert and Gibson, 1974, ICHUM 5113 (A, B), 5112 (C), photographs taken in life. A, Entire body; B, magnification of body surface in intestinal region, showing minute oval inclusions in epidermis, these appearing white with lateral strobe illumination; C, anterior region.
Fig. 4 in Ephemeral Occurrence of the Echiuran Listriolobus brevirostris (Annelida: Echiura) in Osaka Bay between 1995 and 2002; a New Record for Japan, Probably Resulting from Human-mediated Introduction
Fig. 4. Relationship between trunk length and proboscis length in 52 fixed specimens of Listriolobus brevirostris, collected from Osaka Bay in 1999 (NSMT-Ec 164 to 183).
Fig. 3 in Ephemeral Occurrence of the Echiuran Listriolobus brevirostris (Annelida: Echiura) in Osaka Bay between 1995 and 2002; a New Record for Japan, Probably Resulting from Human-mediated Introduction
Fig. 3. Internal morphology (dorsal view) of Listriolobus brevirostris from Osaka Bay, collected off Kobe on 26 November 2001 (NSMT-Ec 186). A, anterior end of trunk; B, posterior end of trunk (ventral vessel undetectable due to deterioration). Abbreviations: al, alimentary canal; av, anal vesicle; dv, dorsal vessel; gd, gonoduct; gl, gonostomal lip; im, interbasal muscle; nv, neurointestinal vessel; rc, rectal caecum; re, rectum; rv, ring vessel; tb, terminal bulb; vn, ventral nerve cord: vs, ventral seta; vv, ventral vessel. Scale bars: 1 mm.
Fig. 5 in Ephemeral Occurrence of the Echiuran Listriolobus brevirostris (Annelida: Echiura) in Osaka Bay between 1995 and 2002; a New Record for Japan, Probably Resulting from Human-mediated Introduction
Fig. 5. Seasonal changes in trunk length of Listriolobus brevirostris from Osaka Bay in 1999. Solid bars indicate mature specimen(s), dotted lines, measurements from live specimens, and double-headed arrow of dotted line, the length range in live specimens (see text).
FIG. 1 in New occurrences of crabs (Decapoda, Brachyura, Eubrachyura) in the Pliocene of Florida (United States)
FIG. 1. — Location map of the two fossiliferous localities of the Pliocene Tamiami Formation in Sarasota County, Florida (United States). Locality A: SMR Aggregates quarry (27°20'05"N, 82°19'58"W). Locality B: Old APAC Shell quarry (27°14'18"N, 82°27'11"W). Maps modified after different sources and ViaMichelin.
FIG. 2 in New occurrences of crabs (Decapoda, Brachyura, Eubrachyura) in the Pliocene of Florida (United States)
FIG. 2. — Persephona cf. P. subovata (Rathbun, 1893), USNM PAL 720104 from the Pinecrest Member of Tamiami Formation (middle Piacenzian, Pliocene) of locality A in Sarasota County, Florida (United States): A, dorsal view; B, frontal view; C, left lateral view; D, posterior view. Scale bar: 10 mm. Photographs by À. Ossó.
FIG. 3 in New occurrences of crabs (Decapoda, Brachyura, Eubrachyura) in the Pliocene of Florida (United States)
FIG. 3. — Paractaea cf. P. nodosa (Stimpson, 1860), USNM PAL 720105 from the Pinecrest Member of Tamiami Formation (middle Piacenzian, Pliocene) of locality B in Sarasota County, Florida (United States): A, dorsal view; B, frontal view; C, posterior view. Scale bar: 10 mm. Photographs by À. Ossó.
Figure 1 in First report on the occurrence of Typhlodromus (Anthoseius) transvaalensis (Nesbitt) (Acari: Phytoseiidae) in India with a redescription of the species
Figure 1 Typhlodromus (Anthoseius) transvaalensis(adult female): sparsely plumose and knobbed setae on the dorsal shield, 630×, differential interference contrast microscopy.
Figure 2 in First report on the occurrence of Typhlodromus (Anthoseius) transvaalensis (Nesbitt) (Acari: Phytoseiidae) in India with a redescription of the species
Figure 2 Typhlodromus (Anthoseius) transvaalensis(adult female): chelicera, 630×, differential interference contrast microscopy.
Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology
<p>Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of "total-evidence" analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct the past number of lineages.</p> <p>Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.</p> <p>We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the COVID-19 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.</p>
Sentiment analysis of tech media articles using VADER package and co-occurrence analysis (01.2016-04.2021)
<p>Sentiment analysis of tech media articles using VADER package and co-occurrence analysis</p> <p>Sources with weights:</p> <ul> <li>Euractiv 5%</li> <li>The Conversation 5%</li> <li>Politico Europe 5 %</li> <li>IEEE Spectrum 5 %</li> <li>Techforge 5%</li> <li>Fastcompany 5%</li> <li>The Guardian (Tech) 12%</li> <li>Arstechnica 5%</li> <li>Reuters 5%</li> <li>Gizmodo 9%</li> <li>ZDNet 9%</li> <li>The Register 12%</li> <li>The Verge 9%</li> <li>TechCrunch 9%</li> </ul> <p>Methodology</p> <p>The sentiment analysis has been prepared using VADER*, an open-source lexicon and rule-based sentiment analysis tool. VADER is specifically designed for social media analysis, but can be also applied for other text sources. The sentiment lexicon was compiled using various sources (other sentiment data sets, Twitter etc.) and was validated by human input. The advantage of VADER is that the rule-based engine includes word-order sensitive relations and degree modifiers.</p> <p>As VADER is more robust in the case of shorter social media texts, the analysed articles have been divided into paragraphs. The analysis have been carried out for the social issues presented in the co-occurrence exercise.</p> <p>The process included the following main steps:</p> <ul> <li>The 100 most frequently co-occurring terms are identified for every social issue (using the co-occurrence methodology)</li> <li>The articles containing the given social issue and co-occurring term are identified</li> <li>The identified articles are divided into paragraphs</li> <li>Social issue and co-occurring words are removed from the paragraph</li> <li>The VADER sentiment analysis is carried out for every identified and modified paragraph</li> <li>The average for the given word pair is calculated for the final result</li> </ul> <p>Therefore, the procedure has been repeated for 100 words for all identified social issues.</p> <p>The sentiment analysis resulted in a compound score for every paragraph. The score is calculated from the sum of the valence scores of each word in the paragraph, and normalised between the values -1 (most extreme negative) and +1 (most extreme positive). Finally, the average is calculated from the paragraph results. Removal of terms is meant to exclude sentiment of the co-occurring word itself, because the word may be misleading, e.g. when some technologies or companies attempt to solve a negative issue. The neighbourhood's scores would be positive, but the negative term would bring the paragraph's score down.</p> <p> </p> <p>*Hutto, C.J. & Gilbert, E.E. (2014). VADER: A Parsimonious Rule-based Model for Sentiment Analysis of Social Media Text. Eighth International Conference on Weblogs and Social Media (ICWSM-14). Ann Arbor, MI, June 2014.</p>
Figures 1–6 in Occurrence of an exotic whitefly, Siphoninus phillyreae (Haliday) (Hemiptera: Aleyrodidae) in South Korea and its potential pathway analysis
Figures 1–6. Ash whitefly (Siphoninus phillyreae (Haliday)) and regional map of South Korea. 1–2) Several life stages of the ash whitefly on the underside of leaves of a pomegranate tree (GN: Jinju, 3-viii-2021 (S.J. Suh)). 3) Puparium (slide-mounted). 4) Siphons on marginal and submarginal areas of dorsum. 5) Vasiform orifice. 6) Distribution map of ash whitefly in South Korea.
Pesticide metabolites database and occurrence data in wine
<p>Pesticide metabolites database is the overview of potential pesticide metabolites originated from selected parent compounds. These metabolites can be found in various source including JMPR (FAO/WHO) documents, EU pesticide database, EFSA etc. Based on their elemental formula respective ions (protonated / deprotonated molecules, their adducts) originated in ESI source can be derived for ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS).</p> <p>Occurrence data were obtained from determination of pesticide residues and their metabolites in samples of grapevine and wine, using UHPLC-HRMS, with the objective of supporting the possibility of the verification of the method of farming. It documents the identification of pesticide metabolites commonly used in conventional farming and provides a characterization of pesticide degradation during grapevine growth, maturation and during the wine-making process.</p> <p>The dataset is useful for anyone working on authentication of organic fruits and vegetables.</p>
State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data
<p>These files can be categorized into three groups: (1) raw datasets obtained from public databases (i.e., GBIF, BOLD, and GenBank), (2) manually edited files needed for parsing and analysis, and (3) supplementary files for spatial analysis. All are used in the examination of gaps and biases present in Philippine biodiversity data, which can direct research on the taxa and spatial regions that need more sampling.</p>
APPENDIX 2 in Cholevinae (Coleoptera: Leiodidae) of the Sierra de Guadarrama National Park, Spain: occurrence in the MSS of a siliceous landscape
APPENDIX 2. — Distribution maps of all the Cholevinae species collected in the MSS of the Sierra de Guadarrama National Park, except for Choleva (Cholevopsis) punctata Brisout, 1866.
FIG. 6 in Cholevinae (Coleoptera: Leiodidae) of the Sierra de Guadarrama National Park, Spain: occurrence in the MSS of a siliceous landscape
FIG. 6. — Relation between the pronotum width (PWmid) and the pronotum length (PL) of both sexes of Choleva (Cholevopsis) punctata Brisout, 1866.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.