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608 results for “Species Recognition”
Fig. 3 in A Revision Of The Portunus Pelagicus (Linnaeus, 1758) Species Complex (Crustacea: Brachyura: Portunidae), With The Recognition Of Four Species
Fig. 3. Minimum Evolution bootstrap tree incorporating all unique COI haplotypes. Haplotypes of specimens obtained from Portunus pelagicus, P. segnis, P. reticulatus and P. armatus with P. trituberculatus, P. sanguinolentus and Charydis lucifera as outgroups. '*' Indicates the dominant haplotype found in P. pelagicus shared with eight P. reticulatus individuals. '**' Denotes two individuals collected from Japan that may constitute a possible cryptic species.
Fig. 2 in A Revision Of The Portunus Pelagicus (Linnaeus, 1758) Species Complex (Crustacea: Brachyura: Portunidae), With The Recognition Of Four Species
Fig. 2. Scatter plot of canonical scores from forward stepwise discriminant function analysis. Group 1, Portunus armatus; 2, P. reticulatus; 3, P. segnis; 4, P. pelagicus.
Fig. 14 in A Revision Of The Portunus Pelagicus (Linnaeus, 1758) Species Complex (Crustacea: Brachyura: Portunidae), With The Recognition Of Four Species
Fig. 14. Portunus segnis (Forskål, 1775) (specimen not preserved), Doha fish market, Qatar, (photograph: H. Q. Ng).
Rapid resource depletion on coral reefs disrupts competitor recognition processes among butterflyfish species
<p>Avoiding costly fights can help conserve energy needed to survive rapid environmental change. Competitor recognition processes help resolve contests without escalating to attack, yet we have limited understanding of how they are affected by resource depletion and potential effects on species coexistence. Using a mass coral mortality event as a natural experiment and 3,770 field observations of butterflyfish encounters, we test how rapid resource depletion could disrupt recognition processes in butterflyfishes. Following resource loss, heterospecifics approached each other more closely before initiating aggression, fewer contests were resolved by signalling, and the energy invested in attacks was greater. In contrast, behaviour towards conspecifics did not change. As predicted by theory, conspecifics approached one another more closely and were more consistent in attack intensity yet, contrary to expectations, resolution of contests via signalling was more common among heterospecifics. Phylogenetic relatedness or body size did not predict these outcomes. Our results suggest that competitor recognition processes for heterospecifics became less accurate after mass coral mortality, which we hypothesise is due to altered resource overlaps following dietary shifts. Our work implies that competitor recognition is common among heterospecifics, and disruption of this system could lead to suboptimal decision-making, exacerbating sublethal impacts of food scarcity.</p>
FIG. 7 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 7. — Median-joining networks based on trnSGG and rps4-trnS sequences: A, the Ptisana attenuata clade; B, the P. salicina/P. soluta comb. nov., stat. nov./P. smithii clade. The size of each circle is proportional to the haplotype frequency. Undetected intermediate haplotypes on nodes are shown as black circles and hatch marks represent mutational steps separating haplotypes.
FIG. 6 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 6. — Phylogram from the Bayesian phylogenetic analysis of the chloroplast DNA sequence data for Ptisana Murdock. Support values for branches are given in the order of Bayesian inference posterior probability; maximum parsimony bootstrap support; and maximum likelihood bootstrap support. Only values>0.80 PP and 60% BS are shown.
FIG. 4 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 4. — Distribution map for the New Caledonian endemic species of Ptisana attenuata (Labill.) Murdock (), P. rolandi-principis (Rosenst.) Christenh. (Δ), and P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov. (, with unvouchered field observations indicated by a broken outline). Shaded areas are ultramafic substrates. The collecting sites of the sequenced P. attenuata samples are indicated.
FIG. 5 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 5. — The holotype of Ptisana soluta (Compton) Murdock & Perrie, comb. nov., stat. nov. (Compton 1674, Ignambi, 1914, BM[BM000787128]) showing how the lamina transitions from 3-pinnate proximally to 2-pinnate distally. CC BY The Trustees of the Natural History Museum, London.
FIG. 3 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 3. — Ptisana soluta (Compton) Murdock & Perrie, comb. nov., stat. nov., field photos: A, frond with lamina 3-pinnate proximally and 2-pinnate distally. The frond at top-right is P. attenuata (Labill.) Murdock; B, stipes are greenish-brown at a distance; C, abaxial surface of costae and fertile lamina, showing transition from 3-pinnate to 2-pinnate; D, stipe greenish-brown and smooth; E, stipules around stipe bases. Photos: A-D, Leon Perrie from near Nouméa; E, Rémy Amice, from near Nouméa.
FIG. 1 in A synopsis of Ptisana Murdock ferns (Marattiaceae) in New Caledonia based on sequence data and morphology with the recognition of a new vulnerable species, P. soluta (Compton) Murdock & Perrie, comb. nov., stat. nov.
FIG. 1. — Ptisana attenuata (Labill.) Murdock, field photos: A, 3-pinnate frond; B, stipes are dark at a distance; C, abaxial surface of costae and lamina, with synangia; D, stipe dark and wrinkled; E, divided stipules around stipe bases. Photos: Leon Perrie, from near Nouméa.
LivingNER corpus: Named entity recognition, normalization & classification of species, pathogens and food
<p><strong>LivingNER Gold Standard corpus (includes training, validation, test and background sets + MULTILINGUAL RESOURCES</strong>)</p><p> </p><p><strong>Please cite if you use this dataset:</strong></p><p>A. Miranda-Escalada, E. Farré-Maduell, S. Lima-López, D. Estrada, L. Gascó, M. Krallinger, Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources, <i>Procesamiento del Lenguaje Natural</i> (2022)</p><p>@article{amiranda2022nlp, title={Mention detection, normalization \& classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources}, author={Miranda-Escalada, Antonio and Farr{\'e}-Maduell, Eul{`a}lia and Lima-L{\'o}pez, Salvador and Estrada, Darryl and Gasc{\'o}, Luis and Krallinger, Martin}, journal = {Procesamiento del Lenguaje Natural}, year={2022} }</p><p> </p><p><i><strong>1. Introduction</strong></i></p><p>The LivingNER Gold Standard corpus is a collection of<strong> 2000 clinical case reports</strong> covering a <strong>broad range of medical specialities</strong>, i.e. infectious diseases (including Covid-19 cases), cardiology, neurology, oncology, dentistry, pediatrics, endocrinology, primary care, allergology, radiology, psychiatry, ophthalmology, urology, internal medicine, emergency and intensive care medicine, tropical medicine, and dermatology <strong>annotated with species</strong> [SPECIES] (including <strong>living organisms</strong> and <strong>microorganisms</strong>) and <strong>infectious diseases</strong> [ENFERMEDAD] mentions. Species mentions include many <strong>pathogens</strong> and infectious agents, but also <strong>food</strong>, allergens, <strong>pets</strong> or other species, taxonomic groups and organisms of clinical relevance. </p><p>The LivingNER corpus has also annotations of mentions of <strong>humans</strong> (tag HUMAN), including the patients itself, <strong>family members</strong>, healhcare professionals or other persons mentioned in the case reports. Thus it can be useful to extract family history information of patients or information about the social and healthcare personal environment and interactions.</p><p>All mentions have been exhaustively manually mapped by experts to their corresponding <a href="https://www.ncbi.nlm.nih.gov/taxonomy"><strong>NCBI Taxonomy</strong></a> identifiers. </p><p>It was used for the <a href="https://temu.bsc.es/livingner/">LivingNER</a> Shared Task on pathogens and living beings detection and normalization in Spanish medical documents, which was celebrated as part of IberLEF 2022.</p><p> </p><p><i><strong>2. Training, validation, test and background sets</strong></i></p><p>The training set is composed of 1000 clinical case reports. The validation set includes 500 clinical case reports with the same characteristics and the test set includes 485. The background set is a collection of around 13k unannotated case reports that were originally added to prevent manual annotations in the test set during the competition and to create a Silver Standard.</p><p><i><strong>2.1 Annotations format</strong></i></p><p>Annotations and text files are distributed separately. The texts are in plain text (.txt in UTF-8) format, while the annotations are are distributed in a tab-separated file (.tsv) file with one row per annotation:</p><p>- For <strong>subtask 1 (LivingNER-Species NER track)</strong>, the .tsv file has the following columns:</p><ul><li>filename: document name</li><li>mark: identifier mention mark</li><li>label: mention type (SPECIES or HUMAN)</li><li>off0: starting position of the mention in the document</li><li>off1: ending position of the mention in the document</li><li>span: textual span</li></ul><p> - For <strong>subtask 2 (LivingNER-Species Norm track)</strong>, the .tsv file has the same columns as the previous one, plus:</p><ul><li>isH: whether the span is narrower than the NCBITax assigned code</li><li>isN: whether the mention corresponds to a nosocomial infection</li><li>iscomplex: whether the span has assigned a combination of NCBITax codes</li><li>NCBITax: mention code in the NCBI Taxonomy</li></ul><p>- For <strong>subtask 3 (LivingNER-Clinical IMPACT track)</strong>, the .tsv file has the following columns:</p><ul><li>filename</li><li>isPet (Yes/No)</li><li>PetIDs (NCBITaxonomy codes of pet & farm animals present in document)</li><li>isAnimalInjury (Yes/No)</li><li>AnimalInjuryIDs (NCBITaxonomy codes of animals causing injuries present in document)</li><li>IsFood (Yes/No)</li><li>FoodIDs (NCBITaxonomy codes of food mentions present in document)</li><li>isNosocomial (Yes/No)</li><li>NosocomialIDs (NCBITaxonomy codes of nosocomial species mentions present in document)</li></ul><p><i><strong>2.2 Important notes about subtask 3 (LivingNER-Clinical IMPACT track):</strong></i></p><ul><li><strong>Less clinical case reports</strong>. Subtask 3 (LivingNER-Clinical IMPACT track) contains half of the clinical case reports (500 in the training partition, 250 in the validation partition). The list of valid clinical case reports for task 3 is included in the data (train_files_task3.txt and validation_files_task3.txt)</li><li><strong>Enriched dataset.</strong> The GS format is the one described above (a TSV with one line per clinical case report). However, we believe participants may find useful and <strong>enriched dataset. </strong>Then, we provide an additional dataset, with the mentions of the NER track classified in the 4 Clinical impact categories (food, pet&farm animals, animals causing injuries and nosocomial). It is a TSV file with one row per annotation, and with the following columns: filename, mark, label, off0, off1, span, isPet, isAnimalInjury, isFood, isNosocomial, isH, iscomplex, code</li></ul><p> </p><p><i><strong>3. Multilingual resources</strong></i></p><p>We have generated the annotated training and validation sets in <strong>7 languages</strong>:</p><ul><li><i><strong>English</strong></i></li><li><i><strong>Portuguese</strong></i></li><li><i><strong>Catalan</strong></i></li><li><i><strong>Galician</strong></i></li><li><i><strong>Italian</strong></i></li><li><i><strong>French</strong></i></li><li><i><strong>Romanian</strong></i></li></ul><p> </p><p>The process was:</p><ol><li>The text files were translated with a neural machine translation system.</li><li>The annotations were translated with the same neural machine translation system.</li><li>The translated annotations were transferred to the translated text files using an annotation transfer technology.</li></ol><p>The text files are stored in the multilingual_resources/<strong>training-text-files</strong> and multilingual_resources/<strong>validation-text-files </strong>subfolders.</p><p>The annotated TSV files are stored in the multilingual_resources/<strong>annotation_transfer </strong>subfolder.</p><p>For the sake of comparison, we incorporate as well the annotations that resulted from the <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-85">LINNAEUS tool</a> in the multilingual_resources/<strong>linneaus</strong> subfolder.</p><p>If you want to visualize the multilingual resources, check out this Brat server: <a href="https://temu.bsc.es/mLivingNER/#/translations/">https://temu.bsc.es/mLivingNER/#/translations/</a></p><p>For instance, you can see the parallel annotations in <a href="https://temu.bsc.es/mLivingNER/diff.xhtml#/translations/en/annotation_transfer/train/casos_clinicos_cardiologia34?diff=/translations/fr/annotation_transfer/train/">English vs in French</a>, or <a href="https://temu.bsc.es/mLivingNER/diff.xhtml#/translations/cat/annotation_transfer/train/casos_clinicos_cardiologia35?diff=/gold-standard/train/">in Spanish (the gold standard) vs in Catalan.</a></p><p> </p><p><strong>Resources</strong></p><ul><li><a href="https://temu.bsc.es/livingner/"><strong>Task Web</strong></a></li><li><strong>Citation: </strong>A. Miranda-Escalada, E. Farré-Maduell, S. Lima-López, D. Estrada, L. Gascó, M. Krallinger, Mention detection, normalization & classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources, <i>Procesamiento del Lenguaje Natural</i> (2022)</li><li><a href="https://doi.org/10.5281/zenodo.6385162"><strong>Annotation guidelines</strong></a></li><li><a href="https://github.com/tonifuc3m/livingner-evaluation-library"><strong>Evaluation library</strong></a></li><li><a href="https://doi.org/10.5281/zenodo.6390506">LivingNER terminology</a></li><li><a href="http://journal.sepln.org/sepln/ojs/ojs/index.php/pln/article/view/6444"><strong>Overview paper</strong></a></li><li><a href="https://ceur-ws.org/Vol-3202/"><strong>Proceedings participant papers</strong></a></li><li><a href="https://www.youtube.com/watch?v=8VcZw8ywyJY&list=PL5uSCzf1azhA_gMLC3DBZe6NvmMJiggTg"><strong>Youtube videos</strong></a></li><li><a href="https://www.slideshare.net/MartinKrallinger/mention-detection-normalization-classification-of-species-pathogens-humans-and-food-in-clinical-documents-overview-of-the-livingner-shared-task-and-resources-talk-at-iberlef-sepln-2022"><strong>LivingNER overview talk sides at IberLEF/SEPLN</strong></a></li></ul><p> </p><p><strong>License</strong></p><p>This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p><p><strong>Contact</strong></p><p>If you have any questions or suggestions, please contact us at:</p><p><br>- Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>)</p><p><strong>Additional resources and corpora</strong></p><p>If you are interested in SympTEMIST, you might want to check out these corpora and resources:</p><ul><li><a href="https://zenodo.org/records/7614764">DisTEMIST</a> (Corpus of disease mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/8413866">SympTEMIST</a> (Corpus of symptoms, sign and findings mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/8224056">MedProcNER </a>(Corpus of clinical procedure mentions and normalization to SNOMED CT, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/4270158">PharmaCoNER</a> (Corpus of medications, drugs, chemical substances, genes, proteins and vaccine mentions and normalization, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/7116201">MEDDOPROF</a> (Corpus of mentions of professions, occupations and working status and normalization, different document collection)</li><li><a href="https://zenodo.org/records/8403498">MEDDOPLACE</a> (Corpus of mentions of place-related entity mentions, including departments, nationalities or patient movements etc.. and normalization, different document collection)</li><li><a href="https://zenodo.org/records/4279323">MEDDOCAN</a> (Corpus of mentions of Personal Health Identifiers (PHI), differentdocument collection)</li><li><a href="https://zenodo.org/records/3978041">CANTEMIST</a> (Corpus of cancer tumor morphology mentions and normalization, different document collection)</li><li><a href="https://zenodo.org/records/3837305">CodiESp</a> (Corpus of clinical case reportes with assigned clinical codes from ICD10, Spanish version, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560344">SPACCC-POS</a> (Corpus of clinical case reports in Spanish annotated with POS-tags, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560338">SPACCC-TOKEN</a> (Corpus of clinical case reports in Spanish annotated with token-tags (word mention boundaries), different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/2560338">SPACCC-SPLIT</a> (Corpus of clinical case reports in Spanish annotated with sentence boundary-tags, different document collection, some overlapping documents)</li><li><a href="https://zenodo.org/records/5602914">MESINESP-2</a> (Corpus of manually indexed records with DeCS /MeSH terms comprising scientific literature abstracts, different document collection, some overlapping documents)</li></ul>
Fig. 20 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 20. Libitioides sayi (Simon, 1879), ♂ (MNRJ 58916) from Lake Kirby, Texas. a. Dorsal view of body. b. Left femur and trochanter IV, dorsal view. c. Left metatarsus and tarsomeres of leg I, lateral view. Scale bars = 1 mm.
Fig. 5 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 5. Southeastern USA, with the Köppen-Geiger climate regions superimposed, showing the distribution of the American Cosmetidae C.L. Koch, 1839.
Fig. 4 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 4. Libitioides sayi (Simon, 1879), morph C, syntype, ♂ (ZMUC). a. Habitus, dorsal view. b. Same, sinistrolateral view. c. Same, ventral view. d. Same, detail of carapace, dorsal view. e. Labels.
Fig. 2 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 2. Libitioides spp. from USA, in vivo. a. L. ornata (Say, 1821) (morph A), ♂ and ♀, Florida, Orange, Orlando Wetlands Park (©Mary Keim). b. L. sayi (Simon, 1879) (morph B, "clean"), ♂, Texas, Sherman Co. (©Kate Farkas). c. L. sayi (morph C, "depressa"), ♂, Texas, Kleberg Co., Padre Island National Seashore (©Meghan Cassidy). d. L. albolineata (Sørensen, 1884) (typical morph D), ♂, Georgia, Fulton Co. (©E. Christina Butler). Photos are somewhat cropped. All images used here under written permission.
Fig. 21 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 21. Libitioides sayi (Simon, 1879), (MNRJ 58916) from Lake Kirby, Texas. Habitus. a. Male, dorsal view. b. Sinistrolateral view. c. Frontal view. d. Ventral view. e. Panoramic, dorsal view. f. Female, dorsal view (MNRJ 58916). Scale bars = 1 mm.
Fig. 3 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 3. Libitioides modesta (Banks, 1909), holotype ♂ of Platycynorta secunda Roewer 1947 (SMF RII 130) from Cuba. a. Habitus, dorsal view. b. Same, ventral view. c. Original Roewer's label. d. Same as (a), detail of dorsal scutum and basal part of legs. e. Same, detail of basichelicerite, trochanters I–III, protoglyphs and deutoglyphs. f. Same, dextrolateral view. Images courtesy Abel Pérez-González.
Fig. 16 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 16. Libitioides albolineata (Sørensen, 1884) (USNMENT 0153862) from Palmyra, Virginia, distal part of penis. a. Dorsal view. b. Ventral view. c. Dextrolateral view. d. Detail of glans, dextrolateral view. e. Apical view. Scale bars: a–c = 50 μm; d = 20 μm; e = 40 μm.
Fig. 17 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 17. Libitioides ornata (Say, 1821), ♂ (USNMENT 01538061) from Hillsborough County, Florida. a. Dorsal view of body. b. Left femur and trochanter IV, dorsal view. c. Left metatarsus and tarsomeres of leg I, lateral view. d. left chelicera dorsal view. Scale bars = 1 mm.
Fig. 18 in Once upon a time in America: recognition of the species of Libitioides from USA, with comments on other American Cosmetidae (Opiliones, Laniatores)
Fig. 18. Libitioides ornata (Say, 1821) (USNMENT 0153861) from Hillsborough, Florida. Habitus. a. Male, dorsal view. b. Sinistrolateral view. c. Frontal view. d. Ventral view. e. Panoramic, dorsal view. f. Female, dorsal view (USNMENT 0153861). Scale bars: a–c = 1 mm; d–f = 2 mm.
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.