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356 results for “Species concepts”
Figure 2 in A new species of Planipapillus (Onychophora: Peripatopsidae) that defies the original concept of its genus
Figure 2. Planipapillus absonus sp. nov.: male reproductive tract and associated glands, composite image drawn from holotype and paratype male. aag, anterior accessory gland; cg, crural gland; pa, posterior accessory gland; sv, seminal vesicle; t, testis; vd, vas deferens; ve, vas efferens.
Figure 1 in A new species of Planipapillus (Onychophora: Peripatopsidae) that defies the original concept of its genus
Figure 1. Planipapillus absonus sp. nov.: a, dorsolateral view in natura, ©David Paul; b, dorsal view; c, ventral view; d, anteriodorsal view; e, primary papilla; f, secondary papilla; g, crural papilla, leg 6; h, leg 5; i, nephridiopore, leg 5. b–d, stacked stereomicrographs, holotype ♂ 0.84 mm HWE (MV K7279), scale bars = 1 mm; e–i, scanning electron micrographs, paratypes MV K7280, scale bars = 30 µm; e, f, h, I, ♀ 1.04 mm HWE; g, ♂ 0.77 mm HWE.
Fig. 5 in A New Species from Mountain Forest Soils in Japan: Porosia paracarinata sp. nov., and Taxonomic Concept of the Genus Porosia Jung, 1942
Fig. 5. Schematic demonstration of relationship of Porosia paracarinata sp. nov. and two closely related species, such as Nebela carinata and Porosia bigibbosa, based on morphological characters (average morphometric characteristics of species based on literature data and personal observations*).
Fig. 4 in A New Species from Mountain Forest Soils in Japan: Porosia paracarinata sp. nov., and Taxonomic Concept of the Genus Porosia Jung, 1942
Fig. 4. Keel variation in Porosia paracarinata sp. nov. A – SEM image of P. paracarinata with narrow keel; B – LM images of P. paracarinata with narrow; C – very narrow and D – almost disappearing keel. Scale bars: 50 μm.
Fig. 3 in A New Species from Mountain Forest Soils in Japan: Porosia paracarinata sp. nov., and Taxonomic Concept of the Genus Porosia Jung, 1942
Fig. 3. Porosia paracarinata sp. nov. A – SEM image of P. paracarinata with wider keel; B – LM image of P. paracarinata with wider keel; C – P. paracarinata in profile view; D – schematic draw of P. paracarinata. Scale bars: 50 μm.
Fig. 1 in A New Species from Mountain Forest Soils in Japan: Porosia paracarinata sp. nov., and Taxonomic Concept of the Genus Porosia Jung, 1942
Fig. 1. Map of Japan, with indication of Mount Tateyama (in the first figure) and with the detailed locality called Bijodaira (in the second figure) where Porosia paracarinata was found (figure modi- fied from http://klettertechnik-bauservice.de/images/pulau-honshu).
Fig. 2 in A New Species from Mountain Forest Soils in Japan: Porosia paracarinata sp. nov., and Taxonomic Concept of the Genus Porosia Jung, 1942
Fig. 2. Outline of Porosia paracarinata: ventral (left) and lateral (right) views. 1–7 – measured characters of the test (see Table 1). Scale bar: 50 µm.
Linked collectors and determiners for: A new species of the Chaleponcus dabagaensis - group from Mount Rungwe, Tanzania-support for an extended concept of the Eastern Arc Mountains (Diplopoda, Spirostreptida, Odontopygidae).
Natural history specimen data linked to collectors and determiners held within, "A new species of the Chaleponcus dabagaensis - group from Mount Rungwe, Tanzania-support for an extended concept of the Eastern Arc Mountains (Diplopoda, Spirostreptida, Odontopygidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/d71f3b4a-f7a9-4f8b-92a3-f4dcbe49ae17">https://bionomia.net/dataset/d71f3b4a-f7a9-4f8b-92a3-f4dcbe49ae17</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/d71f3b4a-f7a9-4f8b-92a3-f4dcbe49ae17">https://gbif.org/dataset/d71f3b4a-f7a9-4f8b-92a3-f4dcbe49ae17</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Unexpected diversity of Lacon Laporte, 1838 (Coleoptera: Elateridae: Agrypninae) in the Levant: revised species concepts, new species, and an identification key.
Natural history specimen data linked to collectors and determiners held within, "Unexpected diversity of Lacon Laporte, 1838 (Coleoptera: Elateridae: Agrypninae) in the Levant: revised species concepts, new species, and an identification key". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c6d3d19c-627e-425f-8824-193a7213994a">https://bionomia.net/dataset/c6d3d19c-627e-425f-8824-193a7213994a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c6d3d19c-627e-425f-8824-193a7213994a">https://gbif.org/dataset/c6d3d19c-627e-425f-8824-193a7213994a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013.
Natural history specimen data linked to collectors and determiners held within, "Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e">https://bionomia.net/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e">https://gbif.org/dataset/af97dd93-ad80-4dcf-af96-c67a1cc0901e</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Two new species of Lamiinae, synonymies in Hemilophini, and corrections on the concept of four genera with transfers of three species (Coleoptera, Cerambycidae).
Natural history specimen data linked to collectors and determiners held within, "Two new species of Lamiinae, synonymies in Hemilophini, and corrections on the concept of four genera with transfers of three species (Coleoptera, Cerambycidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9e0cb1dc-1a39-470d-8bdb-ce3fd619a6a0">https://bionomia.net/dataset/9e0cb1dc-1a39-470d-8bdb-ce3fd619a6a0</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9e0cb1dc-1a39-470d-8bdb-ce3fd619a6a0">https://gbif.org/dataset/9e0cb1dc-1a39-470d-8bdb-ce3fd619a6a0</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Taxonomic utility of niche models in validating species concepts: A case study in Anthophora (Heliophila) (Hymenoptera: Apidae).
Natural history specimen data linked to collectors and determiners held within, "Taxonomic utility of niche models in validating species concepts: A case study in Anthophora (Heliophila) (Hymenoptera: Apidae)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/1363c785-b3e0-4322-9283-a6d272748735">https://bionomia.net/dataset/1363c785-b3e0-4322-9283-a6d272748735</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/1363c785-b3e0-4322-9283-a6d272748735">https://gbif.org/dataset/1363c785-b3e0-4322-9283-a6d272748735</a>. Formatted as a Frictionless Data package.
Figure 6 in On a new species and genus in the Cypridini (Crustacea, Ostracoda, Cyprididae) from South Africa, with a phylogenetic analysis of the tribe and a discussion on the genus concept in this group
Figure 6. Phylogenetic analyses of matrix given in Appendix 1. Trees are phylograms computed by NJ method, but for all three situations at least some of the equally parsimonious MP phylograms (as computed by branch-andbound routine) had an identical topology. Values without brackets represent distance bootstraps (10,000 replicates) using NJ, values in brackets are MP bootstrap values (10,000 replicates) using full heuristic method. (A) Weight of all characters (1–17)51; (B) weight of valve characters (1–9)55, of soft part characters (10–17)51; (C) weight of all soft part characters (10–17)55, of valves characters (1–9)51.
Figure 5. Mnementh brennei n. gen. n in On a new species and genus in the Cypridini (Crustacea, Ostracoda, Cyprididae) from South Africa, with a phylogenetic analysis of the tribe and a discussion on the genus concept in this group
Figure 5. Mnementh brennei n. gen. n. sp., male, Western Cape, South Africa. (A) T3 (OC.2917); (B) T2 (OC.2915); (C) attachment of caudal ramus (OC.2915); (D) caudal ramus (OC.2915). Scale: 20× (A, B); 10× (C, D).
Figure 2. Mnementh brennei n. gen. n in On a new species and genus in the Cypridini (Crustacea, Ostracoda, Cyprididae) from South Africa, with a phylogenetic analysis of the tribe and a discussion on the genus concept in this group
Figure 2. Mnementh brennei n. gen. n. sp., Western Cape, South Africa. (A) Female, LV, internal view (OC.2922); (B) female, RV, internal view (OC.2922); (C) male, LV, internal view (OC.2915); (D) male, RV, internal view (OC.2915); (E) male, carapace, right lateral view (OC.2921); (F) female, carapace left lateral view (OC.2919); (G) female, RV, internal view, detail of anterior part (OC.2922); (H) female, LV, internal view, detail of anterior part (OC.2922); (I) male, RV, internal view, detail of anterior part (OC.2915); (J) female, RV, internal view, detail of posterior part (OC.2922); (K) female, carapace, ventral view, detail of anterior part (specimen lost); (L) male, carapace, right lateral view, detail of anterior part (OC.2921); (M) female, carapace, ventral view (specimen lost); (N) male, carapace, dorsal view (OC.2920). Scale bar: 2170 mm (A–F, M, N); 926 mm (G–L).
Figure 1 in On a new species and genus in the Cypridini (Crustacea, Ostracoda, Cyprididae) from South Africa, with a phylogenetic analysis of the tribe and a discussion on the genus concept in this group
Figure 1. Map showing localities of Mnementh brennei n. gen. n. sp. in the Western Cape Province of South Africa.
Data for: An AAV-CRISPR/Cas9-strategy for gene editing across divergent rodent species: Targeting neural oxytocin receptors as a proof of concept
<p>A major issue in neuroscience is the poor translatability of research results from preclinical studies in animals to clinical outcomes. Comparative neuroscience can overcome this barrier by studying multiple species to differentiate between species-specific and general mechanisms of neural circuit functioning. Targeted manipulation of neural circuits often depends on genetic dissection, and use of this technique has been restricted to only a few model species, limiting its application in comparative research. However, ongoing advances in genomics make genetic dissection attainable in a growing number of species. To demonstrate the potential of comparative gene editing approaches, we developed a viral-mediated CRISPR/Cas9 strategy that is predicted to target the oxytocin receptor (<em>Oxtr</em>) gene in >80 rodent species. This strategy specifically reduced OXTR levels in all evaluated species (n=6), without causing gross neuronal toxicity. Thus, we show that CRISPR/Cas9-based tools can function in multiple species simultaneously. Thereby, we hope to encourage comparative gene editing and improve the translatability of neuroscientific research.</p>
FIG. 2 in Structural and functional genes, and highly repetitive sequences commonly used in the phylogeny and species concept of the phylum Cyanobacteria
FIG. 2. — Phylogeny of common or less studied genetic markers. According to the literature review,less common studied genetic marker has been highlighted.
FIG. 1. — A in Structural and functional genes, and highly repetitive sequences commonly used in the phylogeny and species concept of the phylum Cyanobacteria
FIG. 1. — A summary of structural and functional genes, and highly repetitive sequences commonly used in the phylogeny of cyanobacteria.
Data from: Automatic patient-level recognition of four Plasmodium species on thin blood smear by a Real Time Detector Transformer (RT-DETR) object detection algorithm: a proof-of-concept and evaluation
<p>Automatic patient-level recognition of four <em>Plasmodium</em> species on thin blood smear by a Real Time Dectector Transformer (RT-DETR) object detection algorithm: a proof-of-concept and evaluation</p> <p>Emilie Guemas, Baptiste Routier, Théo Ghelfenstein-Ferreira, Camille Cordier, Sophie Hartuis, Bénédicte Marion, Sébastien Bertout, Emmanuelle Varlet-Marie, Damien Costa, Grégoire Pasquier</p> <p><strong>Abstract:</strong></p> <p>Malaria remains a global health problem with 247 million cases and 619,000 deaths in 2021. Diagnostic of <em>Plasmodium</em> species is important for administering the appropriate treatment. The gold-standard diagnosis from accurate species identification remains the thin blood smear. Nevertheless, this method is time-consuming and requires highly skilled and trained microscopists. To overcome these issues, new diagnostic tools based on deep learning are emerging. This study aimed to evaluate the performances of a RT-DETR (Real-Time Detection Transformer)object detection algorithm to discriminate <em>Plasmodium</em> species on thin blood smears images. The algorithm was trained and validated on a dataset consisting in 24,720 images from 475 thin blood smears corresponding to 2,002,597 labels. Performances were calculated with a test dataset of 4,508 images from 170 smears corresponding to 358,825labels coming from six French university hospital. At the patient level, the RT-DETR algorithm exhibited an overall accuracy of 79.4% (135/170) with a recall of 74% (40/54) and 81.9% (95/116) for negative and positive smears, respectively. Among <em>Plasmodium </em>positive smears, the global sensitivity was 82.7% (91/110) with a sensitivity of 90% (38/42), 81.8% (18/22) and 76.1% (35/46) for <em>P. falciparum</em>, <em>P. malariae </em>and <em>P. ovale/vivax,</em> respectively. The YOLOv5 model achieved a World Health Organization (WHO) competence level 2 for species identification. Besides, the RT-DETR algorithm may be run in real-time on low-cost devices such as a smartphone and could be suitable for deployment in low-resource setting areas where microscopy experts are lacking.</p> <p><strong>Data collection:</strong></p> <p>The training and validation dataset included 24,720 pictures taken from 475 manually May Grunwald-Giemsa (MGG)-stained thin blood smears from the Montpellier University Hospital collection and for a smaller part from the Toulouse University Hospital collection. In Montpellier, the pictures were taken with a Flexcam C1 microscope camera (Leica) attached to a Leica DM 2000 microscope and Leica DF450C microscope camera adapted with a Leica DM2500 microscope at X1000 magnification. Labelling of pictures was performed manually, and then automatically with manual correction with a Computer Visual Annotation Tools (CVAT) free software. Nine categories of labels were used: white blood cells (n=3,338), red blood cells (n=1,887,781), platelets (n=48,520), <em>Trypanosoma brucei </em>(n=2,773), and red blood cells infected by <em>P. falciparum </em>(n=43,545), <em>P. ovale </em>(n=4,651), <em>P. vivax </em>(n=4,115), <em>P. malariae </em>(n=2,849) and <em>Babesia divergens</em> (n=5,142).</p> <p>The test dataset included 4,508 pictures taken from 170 thin blood smears from the same number of patients from the Parasitology laboratories of University Hospitals of Montpellier, Toulouse, Rouen, Lille, Nantes and Saint-Louis in Paris (Table 1). Among these 170 patients, 54 were not infected, including two patients with Howell-Jolly bodies, and 116 were infected with hematozoa. For each patient, between 20 and 30 photos were taken from one thin blood smear with at least one hematozoan parasite per picture for infected patients.</p> <p>Accurate species diagnostic was made by a senior parasitologist, and for recent smears, it was confirmed by specific PCR, either performed locally (Toulouse) or at the Malaria French National Reference Center (Montpellier, Saint Louis, Rouen, Lille, Nantes).</p>
ScienceDex guides
Understand access before you commit
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.