Find research datasets worth reusing

Figure 5 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 5. Internal organization of the exogenous ovary in Opisthopatus roseus (A–C, E, F) and Peripatopsis balfouri (D). Transmission electron micrographs. A, detail of ovarian epithelia and lumen. Arrowheads indicate apical junctions connecting epithelial cells. B, mitotically dividing oogonium (og) from the germinal epithelium. C, maturating oocyte (oc) with associated cells (ce) of modified germinal epithelium. Arrows point to the basal lamina which is strongly folded. D, maturating oc in the process of breaking through the connective tissue and growing out into the haemocoel. E, detail of dorsal ovarian wall showing the sterile epithelium (se) and the connective tissue (ct), which contains the musculature (mc). F, higher magnification of connective tissue showing muscle cells and collagen fibres. Abbreviations: bl, basal lamina; ce, cells associated with an oocyte (sometimes referred to as 'follicle cells' in the literature); cg, collagen fibres; ct, connective tissue; ge, germinal epithelium; hc, haemocoel; he, haemocyte; lu, ovarian lumen; mc, muscle cell; mt, mitochondria; mv, microvilli; nl, nucleolus; nu, nucleus; oc, maturating oocyte; og, oogonium; se, sterile epithelium; st, growing stalk.

Figure 4 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 4. Internal organization of the exogenous ovary in Opisthopatus roseus (A, B) and Peripatopsis balfouri (C). Transmission electron micrographs. A, cross-section through the middle of the ovary. Dorsal is up. Note the unpaired lumen (lu) and the separation of the ovarian epithelium into a dorsal sterile epithelium (se) and a ventral germinal epithelium (ge). B, stalked oocytes enclosed by a vitelline membrane (= primary egg membrane). C, detail of a stalk. Arrows indicate intermediate filaments, arrowheads point to hemidesmosomes. Inset shows continuity of the basal lamina covering a stalk and a maturating oocyte that bulges into the haemocoel of the female. Abbreviations: bl, basal lamina; ct, connective tissue; ge, germinal epithelium; hc, haemocoel; lu, ovarian lumen; nl, nucleolus; nu, nucleus; oc, maturating oocytes; se, sterile epithelium; st, stalk; vm, vitelline membrane.

Figure 6 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 6. Internal organization of the pseudoendogenous ovary in Metaperipatus inae (A–E) and Metaperipatus blainvillei (F). Light micrographs (A, B) and transmission electron micrographs (C–F). A, cross-section of the ovary (dorsal is up). Note the lateral position of the crescent-shaped ovarian lumen (lu) and the central position of the germinal epithelium (ge). B, detail of stalked oocytes (oc) from the germinal epithelium, which do not bulge into the haemocoel but retain their position within the ovary. C, detail of cells (ce) surrounding a maturating oocytes in the germinal epithelium. D, detail of a stalk. Arrows indicate the intermediate filaments. E, detail of the lumen and ovarian epithelia. The epithelial cells are connected by an apical junction (arrowhead). F, lateral ovarian wall consisting of the sterile epithelium (se) and connective tissue containing muscle cells (mc), a haemocyte (he), and sperm (sh). Abbreviations: bl, basal lamina; ce, cells associated with an oocyte; cg, collagen fibres; ct, connective tissue; ge, germinal epithelium; hc, haemocoel; he, haemocyte; lu, ovarian lumen; mc, muscle cell; mv, microvilli; nl, nucleolus; nu, nucleus; oc, maturating oocyte; se, sterile epithelium; sh, sperm head; st, stalk; sw, sterile ovarian wall.

Figure 3 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 3. Diagram of internal organization of the three major ovarian types in Onychophora: exogenous ovary (A, D), pseudoendogenous ovary (B, E), and endogenous ovary (C, F). A, cross-section of the exogenous ovary with separate ovarian tubes that occur, e.g. in Euperipatoides rowelli, Phallocephale tallagandensis, and Ooperipatellus insignis (Australian Peripatopsidae). B, cross-section of the pseudoendogenous ovary of Metaperipatus inae (Peripatopsidae, Chile). C, cross-section of the endogenous ovary of Epiperipatus biolleyi (Peripatidae, Costa Rica). Note the complete lack of a sterile epithelium. D, detail of the composition of the ovarian wall in Opisthopatus roseus (Peripatopsidae, South Africa). E, detail of the ovary in Met. inae. F, detail of the ovarian wall in Ep. biolleyi. Abbreviations: bl, basal lamina; ct, connective tissue; fc, flattened cell; ge, germinal epithelium; hc, haemocoel; lu, ovarian lumen; mc, muscle cell; oc, oocyte; se, sterile epithelium; st, stalk; tr, tracheae.

Figure 1 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 1. Simplified diagrams of paired versus variously fused structure of the ovarian tubes in Onychophora. Tissues are represented in light grey, ovarian lumen in dark grey. A, exogenous ovary of Typhloperipatus williamsoni (South-East Asian Peripatidae). Modified and complemented according to descriptions given by Kemp (1914). B–D, exogenous ovaries in three species of Peripatopsidae. B, Euperipatoides rowelli (Australia). Note the completely separate ovarian tubes in the middle of the ovary and the fused ovarian lumens at the anterior and posterior ends. A similar ovarian organization has been described in Peripatoides novaezealandiae from New Zealand (Sheldon, 1890: fig. 26). C, Peripatopsis balfouri (South Africa, cf. Fig. 2A). Although the ovarian tubes are fused, their lumens are separate along their entire length. D, Opisthopatus roseus (South Africa). Note the unpaired ovarian structure with a single lumen. E, pseudoendogenous ovary of Metaperipatus inae (Peripatopsidae, Chile, cf. Fig. 2B) with fused ovarian tubes but separate lumens. F, endogenous ovary of Epiperipatus biolleyi (Neotropical Peripatidae, cf. Fig. 2C) with lumens communicating only at the posterior end. G, endogenous ovary of Mesoperipatus tholloni (Peripatidae, Tropical Africa), modified and complemented after Bouvier (1905). Each ovarian tube is completely separate in this species.

Figure 10 in Position and development of oocytes in velvet worms shed light on the evolution of the ovary in Onychophora and Arthropoda

Figure 10. Mapping of three major types of onychophoran ovaries on simplified trees representing three different hypotheses on the phylogenetic relationships of Onychophora. Onychophoran subgroups are designated by their geographical distribution. Note that the suggestion of the exogenous type as an ancestral feature of Onychophora is consistent with all three phylogenetic hypotheses. A, both Peripatopsidae and Peripatidae are monophyletic (phylogeny modified from Monge-Nájera, 1995: fig. 10). B, Peripatidae are nonmonophyletic (phylogeny simplified from Reid, 1996: fig. 29). C, Peripatopsidae are nonmonophyletic (phylogeny simplified from Reid, 1996: fig. 28).

opencc-by-4.0Jul 2008View details →

Figure 2 in Brittle stars (Echinodermata: Ophiuroidea) from La Réunion and the systematic position of Ophiocanops Koehler, 1922

Figure 2. SEM images of Ophiocanops multispina sp. nov. holotype (MNHN EcOs 23818–23820). A, dorsal view; B, dorsal disc; C, dorsal arm plates beyond gonadal chamber; D, disc spine; E, arm laterally; F, dorsal arm spine; G, ventral arm spines; H, lateral arm plate; I, base of dorsal arm spine; J, ventral overview; K, first ventral arm plate; L, arm ventrally; M, proximal face of vertebra; N, distal face of vertebra. Abbreviations: AS, adoral shield; DAP, dorsal arm plate; LAP, lateral arm plate; M, madreporite; NO, nerve opening; OP, oral papillae; SA, spine articulation; VAP, ventral arm plate. Scale bars in millimetres.

opencc-by-4.0Jul 2008View details →

Figure 4 in Brittle stars (Echinodermata: Ophiuroidea) from La Réunion and the systematic position of Ophiocanops Koehler, 1922

Figure 4. Digital images of Amphioplus sp.; A, ventral view; B, dorsal view; C, arm in dorsal view; SEM images of Amphipholis squamata; D, dorsal view; E, ventral view. Abbreviations: AS, adoral shield; DAP, dorsal arm plate; GP, genital plates; LAP, lateral arm plate; OP, oral papillae; OS, oral shield; RS, radial shield; VAP, ventral arm plate. Scale bars in millimetres.

opencc-by-4.0Aug 2008View details →

Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g in Termite soldier defence strategies: a reassessment of Prestwich's classification and an examination of the evolution of defence morphology using extended eigenshape analyses of head morphology

Figure 9. Mapped and reconstructed soldier head shapes positioned across a Termitidae phylogeny. Nodes a–g are referred to in the text.

opencc-by-4.0Mar 2021View details →

CNN models and training, validation and test datasets for "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"

Convolutional neural network (CNN) models and their respective training, validation and test datasets used in manuscript: Tuomo Hartonen, Teemu Kivioja and Jussi Taipale, "PlotMI: interpretation of pairwise interactions and positional preferences learned by a deep learning model from sequence data"

opencc-by-4.0Sep 2021View details →

Data Materials for Fortune Telling Studies: Positive Fortune Telling Enhances Men's Financial Risk Taking

We share the data materials for three studies and a meta-analysis on the effects of positive fortune telling on enhancing men's financial risk taking. A paper entitled as "Positive Fortune Telling Enhances Men’s Financial Risk Taking" was written up for publication.

opencc-by-4.0Sep 2021View details →

Realistic complex geoelectric model with topography, curved layers with the airborne electromagnetic (AEM) system positions and dBz/dt signals

The uploaded files contain the description of the complex model that is used to provide some computational experiments.It is a realistic complex geoelectric model with topography, curved layers, 3-D objects of complex shape, and a fragment of a real observation system containing several thousand AEM system positions. The observation system file also includes dBz/dt values obtained in the measuring points. The model is described with several archieved text files which format is explained in the "readme.txt" file.

opencc-by-4.0Feb 2021View details →

Atlas of false-positive bundles for RecobundlesX

This data is made to be used with the <a href="https://zenodo.org/record/4630660">Atlas for RecobundlesX</a>. In the study performed by MaierHein et al. (2017) about the ISMRM 2015 Tractography Challenge, several bundles from the submitted tractograms were labeled as false positives because they were not in the ground-truth tractogram. Quality control was performed on these bundles to select those with the most anatomical implausible trajectory. From these bundles, 44 were selected and refined to obtain smooth bundle models. v2. Streamlines outliers that were not removed with an automatic pruning step were removed manually. Maier-Hein KH, Neher PF, Houde J-C, Côté M-A, Garyfallidis E, Zhong J, et al. 2017. The challenge of mapping the human connectome based on diffusion tractography. Nat Commun 8:1349.

dryad40/100

Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

Pathogen-mediated selection and sexual selection are important drivers of evolution. Both processes are known to target genes of the major histocompatibility complex (MHC), a gene family encoding cell-surface proteins that display pathogen peptides to the immune system. The MHC is also a model for understanding processes such as gene duplication and trans-species allele sharing. The class II MHC protein is a heterodimer whose peptide-binding groove is encoded by an MHC-IIA gene and an MHC-IIB gene. However, our literature review found that class II MHC papers on infectious disease or sexual selection included IIA data only 18% and 9% of the time, respectively. To assess whether greater emphasis on MHC-IIA is warranted, we analyzed MHC-IIA sequence data from 50 species of vertebrates (fish, amphibians, birds, mammals) to test for polymorphism and positive selection. We found that the number of MHC-IIA alleles within a species was often high, and covaried with sample size and number of MHC-IIA genes assayed. While MHC-IIA variability tended to be lower than that of MHC-IIB, the difference was only ~25%, with ~3 fewer IIA alleles than IIB. Furthermore, the unexpectedly high MHC-IIA variability showed clear signatures of positive selection in most species, and positive selection on MHC-IIA was stronger in fish than in other surveyed vertebrate groups. Our findings underscore that MHC-IIA can be an important target of selection. Future work should therefore expand the characterization of MHC-IIA at both allelic and genomic scales, and incorporate MHC-IIA into models of fitness consequences of MHC variation.

opencc-zeroNov 2022View details →

An in silico guided directed evolution of protease: Spotlighting the beneficial positions

Supplementary Information for "An in silico guided directed evolution of protease: Spotlighting the beneficial positions".

opencc-by-4.0Oct 2022View details →

Figures 1–2 in First host record, nesting behavior, and taxonomic position of the spider wasp genus Hesperopompilus Evans and some other Evans genera (Hymenoptera: Pompilidae)

Figures 1–2. Hesperopompilus sp. (undescribed). 1) Female dragging a Eustala anastera (Araneidae), adult or subadult female, backwards across an exposed tree rootlet, grasping the immobilized orb-weaver spider by its left second coxa with her mandibles. The spider was held slightly above the substrate in a cephalothorax upright position. 2) Female in front of her nest entrance excavating a burrow in sandy soil using her forelegs alternately. She held her apical antenna segments against the floor of the opening and wings flat on her dorsum. Photographs © Yukioz.

opencc-by-4.0Oct 2022View details →

Figures 3–4. Pompilid spp. and their hosts. 3 in First host record, nesting behavior, and taxonomic position of the spider wasp genus Hesperopompilus Evans and some other Evans genera (Hymenoptera: Pompilidae)

Figures 3–4. Pompilid spp. and their hosts. 3) Ammosphex anomalus, identified initially as Perissopompilus phoenix, female dragging a Xysticus sp. (Thomisidae), adult female, backwards across stony ground, grasping the femur of its right hind leg with her mandibles. Photograph © Alice Abela. 4) Xerochares expulsus female dragging an Olios giganteus (Sparassidae), immature male, backwards across the ground, grasping the trochanter of its left foreleg with her mandibles. Photograph © Kelly Harrington.

A brain-wide, annotated dataset of WFA-positive perineuronal nets and parvalbumin neurons in the adult mouse brain

Microscopy dataset for perineuronal nets and parvalbumin-positive interneurons in the adult mouse brain This dataset contains the data used in the paper titled: A Comprehensive Atlas of Perineuronal Net Distribution and Colocalization with Parvalbumin in the Adult Mouse Brain Content The dataset contains microscopy images of coronal brain slices of 7 adult mice and several kinds of biological annotations. For each mouse, the annotations contain information about: <ul> <li>Several files related to the alignment of each brain slice to the Allen Brain Institute CCFv3 atlas (for a more detailed description see <a href="https://github.com/LeonardoLupori/brainAlignment">here</a>)</li> <li>Location of individual PNNs and PV cells in each slice</li> </ul> Folder Structure There are separate folders for each mouse. Each folder is named with the ID of that mouse. Each mouse folder contains: <ol> <li>a MOUSEID-info.xml file - Contains general information for the mouse and images</li> <li>a MOUSEID-quicknii.xml file - Contains information for the alignment to the Allen Brain Atlas CCFv3</li> <li>a MOUSEID-visualign.json file - Contains information for the alignment to the Allen Brain Atlas CCFv3</li> <li>a counts folder - Contains annotations for PNNs and PV cell locations for each slice</li> <li>a dispField folder - Contains displacement fields for non-rigid alignment to the Allen Brain Atlas CCFv3</li> <li>a hiRes folder - Contains original, full-resolution, experimental images</li> <li>a masks folder - Contains binary masks for restricting the analysis</li> <li>a thumbnails folder - Contains low-resolution</li> </ol> Files Description <ul> <li>MOUSEID-info.xml <ul> <li>XML file containing information about this mouse and details on each image</li> </ul> </li> <li>MOUSEID-quicknii.xml <ul> <li>XML file used for global alignment of all the images to the CCFv3 using the software <a href="https://www.nitrc.org/projects/quicknii">QuickNII</a></li> </ul> </li> <li>MOUSEID-visualign.json <ul> <li>JSON file used for the interactive local non-rigid alignment of brain slices to the CCFv3 using the software <a href="https://www.nitrc.org/projects/visualign">VisuAlign</a></li> </ul> </li> <li>counts folder <ul> <li>Folder containing two .csv files for each high-resolution image. Each .csv file contains the (x,y) location of all PNNs (channel 1) and PV cells (channel 2) detected in that image</li> </ul> </li> <li>dispField folder <ul> <li>This folder contains displacement fields in the X and Y direction for each image. These files are meant to be loaded in MATLAB and fed to the function <a href="https://it.mathworks.com/help/images/ref/imwarp.html">imwarp</a>. This function can be used to apply a non-rigid transformation to the reference volume slices in order for it to closely match experimental images.</li> </ul> </li> <li>hiRes folder <ul> <li>Folder containing high-resolution experimental images split by channels</li> </ul> </li> <li>masks folder <ul> <li>Folder containing binary masks. These files are used to restrict the analysis to portions of the image containing biological tissue and to exclude areas where the tissue was damaged or presented artifacts</li> </ul> </li> <li>thumbnails folder <ul> <li>Folder containing a low-resolution RGB version of the experimental images </li> </ul> </li> </ul>

Positive Thompson Permutations of width 7

Almost a decade ago Vaughan Jones introduced a method to produce knots from elements of the Thompson groups $F$. Later, it was extended to the Brown-Thompson group $F_3$. We defined a way to produce permutations out of elements of these groups. We call these permutations Thompson permutations. The number of orbits of each Thompson permutation coincides with the number of connected components of the link. Here are 1350210 Thompson permutations produced by positive elements of width 7.

Text-fig. 2. Geological setting of the studied sites. a: Stratigraphic position of the Mospyne Formation in the Carboniferous succession of the Donets Basin. b: Stratigraphic position of the studied locality of ammonoids (numbers in circles to the right of the lithological column). c–f: Some studied localities, c – stratigraphic level with ammonoids No. 8, d – stratigraphic level No. 4, e – stratigraphic level No. 3, f – part of the section of the Mospyne Formation in Sukha Ravine and the position of stratigraphic levels with ammonoids. Abbreviations: Tour. – Tournaisian, Serpukhov. – Serpukhovian, Kasimov. – Kasimovian. in Late Bashkirian Ammonoids From The Mospyne Formation Of The Donets Basin, Ukraine

Text-fig. 2. Geological setting of the studied sites. a: Stratigraphic position of the Mospyne Formation in the Carboniferous succession of the Donets Basin. b: Stratigraphic position of the studied locality of ammonoids (numbers in circles to the right of the lithological column). c–f: Some studied localities, c – stratigraphic level with ammonoids No. 8, d – stratigraphic level No. 4, e – stratigraphic level No. 3, f – part of the section of the Mospyne Formation in Sukha Ravine and the position of stratigraphic levels with ammonoids. Abbreviations: Tour. – Tournaisian, Serpukhov. – Serpukhovian, Kasimov. – Kasimovian.