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16807 thoracolumbar osteo-ligamentous spine virtual FE input files (part-16: model 15295 to 16295)
<p><em><strong>16807 thoracolumbar osteo-ligamentous spine virtual FE input files (part-16: model 15295 to 16295)</strong></em></p> <ul> <li>16807 FE input files representing thoracolumbar spine hexahedral models, including point coordinates. To reduce the size of shared virtual finite element (FE) models, only point coordinates are shared here. The mean FE input file "<a href="https://zenodo.org/api/files/bdc067d7-cb7d-40b7-9974-5ada43e1a0c5/Mean_Model%20%28Template%29.inp">Mean_Model (Template).inp</a>" is also shared, which includes point coordinates, mesh connectivity IDs, and element sets. To generate virtual FE input files for any of the 16807 models, the corresponding shared point coordinates can be replaced into the mean FE input file (<a href="https://zenodo.org/api/files/bdc067d7-cb7d-40b7-9974-5ada43e1a0c5/Mean_Model%20%28Template%29.inp">Mean_Model (Template).inp</a>). Mesh connectivity IDs, and element sets are the same in all of FE input files. Mean FE input file includes vertebras and IVDs hexahedral meshes; pelvis, sacrum, and the femoral head triangulated meshes; and ligaments. Each point coordinate file is almost 39MB.</li> <li>An excel file: "<a href="https://zenodo.org/api/files/bdc067d7-cb7d-40b7-9974-5ada43e1a0c5/Descriptive_List%20%2816807_FE_virtual_models%29.xlsx">Descriptive_List (16807_FE_virtual_models).xlsx</a>" reporting measured spinopelvic parameters for 16807 virtual FE hexahedral models. The Excel file includes measured spinopelvic parameters (PI, PT, SS, LL, LL-PI, GT, RPV, RLL, LDI, RSA, TPA, and scoliosis cobb angle), GAP and IVD centric thickness for FE virtual cohort. Model ID in the excel file is correspondent to the model’s name.</li> <li>One video file: "how_to_replace_point_coordinates.mp4". It shows how you can replace point coordinates here to the mean FE input file "<a href="https://zenodo.org/api/files/bdc067d7-cb7d-40b7-9974-5ada43e1a0c5/Mean_Model%20%28Template%29.inp">Mean_Model (Template).inp</a>" in order to generate specific FE input file.</li> </ul> <p><em><strong>Notes:</strong></em></p> <p>1- Model number in "<a href="https://zenodo.org/api/files/bdc067d7-cb7d-40b7-9974-5ada43e1a0c5/Descriptive_List%20%2816807_FE_virtual_models%29.xlsx">Descriptive_List (16807_FE_virtual_models).xlsx</a>" is correspondent to the same model number in the 16807 stereolithography (stl) files (.stl extension) representing the virtual thoracolumbar spine triangulated meshes (DOI: 10.5281/zenodo.7715658; stl.part01.rar to stl.part09.rar).</p> <p>2-These point coordinates are sampled by combining the first 5 shape modes of the morphed-mesh statistical shape model in which each shape mode is discretized into 7 standard deviations: -3, -2, -1, 0, 1, 2, 3.</p> <p>3- Generated FE inp files can be opened by Abaqus 2019 and later. Any other FE software which supports .inp extension also can open the files.</p> <p><em><strong>Developed by: </strong></em>Morteza Rasouligandomani (Ph.D. student in biomedical engineering, Pompeu Fabra university, BCN Med-Tech group, DTIC department, Barcelona, Spain).</p> <p>Email contact: morteza.rasouli@upf.edu</p>
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm in Fossil dipsadid snakes from the Guadeloupe Islands (French West-Indies) and their interactions with past human populations
IG. 6. — A, Trunk vertebra of Alsophis sp. 2 from Pointe du Helleux archaeological site (Square 2 – crab layer) located on Grande-Terre Island; B, trunk vertebra of Erythrolamprus juliae cf. copeae (Parker, 1936) from Sainte-Rose La Ramée archaeological site (US 2058) located on Basse-Terre Island. Abbreviations: cd., condyle; ct., cotyle; di., diapophysis; h. k., hemal keel; m. c., medial constriction; n. a., neural arch; n. s., neural spine; p. c., precondylar constriction; p. d., paracotylar depression; p. n., postero-medial notch of the zygantrum; pa., parapophysis; pz. f., prezygapophyseal facet; pz. p., prezygapophyseal process; s. d., subcentral depression; s. r., subcentral ridge; s. t., sub-cotylar tubercle; zs., zygosphene. Scale bars: 4 mm
Annotated T2-weighted MR images of the Lower Spine
<p><strong>Annotated T2-weighted MR images of the Lower Spine</strong></p> <p>Chengwen Chu, Daniel Belavy, Gabriele Armbrecht, Martin Bansmann, Dieter Felsenberg, and Guoyan Zheng </p> <p><strong>Introduction</strong><br /> The Institute for Surgical Technology and Biomechanics, University of Bern, Switzerland, Charité - University Medicine Berlin, Centre of Muscle and Bone Research, Free University & Humboldt-University Berlin, Germany, Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University Burwood Campus, Australia and Institut für Diagnostische und Interventionelle Radiologie, Krankenhaus Porz Am Rhein gGmbH, Köln, Germany, are making this dataset available as a resource in the development of algorithms and tools for spinal image analysis.</p> <p><strong>Description</strong><br /> The database consists of T2-weighted turbo spin echo MR spine images of 23 anonymized patients, each containing at least 7 vertebral bodies (VBs) of the lower spine (T11 – L5). For each vertebral body, reference manual segmentation is provided in the form of a binary mask. All images and binary masks are stored in the Neuroimaging Informatics Technology Initiative (NIFTI) file format, see details at http://nifti.nimh.nih.gov/. Image files are stored as "Img_xx.nii" while the associated annotation files are stored as "Img_xx_Labels.nii", where "xx" is the internal case number for the patient. </p> <p>Image annotations were prepared by Mr. Chengwen Chu (no professional training in radiology). </p> <p><strong>Acknowledgements</strong></p> <ul> <li>The acquisition of original images was supported by the Grant 14431/02/NL/SH2 from the European Space Agency, grant 50WB0720 from the German Aerospace Center (DLR) and the Charité Universitätsmedizin Berlin.</li> <li>Preparation of this data collection was made possible thanks to the funding from the Swiss National Science Foundation (SNSF) through project: 205321 157207/1.</li> </ul> <p><strong>Reference</strong><br /> C. Chu, D. Belavy, W. Yu, G. Armbrecht, M. Bansmann, D. Felsenberg, and G. Zheng, “Fully Automatic Localization and Segmentation of 3D Vertebral Bodies from CT/MR Images via A Learning-based Method”, <strong>PLoS One</strong>. 2015 Nov 23;10(11):e0143327. doi: 10.1371/journal.pone.0143327. eCollection 2015.</p>
Data and R script for: Shoaling behaviour in response to turbidity in three-spined sticklebacks
<p class="MsoNormal"><span>Many fresh and coastal waters are becoming increasingly turbid because of human activities, which may disrupt the visually-mediated behaviours of aquatic organisms. Shoaling fish typically depend on vision to maintain collective behaviour, which has a range of benefits including protection from predators, enhanced foraging efficiency, and access to mates. Previous studies of the effects of turbidity on shoaling behaviour have focussed on changes to nearest neighbour distance and average group-level behaviours. Here, we investigated whether and how experimental shoals of three-spined sticklebacks (<em><span>Gasterosteus aculeatus</span></em>) in clear (<10 <span>Nephelometric Turbidity Units (NTU))</span> and turbid (~35 NTU<span>) </span>conditions differed in five local-level behaviours of individuals (nearest and furthest neighbour distance, heading difference with nearest neighbour, bearing angle to nearest neighbour, and swimming speed). These variables are important for the emergent group-level properties of shoaling behaviour. We found an indirect effect of turbidity on nearest-neighbour distances driven by a reduction in swimming speed, and a direct effect of turbidity which increased variability in furthest neighbour distances. In contrast, the alignment and relative position of individuals was not significantly altered in turbid compared to clear conditions. Overall, our results suggest that the shoals were usually robust to adverse effects of turbidity on collective behaviour, but group cohesion was occasionally lost during periods of instability.</span></p>
SPIDER - Lumbar spine segmentation in MR images: a dataset and a public benchmark
<p>This is a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 studies of 218 patients with a history of low back pain. The data was collected from four different hospitals. There is an additional hidden test set, not available here, used in the accompanying SPIDER challenge on spider.grand-challenge.org. We share this data to encourage wider participation and collaboration in the field of spine segmentation, and ultimately improve the diagnostic value of lumbar spine MRI.</p> <p>Which MRI studies are assigned to the training and validation sets can be found in the overview file. This file also provides the biological sex for all patients and the age for the patients for which this was available. It also includes a number of scanner and acquisition parameters for each individual MRI study. The dataset also comes with radiological gradings found in a separate file for the following degenerative changes:</p> <p>1.    Modic changes (type I, II or III)</p> <p>2.    Upper and lower endplate changes / Schmorl nodes (binary)</p> <p>3.    Spondylolisthesis (binary)</p> <p>4.    Disc herniation (binary)</p> <p>5.    Disc narrowing (binary)</p> <p>6.    Disc bulging (binary)</p> <p>7.    Pfirrman grade (grade 1 to 5). </p> <p>All radiological gradings are provided per IVD level.</p> <div>This dataset, and the associated public benchmark, are described in this paper: <a href="https://www.nature.com/articles/s41597-024-03090-w" target="_blank" rel="noopener">https://www.nature.com/articles/s41597-024-03090-w</a></div> <div>The public segmenation challenge can be found here: <a href="https://spider.grand-challenge.org/" target="_blank" rel="noopener">https://spider.grand-challenge.org/</a></div> <div> </div> <div>When using this dataset, please cite this dataset with the correct DOI, and also cite the afformentioned paper.</div>
Maternal body condition affects the response of the gut microbiome to a widespread contaminant in larval spined toads
<p>Datasets (metadata and phyloseq object) </p> <p>Scripts used for the statistical analyses</p>
Fig. 1 in First Japanese Records of the Indo-Pacific Scorpionfish (Scorpaenidae) Scorpaenodes corallinus, with a Re-evaluation of Coronal Spines as a Diagnostic Character
Fig. 1. Fresh specimen of Scorpaenodes corallinus (KAUM–I. 58534, 80.0 mm SL, off Tomori, Yoron Island, Amami Islands, Japan).
Fig. 2 in First Japanese Records of the Indo-Pacific Scorpionfish (Scorpaenidae) Scorpaenodes corallinus, with a Re-evaluation of Coronal Spines as a Diagnostic Character
Fig. 2. Underwater photograph of Scorpaenodes corallinus from Japan (KPM-NR 80574, Unanzaki, Aka Island, Kerama Islands, 18 m depth, 26 October 2001, taken by A. Moriyama).
Fig.ç5.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, dorsal view; B, segment 4, dorsal view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; mds, middorsal spine; pac, pachycyclus; pf, pectinate fringe; ps, perforation site; rss, rounded sensory spot. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç5.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 1 and 2, dorsal view; B, segment 4, dorsal view. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; mds, middorsal spine; pac, pachycyclus; pf, pectinate fringe; ps, perforation site; rss, rounded sensory spot.
Fig.ç3.Ec hinoderes ohtsukai sp. nov., scanning electron micrographs. A, B, Paratype, female (ZIHU 3983); C–E, paratype, male (ZIHU 3982). A, General habitus, lateral view; B, neck and segments 1–4, lateral view; C, enlargement of segment 7, lateral view; D, enlargement of segment 9, lateral view; E, enlargement of segments 10 and 11, lateroventral view. Abbreviations: ch, cuticular hair; dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; pf, pectinate fringe; po, pore; ps1, penile spine 1; ps2, penile spine 2; ps3, penile spine 3; rss, rounded sensory spot; si, sieve plate; ss, sensory spot. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç3.Ec hinoderes ohtsukai sp. nov., scanning electron micrographs. A, B, Paratype, female (ZIHU 3983); C–E, paratype, male (ZIHU 3982). A, General habitus, lateral view; B, neck and segments 1–4, lateral view; C, enlargement of segment 7, lateral view; D, enlargement of segment 9, lateral view; E, enlargement of segments 10 and 11, lateroventral view. Abbreviations: ch, cuticular hair; dss, droplet-shaped sensory spot; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; pf, pectinate fringe; po, pore; ps1, penile spine 1; ps2, penile spine 2; ps3, penile spine 3; rss, rounded sensory spot; si, sieve plate; ss, sensory spot.
Fig.ç2.Ec hinoderes ohtsukai sp. nov., camera lucida drawings. A, B, Holotype, male (ZIHU 3976), entire animal, dorsal and ventral view, respectively; C, D, allotype, female (ZIHU 3977), segments 9–11, dorsal and ventral view, respectively. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; lts, lateral terminal spine; lvt, lateroventral tubule; mds, middorsal spine; ne, neck; ps, penile spine; rss, rounded sensory spot; si, sieve plate. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç2.Ec hinoderes ohtsukai sp. nov., camera lucida drawings. A, B, Holotype, male (ZIHU 3976), entire animal, dorsal and ventral view, respectively; C, D, allotype, female (ZIHU 3977), segments 9–11, dorsal and ventral view, respectively. Abbreviations: dss, droplet-shaped sensory spot; gco1, glandular cell outlet type I; gco2, modi ed glandular cell outlet type II; ldt, laterodorsal tubule; lts, lateral terminal spine; lvt, lateroventral tubule; mds, middorsal spine; ne, neck; ps, penile spine; rss, rounded sensory spot; si, sieve plate.
Fig.ç8.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 10 and 11, dorsal view; B, segments 10 and 11, ventral view. Abbreviations: ldt, laterodorsal tubule; lts, lateral terminal spine; ps1, penile spine 1; ps2, penile spine 2. in A New Brackish-water Species of Echinoderes (Kinorhyncha: Cyclorhagida) from the Seto Inland Sea, Japan
Fig.ç8.Ec hinoderes ohtsukai sp. nov., holotype, male (ZIHU 3976), Nomarski photomicrographs. A, Segments 10 and 11, dorsal view; B, segments 10 and 11, ventral view. Abbreviations: ldt, laterodorsal tubule; lts, lateral terminal spine; ps1, penile spine 1; ps2, penile spine 2.
Figure 3. Acanthodian fin spines and scapulocoracoid. A-C in Acanthodian fauna from the Early Devonian (Emsian) of Death Valley, California
Figure 3. Acanthodian fin spines and scapulocoracoid. A-C, Bryantonchus peracutus: A, B complete spine FMNH-PF14564; C, proximal end of spine FMNH-PF14568. D, E, Machaeracanthus sp.: D, incomplete spine FMNH-PF14573, lateral view; E, abraded spine FMNH-PF14574, dorsoventrally compressed. F-H, acanthodian indet. scapulocoracoid: F, counterpart FMNH-PF14575; G, part FMNH-PF14576; H, outline sketch. Abbreviations: IEB, insertion-exsertion boundary; k/w, worn keel or wing; plac, placoderm plate; le, leading edge; te, trailing edge; teg, trailing edge groove. Scale bars=0.5 mm in A, C–E, 0.1 mm in B, F–H.
Fig. 2. Juvenile Orthacanthus platypternus, Stephanian B in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 2. Juvenile Orthacanthus platypternus, Stephanian B (Upper Carboniferous) of Hamilton, USA (A) compared to juvenile of O. bohemicus, Westphalian D (Upper Carboniferous) of Bohemia, Czech Republic (B), showing the relative position of the dorsal spine. A, modified from Zidek (1993b: fig. 1); B, modified from Soler-Gijón (2004: fig. 3C).
Fig. 3 in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 3. External morphology of dorsal spines of Orthacanthus platypternus (Cope, 1884), Lower Permian, Craddock Bone Bed, Texas, USA. A. HMNS-T1, juvenile, lateral view. B. SMU 68799, juvenile, posterior view. C. SMU 68800, juvenile, posterior (C1) and postero-lateral (C2) views. D. SMU 68801, adult, denticulated, postero-lateral view (D1) and non-denticulated, posterior view (D2) regions. Numbers 1 to 17 point to the positions of the denticles along the posterior sides of the spines. Numbers 1' to 17' correspond to the right row of denticles. Grey areas in B–D2 represent sedimentary matrix. Scale bars 5 mm.
Fig. 6 in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 6. Cross-sections of dorsal spines (non-denticulated region) of Orthacanthus platypternus (Cope, 1884), Lower Permian, Craddock Bone Bed, Texas, USA. Comparison between the smallest, specimen HMNS-T1 (A), and the largest Orthacanthus dorsal spine sampled, specimen HMNS-J1 (B). Posterior sides of the spines are pointing to the top of the figure.
Fig. 9 in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 9. Bivariate plots of relationship between width and height in cross sections of Orthacanthus dorsal spines. A. Orthacanthus platypternus (Lower Permian, Craddock Bone Bed, Texas, USA). B. Comparison of O. platypternus with O. meridionalis (Upper Carboniferous, Puertollano, Spain) and Orthacanthus sp. (Upper Carboniferous, Robinson, Kansas, USA). Note the linear regression (y = 0.91x + 0.15; n = 65, r2 = 0.98) calculated by Donelan and Johnson (1997) for the isolated dorsal spines of O. platypternus. The maximum and minimal values are also included here for a comparative reference; values of the rest of the specimens are not included for clarity. Grey shaded areas indicate approximate intervals of the three size clusters corresponding to juveniles and adults according the biometric analysis by Donelan and Johnson (size intervals are based on unpublished data presented in a poster at 57th Annual Meeting of the Society of Vertebrate Paleontology, Chicago, October 1997). Note the ontogenetic trajectories of several individuals of O. platypternus (HMNS-T2 and HMNS-J3), O. meridionalis (PU-XE19, 20, 74 and 76) and Orthacanthus sp. (KUVP-72324) showing stages SP1–n spine proper). Data from O. meridionalis and Orthacanthus sp. after Soler-Gijón (1999: table 1 and figs. 4–8). Vertical grey arrows point to the position in the linear regression for SMU specimens according the maximum width values at the proximal end of denticulated regions: 3.5 mm (SMU 68799), 4.5 mm (SMU 68800) and 8.4 mm (SMU 68801). Abbreviations: SP1–5, spines 1–5; SpPr, spine proper.
Fig. 8. A in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 8. A. Reconstruction of the dorsal spine (mainly the denticulated region) of Orthacanthus platypternus, based on specimens HMNS-T1 and HMNS-T2. B, C. Reconstructions of the dorsal spine of Orthacanthus meridionalis (modified from Soler-Gijón 1999: fig. 10); PU-XE76 (B) PU-XE19 (C). Note that distal denticles belong to the first spine (juvenile). The intersection of the first major growth line and the denticulated border of the spine indicate the proximal end of the denticulated region of the first spine; the following "spines" exhibit the distal denticles and those corresponding to each new growth stage.
Fig. 5 in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 5. Serial cross-sections (A, C, D) of dorsal spine of Orthacanthus platypternus (Cope, 1884), Lower Permian, Craddock Bone Bed, Texas, USA; specimen HMNS-J3, where A represents the most proximal section and D is the most distal. B. Detail of section in A showing three minor growth lines close to the base of the right denticle in the figure (arrows).
Fig. 4 in Morphology and histology of dorsal spines of the xenacanthid shark Orthacanthus platypternus from the Lower Permian of Texas, USA: Palaeobiological and palaeoenvironmental implications
Fig. 4. Serial longitudinal sections of dorsal spine of Orthacanthus platypternus (Cope, 1884), Lower Permian, Craddock Bone Bed, Texas, USA; specimen HMNS-T2, where A represents the most proximal section and E is the most distal. Samples C–E include the denticulate region. Photos of the sections (A1–E1), interpretative drawings (A2–E2). Scale bars 1 mm.
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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.