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861 results for “collagen I”
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences
<p>Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher-order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher-order relationships. Such analyses are rightfully regarded as the 'gold standard' for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. In contrast some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher-order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ~293 million years (Ma), the base of Teleostei at ~211 Ma and the radiation of percomorphs beginning at ~141 Ma (~350 Ma, ~250–283 Ma and ~120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing.</p>
Data manuscript: Preventive training does not interfere with mRNA-encoding myosin and collagen expression during pulmonary arterial hypertension
<p>Supporting Information files of manuscript: Preventive training does not interfere with mRNA-encoding myosin and collagen expression during pulmonary arterial hypertension </p> <p> </p> <p>The values behind the means, standard deviations and values used to build graphs; </p>
Raw, unprocessed SEM data images for: Figure 1: Scanning electron microscope images of "type-1 bone collagen" demineralized bone matrix fibrils
<p>Raw, unprocessed SEM data images for Figure 1 of the manuscript: Scanning electron microscope images of "type-1 bone collagen" demineralized bone matrix fibrils. (A) Fibrils from the <em>B</em>. <em>taurus</em> extant long bone control. Prominent banding (~67nm) is present that is characteristic of type-1 collagen protein fibrils (Boatman et al., 2019; Gottardi et al., 2016; Lin et al., 1993; Rabotyagova et al., 2008; Tzaphlidou, 2005). (B) Permafrost YG 610.2397 <em>M</em>. <em>primigenius</em> demineralized bone matrix fibrils. An ~67nm banding pattern on the fibrils is also observed but is somewhat less distinct in comparison to that of the extant <em>B</em>. <em>taurus</em> specimen. (C) Observed fibril structures in the temperate MOR 91.72 <em>M</em>. <em>columbi</em> specimen. Fibril banding is generally absent, suggesting the original chemical state of the type-1 collagen fibrils/sequences is substantially altered.</p>
Data from: Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons
<p>This dataset is originally used in:</p> <p>I. Silva Barreto, M. Pierantoni, M. Hammerman, E. Törnquist, S. Le Cann, A. Diaz, J. Engqvist, M. Liebi, P. Eliasson, H. Isaksson, <em>Nanoscale characterization of collagen structural responses to in situ loading in rat Achilles tendons</em>, <strong>Matrix Biology</strong> (2022), doi:https://doi.org/10.1016/j.matbio.2022.11.006</p> <p><strong>Abstract:</strong> The specific viscoelastic mechanical properties of Achilles tendons are highly dependent on the structural characteristics of collagen at and between all hierarchical levels. Research has been conducted on the deformation mechanisms of positional tendons and single fibrils, but knowledge about the coupling between the whole tendon and nanoscale deformation mechanisms of more commonly injured energy-storing tendons, such as Achilles tendons, remains sparse. By exploiting the highly periodic arrangement of tendons at the nanoscale, <em>in situ</em> loading of rat Achilles tendons during small-angle X-ray scattering acquisition was used to investigate the collagen structural response during load to rupture, cyclic loading and stress relaxation. The fibril strain was substantially lower than the applied tissue strain. The fibrils strained linearly in the elastic region of the tissue, but also exhibited viscoelastic properties, such as an increased stretchability and recovery during cyclic loading and fibril strain relaxation during tissue stress relaxation. We demonstrate that the changes in the width of the collagen reflections could be attributed to strain heterogeneity and not changes in size of the coherently diffracting domains. Fibril strain heterogeneity increased with applied loads and after the toe region, fibrils also became increasingly disordered. Additionally, a thorough evaluation of radiation damage was performed. In conclusion, this study clearly displays the simultaneous structural response and adaption of the collagen fibrils to the applied tissue loads and provide novel information about the transition of loads between length scales in the Achilles tendon.</p> <p>Any queries related to the data set or the publication may be directed to Hanna Isaksson by email (hanna.isaksson@bme.lth.se).</p>
Abdominal vagus nerve stimulation alleviates collagen-induced arthritis in rats
<p><span>Rheumatoid arthritis (RA) is a chronic, autoimmune inflammatory disease. Despite therapeutic advances, a significant proportion of RA patients are resistant to pharmacological treatment. Stimulation of the cervical vagus nerve is a promising alternative bioelectric neuromodulation therapeutic approach. However, recent clinical trials show cervical vagus nerve stimulation (VNS) was not effective in a significant proportion of drug-resistant RA patients. Here we aim to assess if abdominal vagus nerve stimulation reduces disease severity in a collagen-induced arthritis (CIA) rat model.</span><span> The abdominal vagus nerve of female Dark Agouti rats was implanted and CIA-induced using collagen type II injection. VNS (</span><span>1.6 mA, 200 µs pulse width, 50 µs interphase gap, 27 Hz frequency)</span><span> was applied to awake freely moving rats </span><span>for 3 h/day (</span><span>days 11–17). A</span><span>t 17 days following the collagen injection,</span><span> unstimulated CIA rats (n = 8) had significantly worse </span><span>disease activity index, </span><span>tumour necrosis factor-alpha (</span><span>TNF) and </span><span>receptor activator of NF</span><span>k</span><span>B ligand (</span><span>RANKL) levels, synovitis and cartilage damage than normal rats (n = 8, </span><span>Kruskal-Wallis:</span> <span><em>P</em> </span><span>< 0.05). However, </span><span>stimulated CIA rats (n = 5-6) had significantly decreased inflammatory scores and ankle swelling (Kruskal-Wallis: </span><span>P</span><span> < 0.05) compared to unstimulated CIA rats (n = 8). Levels of tumour necrosis factor-alpha (TNFα) remained at undetectable levels in stimulated CIA rats while levels of receptor activator of NF</span><span>k</span><span>B ligand (RANKL) were significantly less in stimulated CIA rats compared to unstimulated CIA rats (</span><em><span>P</span></em><span> < 0.05). Histopathological score of inflammation and cartilage loss in stimulated CIA rats were no different from that of normal (</span><span><em>P</em> </span><span>></span><span> 0.05). In conclusion, abdominal VNS alleviates CIA and could be a promising therapy for patients with RA.</span></p>
Collagen fiber images and centerline annotations based on SHG imaging
<p>The dataset contains images of collagen fibers collected using SHG and manual annotations of the fiber centerlines, from sections of the pancreas, kidney, and breast.</p>
High-Purity Type I Collagen Nerve Wrapping in Peripheral Nerve Procedures: A Prospective Registry
ClinicalTrials.gov study NCT07360730. IPD Sharing: YES. Countries: 1. Publications: 10.
Multicentric RCT Comparing High Purity Type I Collagen-Skin Substitute vs dHACM in Treatment of Diabetic Foot Ulcers
ClinicalTrials.gov study NCT07046403. IPD Sharing: NO. Countries: 1. Publications: 8.
Safety and Effectiveness of Collagen-phosphorylcholine Bioengineered Cornea in Patients Requiring Lamellar Keratoplasty
ClinicalTrials.gov study NCT02277054. IPD Sharing: NO. Countries: 1. Publications: 2.
Evaluation of OSSIX-Plus Resorbable Collagen Membranes for Alveolar Ridge Preservation Following Exodontia
ClinicalTrials.gov study NCT00639860. IPD Sharing: NO. Countries: 1. Publications: 1.
Treatment of Full-Thickness Wounds: NPWT Combined With Type-I Collagen Based Advanced Skin Substitute Versus NPWT Alone
ClinicalTrials.gov study NCT06873867. IPD Sharing: NO. Countries: 1. Publications: 4.
Comparison of Processed Nerve Allograft and Collagen Nerve Cuffs for Peripheral Nerve Repair
ClinicalTrials.gov study NCT01809002. IPD Sharing: NO. Countries: 1. Publications: 1.
The Horizontal Ridge Augmentation Using Equine Xenograft and a Collagenated Porcine Cortical Lamina
ClinicalTrials.gov study NCT04376060. IPD Sharing: YES. Countries: 1. Publications: 3.
Efficacy, Safety and Pharmacokinetic Profile of a Collagen Bupivacaine Implant in Men After Open Mesh Herniorrhaphy
ClinicalTrials.gov study NCT00626886. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Ologen Collagen Matrix Safety and Effective Comparison With Mitomycin-C(MMC) in Glaucoma Surgery
ClinicalTrials.gov study NCT00538590. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Simultaneous TransPRK and Corneal Collagen Cross-Linking
ClinicalTrials.gov study NCT02208089. IPD Sharing: Not stated. Countries: 1. Publications: 2.
High-Purity Type I Collagen Augmentation in Meniscal Repair
ClinicalTrials.gov study NCT07352410. IPD Sharing: NO. Countries: 1. Publications: 8.
Ridge Preservation Using a Ossix™ Bone vs Bio-Oss® Collagen
ClinicalTrials.gov study NCT04338516. IPD Sharing: NO. Countries: 1. Publications: 1.
HRIPT for Collagen Dressing
ClinicalTrials.gov study NCT06283173. IPD Sharing: NO. Countries: 1. Publications: 1.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.