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FIGURE 5 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 5. Histological transversal section of O. margoi. A, different stage of maturation of clusters of germ cells in the testes. Spermatogonia (sg) and spermatids (st) in each cluster are arranged around the cythophore (cy). In more advanced stages it is possible to observe the tails (t) and degenerating cytophores (asterisk). Scale bar = 100 µm. B, structure of the ovary. The ovisac (os) surround the ovary cord (oc) immersed in the ovary lumen (ol). Elongated follicular cells (fc) envelope the egg string that is composed by numerous immature germ cells (gc). The club-shaped end (cse) and a tiny convoluted central part of the cord are visible in this section. Scale bar = 100 µm. C, maturing oocytes (o) in proximity of nurse cells (nc). The germinal vesicle or nucleus (n) contains pale nucleoplasm (np) and nucleoli (nl). Scale bar = 50 µm.
FIGURE 4 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 4. Histological transversal section of O. margoi. A, section of the two lateral post ceca (pca), showing the central posterior intestine (pi) and empty lateral diverticula (ld). Scale bar = 500 µm. B, section trough the male system. The atrium is folded in two parts. The circular posterior part (pp) tied to the celomic cavity trough a connection (cn) and the dorso-ventrally flattened anterior part (ap) ventrally located with a central elongated empty canal (c). On the top of the atrium there is the muscular bulb (mb). Scale bar = 100 µm. C, the two ovaries (ov) containing the ovary cords develops beneath the posterior crop (pc). One of the two ejaculatory ducts (ed) and the ventral located nerve cord (nc) are visible. Scale bar = 100 µm. D, section at the level of the posterior crop (pc) filled with prey's blood. Beneath the posterior crop is possible to observe the two ovaries (o). The ovary on the left shows the terminal part of the egg string with two maturing irregular shaped oocytes (asterisk). On both sides of the posterior crop is visible one pair of testes (t) connected with the body wall trough connections (cn). In the left testis is visible the vasa efferentia (ve) diverting dorsally. Scale bar = 500 µm.
FIGURE 2 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 2. Scanning electron micrographs of the sensilla. A, B, ventral view of the anterior sucker showing two rings of sensilla (arrows), the external one with smaller sensilla. C, structure of a mouth sensillum showing a central overhead region delimited by a surrounding rime (sr) with cilia (c). D, particular of the anterior sucker showing numerous pores (arrows) beneath the rings of sensilla. E, ventral surface of the body showing regular pattern of sensilla (arrows) disposed in rows and alternate with pores. F, structure of a body sensillum showing short grouped cilia (g) and long single cilia (s) in the proximity of a pore.
FIGURE 3 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 3. Histological transversal section of O. margoi A, section of the anterior crop (ac) including the last part of the oesophagus (oe) and columns of gland cells (gc) ending in a gland duct (gd). Scale bar = 500 µm. B, section trough the female system exposing the vagina (v) with the set of duct of the seminal receptaculum (sr). Laterally two tiny ejaculatory ducts (ed) and the atrium (a) are shown. Scale bar = 500 µm. C, section of the dorsal part of the anterior sucker showing one of the two pigmented cup eyes with pigmented supportive cells (psc) and photoreceptor cells (phc). Scale bar = 50 µm. D, transversal section of the eye showing two photoreceptors. The apical part of those cells is composed by a vacuole-like structure (vls) located above a large cytoplasmic area containing the nucleus (n). Beside the nucleus nerve fibres (nf) are departing. Between the two eyes is visible the body cavity (cc). Scale bar = 50 µm. E, section of the ganglionic mass at the level of the supraesophageal ganglion (sg) surrounding the proboscis (pr). Around the ganglionic mass is visible the body cavity (cc). Scale bar = 200 µm. F, section along the oviducal bridge with the two tubular ovaries (ov) opening in two foramina (fac, fnc) for the passage of the alimentary canal (ac) and the nerve cord (nc). Down of the ovaries there are the two seminal vesicles (sv). Scale bar = 500 µm.
FIGURE 1 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 1. Ozobranchus margoi (Apáthy, 1890) scanning electron micrographs. A, ventral view showing the anterior (as) and posterior sucker (ps). B, dorsal view showing the gills (g) and the typical external annulation (an). C, morphology of the gills (g). Each pair of gills arising from a single biannulate somite of the urosome composed of (a 1 + a 2)> a 3, with a basal stalk (bs) dividing in secondary branches (sb) whence single filaments (f) are departing. D, ventral lateral view of the anterior sucker showing the atrium (a) extruded through the genital aperture (ga). E, ventral view of the branchiate segment showing the approximate position of the genital aperture (ga). F, occasionally a longitudinal canal was observed running the external surface of the filament (lc).
FIGURE 8. 3D in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 8. 3D volume renderings of O. margoi using the micro-CT technology. Contrast enhancement to expose the denser parts. A, dorsal view of the whole body until the posterior sucker (ps) enouncing the digestive system. From the posterior intestine (pi) two lateral post ceca are starting (pca). Four pairs of blind ending lateral diverticula (ld) are diverting from the posterior intestine that finally enlarge to form a sac-like structure. Arrows indicate the two lateral blind-ended sacks in the last sack of the posterior intestine. B, frontal view of the anterior sucker (as) showing the four lines of lateral columnar glands (gl) and a central gland-like structure separated from the other (arrow). Scale bar = 1mm.
FIGURE 7 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 7. Section images of O. margoi using the micro-CT technology. A, antero-coronal section in 3D volume rendering of the dorsal part of the leech, showing the glands (gl) with the gland duct (gd) and the oesophagus (oe). Five pairs of blind sacs (bs) begins on both sides of the posterior crop (pc). B, transversal section with the ganglionic mass (gm) overcome by a glandlike structure (gls) and surrounding the proboscis (pr). C, transversal section on the oviducal bridge (ob) with the two ovaries arching ventrally and separating the anterior (ac) and posterior crop (pc). D, antero-coronal section of the leech showing the oesophagus (oe) and four pairs of testis (T) connected (cn) in two points with the body cavity. On both lateral sides there are five pairs of external gills (g). E, coronal section of the whole body showing the posterior crop (pc), a pair of testes (t) tied to the celomic cavity with two connections (cn), two lateral post ceca (pca) and three of the four central sacs of the posterior intestine. F, transversal section of the not branchiate segment of the urosome showing two ventrally located lateral post ceca (pca), one central expanded posterior intestine (pi) and a dorsally directed lateral diverticula (ld). G, transversal section in proximity of the posterior sucker (ps) showing the posterior intestine (pi) ending in a dorsal anus (da). Scale bar = 1mm.
FIGURE 6 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 6. Section images of O. margoi using the micro-CT technology. A, B, C. Coronal progressive sections of the trachelosome showing the ganglionic mass (gm) surrounding the alimentary tract between the proboscis (pr) and the oesophagus (oe). The proboscis start from a small mouth (m). The first section (a) shows the sopraesophageal ganglion (sg), than the ganglionic mass expand down of the oesophagus (oe) (b, c). D, lateral section at the exact half of the body. The brain (br) overcome by a gland-like structure (gls) and surrounds the proboscis (pr). The oesophagus (oe) is forming a loop on the top of the atrium and in the ventral part is visible the genital atrium (ga). E, lateral section before the half of the body. Two columns of denser glands cells (gl) are passing through the oesophagus's loop (oe). F, transversal section on the male organs. The atrium (oe) is tied to the celomic cavity trough a connection (cn) and overcome by the muscular bulb (mb) and the anterior crop (ac). G, antero-coronal section of the body showing the oesophagus (oe), the four column of glands (gl) and the atrium (a). Scale bar = 1mm.
FIGURE 4 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 4. Histological transversal section of O. margoi. A, section of the two lateral post ceca (pca), showing the central posterior intestine (pi) and empty lateral diverticula (ld). Scale bar = 500 µm. B, section trough the male system. The atrium is folded in two parts. The circular posterior part (pp) tied to the celomic cavity trough a connection (cn) and the dorso-ventrally flattened anterior part (ap) ventrally located with a central elongated empty canal (c). On the top of the atrium there is the muscular bulb (mb). Scale bar = 100 µm. C, the two ovaries (ov) containing the ovary cords develops beneath the posterior crop (pc). One of the two ejaculatory ducts (ed) and the ventral located nerve cord (nc) are visible. Scale bar = 100 µm. D, section at the level of the posterior crop (pc) filled with prey's blood. Beneath the posterior crop is possible to observe the two ovaries (o). The ovary on the left shows the terminal part of the egg string with two maturing irregular shaped oocytes (asterisk). On both sides of the posterior crop is visible one pair of testes (t) connected with the body wall trough connections (cn). In the left testis is visible the vasa efferentia (ve) diverting dorsally. Scale bar = 500 µm.
FIGURE 3 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 3. Histological transversal section of O. margoi A, section of the anterior crop (ac) including the last part of the oesophagus (oe) and columns of gland cells (gc) ending in a gland duct (gd). Scale bar = 500 µm. B, section trough the female system exposing the vagina (v) with the set of duct of the seminal receptaculum (sr). Laterally two tiny ejaculatory ducts (ed) and the atrium (a) are shown. Scale bar = 500 µm. C, section of the dorsal part of the anterior sucker showing one of the two pigmented cup eyes with pigmented supportive cells (psc) and photoreceptor cells (phc). Scale bar = 50 µm. D, transversal section of the eye showing two photoreceptors. The apical part of those cells is composed by a vacuole-like structure (vls) located above a large cytoplasmic area containing the nucleus (n). Beside the nucleus nerve fibres (nf) are departing. Between the two eyes is visible the body cavity (cc). Scale bar = 50 µm. E, section of the ganglionic mass at the level of the supraesophageal ganglion (sg) surrounding the proboscis (pr). Around the ganglionic mass is visible the body cavity (cc). Scale bar = 200 µm. F, section along the oviducal bridge with the two tubular ovaries (ov) opening in two foramina (fac, fnc) for the passage of the alimentary canal (ac) and the nerve cord (nc). Down of the ovaries there are the two seminal vesicles (sv). Scale bar = 500 µm.
FIGURE 5 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 5. Histological transversal section of O. margoi. A, different stage of maturation of clusters of germ cells in the testes. Spermatogonia (sg) and spermatids (st) in each cluster are arranged around the cythophore (cy). In more advanced stages it is possible to observe the tails (t) and degenerating cytophores (asterisk). Scale bar = 100 µm. B, structure of the ovary. The ovisac (os) surround the ovary cord (oc) immersed in the ovary lumen (ol). Elongated follicular cells (fc) envelope the egg string that is composed by numerous immature germ cells (gc). The club-shaped end (cse) and a tiny convoluted central part of the cord are visible in this section. Scale bar = 100 µm. C, maturing oocytes (o) in proximity of nurse cells (nc). The germinal vesicle or nucleus (n) contains pale nucleoplasm (np) and nucleoli (nl). Scale bar = 50 µm.
FIGURE 2 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 2. Scanning electron micrographs of the sensilla. A, B, ventral view of the anterior sucker showing two rings of sensilla (arrows), the external one with smaller sensilla. C, structure of a mouth sensillum showing a central overhead region delimited by a surrounding rime (sr) with cilia (c). D, particular of the anterior sucker showing numerous pores (arrows) beneath the rings of sensilla. E, ventral surface of the body showing regular pattern of sensilla (arrows) disposed in rows and alternate with pores. F, structure of a body sensillum showing short grouped cilia (g) and long single cilia (s) in the proximity of a pore.
FIGURE 1 in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 1. Ozobranchus margoi (Apáthy, 1890) scanning electron micrographs. A, ventral view showing the anterior (as) and posterior sucker (ps). B, dorsal view showing the gills (g) and the typical external annulation (an). C, morphology of the gills (g). Each pair of gills arising from a single biannulate somite of the urosome composed of (a1 + a2)> a3, with a basal stalk (bs) dividing in secondary branches (sb) whence single filaments (f) are departing. D, ventral lateral view of the anterior sucker showing the atrium (a) extruded through the genital aperture (ga). E, ventral view of the branchiate segment showing the approximate position of the genital aperture (ga). F, occasionally a longitudinal canal was observed running the external surface of the filament (lc).
FIGURE 7. Sample sites and climatic suitability for all Alpinobombus species combined estimated using Maxent from climate variables for the year 2000 in The arctic and alpine bumblebees of the subgenus Alpinobombus revised from integrative assessment of species' gene coalescents and morphology (Hymenoptera, Apidae, Bombus)
FIGURE 7. Sample sites and climatic suitability for all Alpinobombus species combined estimated using Maxent from climate variables for the year 2000. Bright yellow and brown areas show where the logistic prediction of occurrence is p> 0.5 (the outlier records with exceptionally low probabilities of suitability were excluded in step-wise iterations); brown spots show all consistent Alpinobombus site records; '?' shows the five records that are in climatically outlying sites. Polar projection, North Pole (starred) at the centre of the map, international boundaries and the Arctic Circle shown as narrow grey lines.
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
A global 0.05° gross primary productivity of sunlit and shaded leaves dataset via combining two-leaf light use efficiency model with random forest over 2002~2020
<p>The TL-CRF model generated a global 0.05´0.05° product for eight-day gross primary productivity (GPP) of sunlit and shaded canopies from 2002 to 2020 by embedding the random forest (RF) submodule into the two-leaf light use efficiency (TL-LUE) model while considering the seasonal differences in the clumping index. The RF technique was used to integrate various environmental stress factors including meteorological, hydrological, soil properties, and elevation, thereby improving the overall scale of the complex environmental conditions to the maximum LUE. This novel GPP product could support further research on spatial and temporal patterns of the carbon cycle and its association with climate change.</p> <p> </p> <p> </p> <p>Variable: GPP, GPP<sub>sh</sub>, and GPP<sub>su</sub></p> <p>Spatial coverage: global</p> <p>Temporal coverage: 2002 to 2020</p> <p>Spatial resolution: 0.05×0.05°</p> <p>Temporal resolution: eight-day</p> <p>Unite: g C m<sup>−2</sup> d<sup>−1</sup></p> <p>Data format: raster (.tif)</p>
Pan-Cancer T cell atlas from "The combined use of scRNA-seq and network propagation highlights key features of pan-cancer Tumor-Infiltrating T cells" (https://doi.org/10.1371/journal.pone.0315980)
<p>The scRNA-seq data were collected from previously published datasets (GSE140228, GSE139555, GSE155698, GSE121636, and GSE139324), adhering to the following selection criteria: 1) presence of T cells, 2) treatment-naïve patients, 3) solid tumors, and 4) inclusion of at least tumor and blood samples.<br>Each scRNA-seq dataset underwent separate preprocessing in R (v4.0.2). We filtered out cells from the original count matrices that had fewer than 200 genes detected or more than 10% mitochondrial UMI counts and we only kept genes detected in at least 3 cells. Then, we applied Seurat (v4.0.5) with default parameters for count data normalization and scaling. Each cell was assigned a cell cycle score using the CellCycleScoring function and we computed the difference between the G2M and S phase scores. This approach allows for the separation of non-cycling from cycling cells while minimizing the differences in cell cycle phase among proliferating cells. The SelectIntegrationFeatures function was ran with the nfeatures parameter set to 3,000 before merging all samples from each dataset. These integration features were then used for Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP). Clustering was performed using the Louvain algorithm with the resolution parameter set to 2.0 for all datasets. Finally, T cells were isolated based on CD3D and CD3G genes expression (CD3D or CD3G expression level > 0).</p> <p>To integrate heterogeneous data from different sources, a two-step procedure was applied. We first concatenated all datasets together and ran the scaling and PCA steps based on the top 3,000 highly variable genes identified by the FindVariableFeatures function with the “vst” method. Harmony was applied for batch effect correction then UMAP and clustering using the Louvain algorithm with the resolution parameter set to 2.0 were performed on the harmony reduction. Examining the result from the first clustering run, we identified contamination clusters and clusters that arose from unwanted factors: we removed the contamination clusters including low quality cells highly expressing marker genes associated with apoptosis and tissue dissociation operation, pancreatic acinar cells (expressing PRSS1, CLPS, PNLIP and CTRB1 among others), myeloid cells (expressing CD68) and B cells (expressing CD79A). Then, we performed the second run of integration and clustering excluding immunoglobulin, ribosome-protein-coding, and T cell receptor (TCR) genes (gene symbol with string pattern "^IGK|^IGH|^IGL|^IGJ|^IGS|^IGD|IGFN1", "^RP([0–9]+-|[LS])", and "^TRA|^TRB|^TRG" respectively) from the top 3,000 highly variable genes and regressing out the cell cycle difference effect as well as the percentage of mitochondrial UMI counts. Harmony (v0.1.0) was applied again for batch effect correction and UMAP was performed on the harmony reduction.<br>T cell subtypes identification and annotation was performed by clustering cells using the Louvain algorithm with the resolution parameter set to 4.1 after iterative testing from 3.5 to 5.0 by 0.1 (more granular than default), computing clusters signatures based on differential gene expression using the FindAllMarkers function with the “MAST” method and interrogating known gene markers expression. A resolution value of 4.1 was notably found to be the lowest resolution value enabling the correct separation of proliferating CD4+ T cells from proliferating CD8+ T cells.</p>
Figure 6 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
Figure 6. Single shortest cladogram for six genes and morphology in combination (14 570 steps) under parameter set 3221. Numbers above branches are jackknife frequencies> 50%. Navajo rugs (as explained in Fig. 5) for the six parameter sets shown below branches.
Figure 5 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
Figure 5. Single shortest cladogram for six genes in combination (14 465 steps) under parameter set 3221. Numbers above branches are jackknife frequencies> 50%. Navajo rugs below branches depict monophyly (black) or nonmonophyly (white) of clades under the six parameter sets shown at left; grey box indicates monophyly in some but not all shortest cladograms.
Figure 4 in A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set
Figure 4. Strict consensus of nine best-fit cladograms based on morphological data in Table 2 under implied weights (k = 2, 3, 4, 5, and 6). GC values> 50% shown above branches for concavity constant k = 3. Position of Scolopocryptops simojovelensis highlighted.
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.