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Fig. 5 in Revision of the genus complex Gibbula: an integrative approach to delineating the Eastern Mediterranean genera Gibbula Risso, 1826, Steromphala Gray, 1847, and Phorcus Risso, 1826 using DNA-barcoding and geometric morphometrics (Vetigastropoda, Trochoidea)
Fig. 5 Lectotype of Steromphala cineraria (Linnaeus, 1758). Located at LSL (LSL.502). Scale bar 5 mm
Fig. 2 Landmark templates for representative a lateral and b in Revision of the genus complex Gibbula: an integrative approach to delineating the Eastern Mediterranean genera Gibbula Risso, 1826, Steromphala Gray, 1847, and Phorcus Risso, 1826 using DNA-barcoding and geometric morphometrics (Vetigastropoda, Trochoidea)
Fig. 2 Landmark templates for representative a lateral and b ventral standardised views. Filled circles show fixed landmarks. Empty circles show semilandmarks, processed as sliding landmarks
Fig. 5 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 5. Phylogenetic tree based on analysis of mitochondrial COI sequences of the Sarcocystidae including the new Sarcocystis sp. examined in this study (black symbols). Other taxa of the Apicomplexa served as root. Evolutionary history was inferred by the Maximum Likelihood (ML) method based on the TamuraNei model, whereby 619 positions were included in the final data set. All positions with less than 95% site coverage were eliminated; that is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. Bootstrap percentages (1000 iterations) are shown next to branches. COI sequences E357-13 and E120-13 (not shown in the tree) are available at GenBank (MN732561 and MN732562, respectively).
Fig. 2 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 2. Ultrastructure of S. scandentiborneensis sp. nov. Note, due to ethanol-fixation some ultrastructural details are poorly resolved (e.g. membranes). A) Longitudinal section through the same sample as in Fig. 1C, showing a gross view of the sarcocyst and its villous protrusions (VP) that are sectioned in different orientations. The inset shows a cross section through various VP that reveals the arrangement of microtubules in their inner core; while in this case 16 microtubules are visible (asterisks), sections through more apical portions of the VP showed lower numbers. B) Longitudinal section through the fingerlike VPs that appear to be anchored in the ground substance (arrow) by microtubules (asterisks) that extend into each protrusion; note the electron-dense, U-shaped structure at each tip of the protrusions (arrowheads) and the apparently serrated surface of the VP (flat arrowheads). The inset shows a higher magnification of the apical part of a single VP with the typical U-shaped apex (asterisk), which appears to be connected with the host cell through an electronlucent contact zone (white arrowheads); interestingly, the protrusion appears fenestrated (also visible in the main image) possessing thorn-like structures (black arrows; the white arrow indicates a crosssectional view) that could be responsible for the serration visible at lower magnification. CZ, cystozoites; HC, host cell; VP, villous protrusion.
Fig. 1 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 1. Light microscopy of Sarcocystis scandentiborneensis sp. nov. A and B, Haematoxylin & Eosinstained histological sections of striated musculature; C and D, Richardson's dye-stained 1.0 μm thin sections of sarcocysts. A) Tissue section of laryngeal muscle with various sarcocysts in cross section (asterisks), indicating a relatively high density of cysts in this part of musculature. B) Longitudinal section through a sarcocyst, showing a cigar-shaped appearance; however, isolated native sarcocysts, which were not available, may look different. C) Part of a longitudinal section through the tip of a sarcocyst, note the very thin ground substance (arrows) and the fine septae extending into the interior of the cyst (arrowheads); cystozoites (CZ) were loosely scattered within chambers while metrocytes were rarely seen, indicating maturity of the cyst; bars indicate the variable thickness of the cyst wall: the wall was thinner in regions where the villous protrusions were bent (right bar); note that the intense staining at the interface between host cell (HC) and parasite is part of the host cell. D) Cross-section through a sarcocyst showing cystozoites and the cyst wall (bar) including its thin ground substance (arrows).
Fig. 4 in Description of Sarcocystis scandentiborneensis sp. nov. from treeshrews (Tupaia minor, T. tana) in northern Borneo with annotations on the utility of COI and 18S rDNA sequences for species delineation
Fig. 4. Mapping (to the Toxoplasma gondii reference molecule M97703) of frequencies (%) of base pair changes observed in sequence comparisons of nu clear 18S rDNA within the new Sarcocystis sp. from treeshrews (intraspecific variation: isolates E364–13 versus E357–13) and between the new species and Sarcocystis zuoi and/or S. clethrionomyelaphis (interspecific variation: E364–13 versus S. zuoi/clethrionomyelaphis). Results were combined for the two latter species to simplify the graph. Here, 87.2% of 2118 alignment positions showed moderate to high levels of consistency, while sections of ambiguous alignment did not relate to the species under investigation. Due to gaps in the alignment, not all of the observed nt changes could be mapped to a homologous position of the reference molecule (i.e., 7 out of 24 bp changes in intraspecific comparison; 33 out of 74 bp changes in interspecific comparison), in which case the position of each nt relative to the helix was inferred from neighboring nt for which such position was known. Gaps were mainly due to insertions in helices V2, V4, and V9 rendering E357-13/E364-13 longer than the sequence of T. gondii. The percentage of parsimony-informative (pi) bp changes per helix is shown for helices V1, V2, V4, V7, and V9 above each column. Also shown is the ratio of transitions versus transversions (Ti/Tv) for selected helices.
Single-cell and spatial transcriptomics delineate molecular traits and immunosuppressive landscape during histological progression of lung adenocarcinoma
<p>Two specimens of lung adenocarcinoma, each corresponding to the lepidic and solid histologic patterns as confirmed through histologic scrutiny, were procured in accordance with standard surgical protocols. These specimens underwent a process of formalin fixation and were subsequently encapsulated within paraffin-embedded tissue blocks. The specimens were then sectioned and subjected to hematoxylin and eosin (H&E) staining to facilitate subsequent imaging at a resolution of 40x (equivalent to 0.25 micron/pixel) via the use of Aperio GT450 scanners. The tissue slides were then conveyed to the Genomics core, where following the decoverslipping of the tissue, the Visium CytAssist device was employed to transfer transcriptomic probes from the original glass slides to capture areas on Visium slides measuring 11mm x 11mm. Comprehensive transcriptomic profiling was achieved post mRNA permeabilization, through poly(A) capture and probe hybridization. The resultant libraries were sequenced utilizing the Illumina Novaseq 6000, using paired-end sequencing with a read length of 150 base pairs.</p>
Data for "Site-Specific Management Zones Delineation Based on Apparent Soil Electrical Conductivity in Two Contrasting Fields of Southern Brazil"
<p>This dataset contains soybean yield, soil property values, and apparent electrical conductivity (ECa) from two farms located in the South of Brazil. The data description and methods can be found in the paper:</p> <p><strong>Bottega, E. L., Safanelli, J. L., Zeraatpisheh, M., Amado, T. J. C., Queiroz, D. M. de, & Oliveira, Z. B. de. (2022). Site-Specific Management Zones Delineation Based on Apparent Soil Electrical Conductivity in Two Contrasting Fields of Southern Brazil. In Agronomy (Vol. 12, Issue 6, p. 1390). MDPI AG. https://doi.org/10.3390/agronomy12061390</strong></p> <p>Abstract:</p> <p>Management practices that aim to increase the profitability of agricultural production with minimal environmental impact must consider within-field soil variability, and this site-specific management can be addressed by precision agriculture (PA). Thus, this work aimed to investigate which key soil attributes are distinguishable management zones (MZ) delineated based on the soil apparent electrical conductivity (ECa), using fuzzy k-means, in two fields with contrasting soil textures in southern Brazil. For this, a grid scheme (50 × 50 m) was applied to measure ECa, conduct soil sampling for analysis, and determine soybean yield. The MZ were delineated based on the ECa spatial distribution, and statistical non-parametric tests (p < 0.05) were employed to compare the soil chemical and physical attributes among MZ. The management zones were able to distinguish the average values of Clay, Silt, pH, Ca<sup>2+</sup>, Mg<sup>2+</sup>, SB, Al<sup>3+</sup>, H<sup>+</sup> + Al<sup>3+</sup>, AS%, and BS%. In the field classified as sandy clay loam texture, management zones were able to differentiate the average values of soybean yield, Clay, Ca<sup>2+</sup>, Mg<sup>2+</sup>, SB, and CEC. Thus, this study supports the ECa as an efficient tool for delineating MZ of contrasting cropland soils in southern Brazil to understand the within-field soil variability and adjust the inputs accordingly.</p>
Linked collectors and determiners for: Checklist of the Red Sea Fishes with delineation of the Gulf of Suez, Gulf of Aqaba, endemism and Lessepsian migrants.
Natural history specimen data linked to collectors and determiners held within, "Checklist of the Red Sea Fishes with delineation of the Gulf of Suez, Gulf of Aqaba, endemism and Lessepsian migrants". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/6c170c2b-8792-4173-ac41-2aa1fe2b7ab7">https://bionomia.net/dataset/6c170c2b-8792-4173-ac41-2aa1fe2b7ab7</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6c170c2b-8792-4173-ac41-2aa1fe2b7ab7">https://gbif.org/dataset/6c170c2b-8792-4173-ac41-2aa1fe2b7ab7</a>. Formatted as a Frictionless Data package.
Fig. 3 in Phylogenetic relationships and sectional delineation within Gentiana (Gentianaceae)
Fig. 3. Distribution of morphological traits relevant for the identification of sections in Gentiana, in the light of phylogenetic relationships among these sections. The phylogenetic tree is identical to the one shown in Fig. 1.
Fig. 2 in Phylogenetic relationships and sectional delineation within Gentiana (Gentianaceae)
Fig. 2. Simplified phylogenetic trees of 254 nuclear anchored loci, plastid genomes and ITS region (rDNA cistron) produced via anchored hybrid enrichment. The upper two phylograms are based upon anchored loci either with tips collapsed according to the sectional delineation presented in this study (left), or with tips collapsed according to the sectional delineation by Ho & Liu (2001, right). Colour coding corresponds to Fig. 1. All nodes are fully supported (BI: 1.00 PP, ML: 100% BS) unless otherwise stated. Arrows in blue (anchored loci) and red (ITS region) show incongruences in phylogenetic relationships among sections, in comparison to the plastid phylogeny. Asterisks indicate nodes that are not supported by any analysis. Corresponding phylograms without collapsed tips are available for the rDNA cistron and the plastid phylogenies as supplementary Fig. S1 and S2.
Fig. 1 in Phylogenetic relationships and sectional delineation within Gentiana (Gentianaceae)
Fig. 1. Phylogram of ingroup species (outgroup removed) derived from 254 nuclear anchored loci produced via anchored hybrid enrichment. Phylogenetic support values for both Bayesian inference and maximum likelihood are shown at nodes only when they differ from 1.00 posterior probability and 100% bootstrap support. The double slash (//) symbolises an artificial shortening of this branch, as sect. Chondrophyllae produced a very long branch. The figure is colour-coded, with each colour referring to a clade in the phylogeny, a section corresponding to our new taxonomic treatment, and a picture illustrating each section. The species displayed are: A, Gentiana hexaphylla; B, G. tongolensis; C, G. frigida; D, G. verna; E, G. harrowiana; F, G. phyllocalyx; G, G. lutea; H, G. acaulis; I, G. aperta; J, G. praeclara; K, G. stipitata; L, G. officinalis; M, G. sceptrum. – Photographs: Adrien Favre.
Figure 1 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 1. Images of the three morphotypes of the Iberus gualtieranus complex. A, Iberus gualtieranus, with a keeled, flattened shell and closed umbilicus. B, Iberus alonensis, with a globose and non-umbilicated shell. C, Iberus campesinus, with a rounded, umbilicated shell and an expanded peristome. Scale bar: 2 cm.
Figure 4 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 4. Neighbour-joining (NJ) tree of the Iberus gualtieranus complex for the combined data set of the cytochrome oxidase subunit I (COI) and 16S rRNA genes. Bootstrap values under NJ (1000 replicates), MrBayes, and maximum parsimony are shown at each node (NJ/BA/MP)> 70%. G1, A2, C3, A4, A5, and A6 are the six major clades obtained. Subclades are indicated with lower case letters (a, b, c).
Figure 5 in Mitochondrial DNA diversity and taxa delineation in the land snails of the Iberus gualtieranus (Pulmonata, Helicidae) complex
Figure 5. The molecular phylogeny of cytochrome oxidase subunit I (COI) (left) and 16S rRNA (right) by neighbourjoining (NJ) analyses. Bootstrap values under NJ (1000 replicates), MrBayes, and maximum parsimony are given at each node (NJ/BA/MP)> 70%. For abbreviations, see the legend to Figure 4.
Figure 7 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 7. The phylogeny most strongly supported by our electrophoretic data. Note that C. reimanni and C. novaeguineae could not be separated electrophoretically, but we retain them as separate on the basis of morphological evidence (Philippen & Grossman, 1990; Rhodin, 1994a). The symbols + show the progressive development of robusticity in both the skull and triturating surfaces.
Figure 6 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 6. The best-supported phylogeny for the Chelodina prior to the present electrophoretic study (Burbidge et al., 1974; Rhodin & Mittermeier, 1976; Georges & Adams, 1992; Rhodin, 1994a,b). The root was chosen on the basis of evidence presented by Georges & Adams (1992), Seddon et al. (1997) and Georges et al. (1998). This phylogeny serves as the working hypotheses against which to compare our data. Only those taxa we regard to be species are included.
Figure 2 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 2. Principal co-ordinates analysis applied to a matrix of Roger's D genetic distances between all individuals of Chelodina expansa. The plot shows a degree of differentiation between coastal Queensland forms (Albert River in the south to Fitzroy–Dawson River in the north, including Fraser Island) (O) and those of the Murray-Darling system (•), but these differences have not moved to fixation at any locus (45 loci).
Figure 3 in Electrophoretic delineation of species boundaries within the genus Chelodina (Testudines: Chelidae) of Australia, New Guinea and Indonesia
Figure 3. Principal co-ordinates analysis applied to a matrix of Roger's D genetic distances between all individuals of Chelodina rugosa (Queensland form) (O), C. rugosa (Northern Territory form) (Z), C. siebenrocki (•), Chelodina burrungandjii (O) and an undescribed form from the Kimberley plateau of Western Australia (Ɨ). A hybrid between Chelodina burrungandjii and C. rugosa (Northern Territory form) is included (). Three groups are evident. Chelodina burrungandjii and the undescribed form from the Kimberley plateau are undifferentiated and probably represent a single taxon. Chelodina seibenrocki and the Queensland form of C. rugosa are undifferentiated, and also probably represent a single taxon. The Northern Territory form of C. rugosa represents the third group. These three groups differ each by only one fixed difference.
Overview of Automatic Preliminary Boundary Delineation Tool developed as part of UC2 (Prefilled Application) in NIVA4CAP
<p>UC2 Pre-filled application seeks to make it easier and more accurate for farmers to annually declare their lands by reducing the time needed to draw the new parcels boundaries or update the existing ones, thus, prevent the mistakes with input of the data on crops grown. The work focussed on (1) Creating an automatic preliminary boundary delineation tool, (2) Testing an early stage corp type/ land use classification tool and (3) Finding and testing a robotic process automation tool suitable for data harvesting from external registers. This document gives an overview of the parcel boundary delineation tool and is supplemented by a complementary report summarising results from tests of that tool in Lithuania and Spain and referenced below.</p>
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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.