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2,788 results for “remodeling”
Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
<p><span>Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish <i>Astatotilapia burtoni</i>. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.</span></p>
Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling
<p>Scripts associated with the analysis and plotting of data for the Cell paper: Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling</p>
Remodeling dental anatomy vs sham therapy for chronic temporomandibular disorders: A placebo-controlled randomized clinical trial
<div><em>Background</em></div> <div>Evidence regarding the etiology or effective treatments for chronic orofacial pain, the majority diagnosed as temporomandibular disorder (TMD), is limited.</div> <div> </div> <div><em>Purpose</em></div> <div>To investigate whether occlusal equilibration therapy (ET) and decreasing the (higher) angle of the lateral guidance on the nonworking-side leads to a reduction in chronic TMDs intensity.</div> <div> </div> <div><em>Methods</em></div> <div>It was conducted a randomized, explanatory, single blind with blinded assessment, placebo-controlled trial with strong protection against bias involving patients with chronic TMDs. Participants were randomly assigned to receive equilibration therapy or sham therapy. ET in this study consisted of minimal invasive occlusal remodeling to obtain balanced occlusion with reduction of the steeper angle of lateral mandibular movement with respect to the Frankfort plane. The primary outcome was a change in the pain intensity score (on a 0–10 point scale, with 0 indicating no pain and 10 the worst possible pain) at month 6. Secondary outcomes include maximum unassisted mouth opening and psychological distress.</div> <div> </div> <div><em>Results</em></div> <div>A total of 77 participants underwent randomization, 39 of whom received ET and 38 sham therapy. The trial was stopped early for efficacy, according to preestablished rules when 67 participants (n = 34, n = 33, respectively) had completed the analysis. At month 6, the mean unadjusted pain intensity score was 2.1 in the ET and 3.6 in the sham therapy group (adjusted mean difference, −1.54; 95% confidence interval [CI] −0.5 to −2.6; P = 0.004; ANCOVA model). The mean increase in maximum unassisted mouth opening (main secondary outcome) was significantly higher in the real therapy group (adjusted mean difference 3.1 mm, 95% CI 0.5–5.7, p = 0.02).</div> <div> </div> <div><em>Conclusion</em></div> <div>ET significantly reduced the intensity of facial pain associated with chronic TMDs and increased maximum unassisted mouth opening, as compared with sham therapy, over the course of 6 months. There were no serious adverse events.</div>
REMODEL. WP5. Cable Manipulation Planning, Execution and Interactive Perception. T5-3. Bimanual wire and cable manipulation. Data related to a paper for the conference SysInt 2022
<p>The datasets contain data recorded during the experiment reported in the paper:</p> <p>G. Laudante, and S. Pirozzi, “An Intelligent System for Human Intent and Environment Detection Through Tactile Data,” 6th International Conference on System-Integrated Intelligence (SysInt 2022), Genova, Italy. (DOI: 10.1007/978-3-031-16281-7_47)</p>
Dataset for "Pan-cancer integrative analyses dissect the remodeling of endothelial cells in human cancers"
<p>This is the dataset for "Pan-cancer integrative analyses dissect the remodeling of endothelial cells in human cancers".</p> <p> </p> <p>File "NSR.panE.exprs.all.h5ad.gz" contains processed expression .h5ad data.</p> <p>File "NSR.panE.obs.meta.csv" contains the meta data for this study.</p> <p>File "umap.zip" contains the .csv files for umap coordinates.</p> <p> </p> <p> </p>
Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition
<p>Unprocessed Solid-state NMR and Molecular Dynamics data sets for the manuscript titled "Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition"</p>
Structural coronary artery remodelling in the rabbit fetus as a result of intrauterine growth restriction
<p>Segmentation of the coronary arteries in synchrotron X-Ray Phase Contrast images from 8fetal rabbit hearts: 4 controls (healthy), and the other 4 with intrauterine growth restriction (IUGR).</p>
Data - Medial gastrocnemius muscle remodeling correlates with reduced plantar flexor kinetics fourteen weeks following Achilles tendon rupture
<p>ultrasound images and biodex data published used in analysis.</p> <p>study timeline:</p> <p>s1 - week 0</p> <p>s2 - week 2</p> <p>s3 - week 4</p> <p>s4 - week 6</p> <p>s5 - week 10</p> <p>s6 - week 14</p>
Data described in the article "Three-step enzymatic remodeling of chitin into bioactive chitooligomers"
<p>The Supporting Information file contains the following data: <span>PCR primers and reaction conditions for the generation of <em>Tf</em>Chit mutants; HPLC chromatogram of chitin hydrolysate; detailed sequence alignment; computational data; additional figures for modeling of <em>Tf</em>Chit;</span><span> <span>MALDI-TOF MS analysis of a mixture of insoluble chitooligomers prepared by Y445N <em>Ao</em>Hex, and <em>m/z</em> values monitored by HPLC-MS of the deacetylation reactions.</span></span></p>
Automated Model Discovery for Tensional Homeostasis: Constitutive Machine Learning in Growth and Remodeling (Source code and data)
<p>This dataset contains</p> <ul> <li>the source code</li> <li>the data and examples</li> <li>the material subroutine with examples of uniaxial strain and stress</li> </ul> <p>of the inelastic Constitutive Artificial Neural Network (iCANN) enhanced by the concept of homeostatic surfaces to discover tensional homeostasis.</p> <p>The corresponding publication is:</p> <p>Holthusen, H., Brepols, T., Linka, K., & Kuhl, E..<em> </em></p> <p><em>Automated Model Discovery for Tensional Homeostasis: Constitutive Machine Learning in Growth and Remodeling.</em></p> <p> </p> <p><strong>Standalone_Materialroutine</strong></p> <ul> <li>00_Materialroutine: Contains the material subroutine implemented in FORTRAN</li> <li>01_uniaxial_strain: Example of the material subroutine in a uniaxial strain driven manner</li> <li>02_uniaxial_stress: Example of the material subroutine in a uniaxial stress driven manner</li> </ul> <p> </p> <p><strong>TensorFlow</strong></p> <ul> <li> <p>iCANN:</p> <ul> <li> <p>01_Biax/biax_l1: Keras/TensorFlow implementation of the iCANN. Example of the cross specimen with L1 (Lasso) regularization</p> </li> <li> <p>01_Biax/biax_l2: Keras/TensorFlow implementation of the iCANN. Example of the cross specimen with L2 (ridge) regularization</p> </li> <li> <p>02_Uniax/uniax_l1: Keras/TensorFlow implementation of the iCANN. Example of the stripe specimen with L1 (Lasso) regularization</p> </li> <li>02_Uniax/uniax_l1: Keras/TensorFlow implementation of the iCANN. Example of the stripe specimen with L2 (ridge) regularization</li> </ul> </li> <li> <p>iCANN_ABS_activation: Same four examples as above, however, with the absolute value activation function</p> </li> <li> <p>installed_packages: File containing a list of installed Python modules used to implement the iCANN</p> </li> </ul> <p>The TensorFlow implementations in all 01_Biax/ and 02_Uniax/ sub-directories are the same.</p> <p>The implementation in iCANN_ABS_activation is different with respect to the activation functions of the pseudo potential.</p> <p> </p> <p>The experimental data for the cross and stripe specimen are taken from the literature:</p> <p>Eichinger, J. F., Paukner, D., Szafron, J. M., Aydin, R. C., Humphrey, J. D., & Cyron, C. J. (2020).</p> <p>Computer-controlled biaxial bioreactor for investigating cell-mediated homeostasis in tissue equivalents. <em>Journal of biomechanical engineering</em>, <em>142</em>(7), 071011.</p> <p><a href="https://doi.org/10.1115/1.4046201">https://doi.org/10.1115/1.4046201</a></p>
Data from: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression
Organismal responses to light:dark cycles can result from two general processes: (i) direct response to light or (ii) a free-running rhythm (i.e., a circadian clock). Previous research in cnidarians has shown that candidate circadian clock genes have rhythmic expression in the presence of diel lighting, but these oscillations appear to be lost quickly after removal of the light cue. Here, we measure whole-organism gene expression changes in 136 transcriptomes of the sea anemone Nematostella vectensis, entrained to a light:dark environment and immediately following light cue removal to distinguish two broadly defined responses in cnidarians: light entrainment and circadian regulation. Direct light exposure resulted in significant differences in expression for hundreds of genes, including more than 200 genes with rhythmic, 24-hour periodicity. Removal of the lighting cue resulted in the loss of significant expression for 80% of these genes after one day, including most of the hypothesized cnidarian circadian genes. Further, 70% of these candidate genes were phase shifted. Most surprisingly, thousands of genes, some of which are involved in oxidative stress, DNA damage response, and chromatin modification, had significant differences in expression in the 24 hours following light removal, suggesting that loss of the entraining cue may induce a cellular stress response. Together, our findings suggest that a majority of genes with significant differences in expression for anemones cultured under diel lighting are largely driven by the primary photoresponse rather than a circadian clock when measured at the whole animal level. These results provide context for the evolution of cnidarian circadian biology and help to disassociate two commonly confounded factors driving oscillating phenotypes.
Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements
<p>Structural variant calls, RepeatMasker annotations, and genome assemblies of diverse mouse genomes. </p>
Microvascular network remodeling in the ischemic brain defined by light sheet microscopy
<p>This dataset contains the raw image data set used in the study entitled "Microvascular network remodeling in the ischemic brain defined by light sheet microscopy" by Hagemann et al.. Images were analysed using VesselExpress software (see also <a href="https://pubmed.ncbi.nlm.nih.gov/37056368/">https://pubmed.ncbi.nlm.nih.gov/37056368/</a>) using the provided config file with gamma values ranging from 50 to 400.</p>
Mathematical model results for: Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration
<p>Collective cell migration plays an essential role in vertebrate development, yet the extent to which dynamically changing microenvironments influence this phenomenon remains unclear. Observations of the distribution of the extracellular matrix (ECM) component fibronectin during the migration of loosely connected neural crest cells (NCCs) lead us to hypothesize that NCC remodeling of an initially punctate ECM creates a scaffold for trailing cells, enabling them to form robust and coherent stream patterns. We evaluate this idea in a theoretical setting by developing an agent-based model that incorporates reciprocal interactions between NCCs and their ECM. ECM remodeling, haptotaxis, contact guidance, and cell-cell repulsion are sufficient for cells to establish streams in silico, however additional mechanisms, such as chemotaxis, are required to consistently guide cells along the correct target corridor. Further investigations of the model imply that contact guidance and differential cell-cell repulsion between leader and follower cells are key contributors to robust collective cell migration by preventing stream breakage. Global sensitivity analysis and simulated underexpression/overexpression experiments suggest that long-distance migration without jamming is most likely to occur when leading cells specialize in creating ECM fibers, and trailing cells specialize in responding to environmental cues by upregulating mechanisms such as contact guidance. This dataset contains summary statistics, movies, parameter values, and photos obtained from individual realizations of the mathematical model.</p>
Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"
<p># Code and data for "Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages"</p> <p><br> - `pipeline` contains scripts for processing raw reads with `nf-core/rnaseq` Nextflow pipeline<br> - `setup_conda.sh` sets up a conda environment for Nextflow<br> - `samplesheet.csv` describes the samples<br> - `rna-seq-nextflow.sh` runs the analysis<br> - `data` contains the quantifications by Salmon from the pipeline and data for the CRE motif (see `analysis.Rmd` for more details)<br> - `analysis.Rmd` an R notebook containing a code to reproduce conclusions and figures in the paper and additional comments.</p> <p>The R environment (all packages) is reproducibly reconstructed via `renv` - run `renv::restore()` after loading the project.</p> <p>The generated figures and tables are stored in the `outputs` directory.</p> <p> </p>
Balloon REmodeling Antrostomy THErapy Study
ClinicalTrials.gov study NCT00645762. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Impact of Diabetes on Left Ventricular Remodeling
ClinicalTrials.gov study NCT01052272. IPD Sharing: Not stated. Countries: 1. Publications: 39.
Role of Nitric Oxide in the Impact of Aging on Myocardial Remodeling
ClinicalTrials.gov study NCT00603720. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Anakinra to Prevent Adverse Post-infarction Remodeling (2)
ClinicalTrials.gov study NCT01175018. IPD Sharing: NO. Countries: 1. Publications: 5.
The Effects of Sacubitril/Valsartan Compared to Valsartan on LV Remodelling in Asymptomatic LV Systolic Dysfunction After MI
ClinicalTrials.gov study NCT03552575. IPD Sharing: NO. Countries: 1. Publications: 2.
ScienceDex guides
Understand access before you commit
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.