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1,036 results for “Cell mechanics”
Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells
<p>Contains animations, data, and source code used for the paper "Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells" by the same authors. </p> <p><br>This repository contains all the data and analysis scripts to support the manuscript<br>The file structure is as follows:<br>- "analysis" contains all the analysis scripts<br>- "gfx" and "animations" the figures and supporting animations<br>- "1-SCpair", "2-SCtissue", "3-BDsimulation", "4-tissue-stochdiv", "6-inertia-effects" all the source code and data for the respective models.</p>
Schiff Base Crosslinked Hyaluronic Acid Hydrogels with Tunable and Cell Instructive Time-Dependent Mechanical Properties
<p>This folder contains raw data for the paper titled "<strong>Schiff Base Crosslinked Hyaluronic Acid Hydrogels</strong><strong> with Tunable and Cell Instructive Time-Dependent Mechanical Properties</strong>" authored by Taha Behroozi Kohlan, Yanru Wen, Carina Milena Mini, and Anna Finne-Wistrand, published in <em>Carbohydrate Polymers</em> journal. The raw data presented here contains NMR, FTIR, SEC, swelling and stability, and rheology data used to create figures.</p> <p><strong>Abstract:</strong></p> <p>The dynamic interplay between cells and their native extracellular matrix (ECM) influences cellular behavior, imposing a challenge in biomaterial design. Dynamic covalent hydrogels are viscoelastic and show self-healing ability, making them a potential scaffold for recapitulating native ECM properties. We aimed to implement kinetically and thermodynamically distinct crosslinkers to prepare self-healing dynamic hydrogels to explore the arising properties and their effects on cellular behavior. To do so, aldehyde-substituted hyaluronic acid (HA) was synthesized to generate imine, hydrazone, and oxime crosslinked dynamic covalent hydrogels. Differences in equilibrium constants of these bonds yielded distinct properties including stiffness, stress relaxation, and self-healing ability. The effects of degree of substitution (DS), polymer concentration, crosslinker to aldehyde ratio, and crosslinker functionality on hydrogel properties were evaluated. The self-healing ability of hydrogels was investigated on samples of the same and different crosslinkers and DS to obtain hydrogels with gradient properties. Subsequently, human dermal fibroblasts were cultured in 2D and 3D to assess the cellular response considering the dynamic properties of the hydrogels. Moreover, assessing cell spreading and morphology on hydrogels having similar modulus but different stress relaxation rates showed the effects of matrix viscoelasticity with higher cell spreading in slower relaxing hydrogels.</p>
Correlating single-molecule rupture mechanics with cell population adhesion by yeast display
<p>Data underlying the figures in the publication “Correlating single-molecule rupture mechanics with cell population adhesion by yeast display”, published in <em>Biophysical Reports, </em><em><strong>2022</strong></em><em>, Volume 2, Issue 1, 100035, ISSN 2667-0747.</em></p> <p><em><a href="https://doi.org/10.1016/j.bpr.2021.100035">https://doi.org/10.1016/j.bpr.2021.100035</a></em></p> <p>Table of contents:</p> <p><strong>1. Fig2_SMFS.xlsx</strong>: Contour Length vs probability density values for <em>Figure 2D</em>. Rupture Force and Loading rate values for all SMFS curves analysed for <em>Figure 2E</em> and <em>2F</em>.</p> <p><strong>2. Fig3_SDA.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values of all replicates and speeds for F<em>igures 3D</em> and <em>3E</em>.</p> <p><strong>3. FigS1_SPR curves.xlsx</strong>: SPR curves reported in Supplementary <em>Figure 1</em>.</p> <p><strong>4. FigS2_one step FLN.xlsx</strong>: Force <em>vs</em> Extension trace and Contour Length Histogram values for one step FLN unfolding shown in <em>Supplementary Figure 2</em>.</p> <p><strong>5. FigS3_SMFS_internal control.xlsx</strong>: Rupture Force and Loading rate values for N-S25H reported in <em>Supplementary Figure 3</em>.</p> <p><strong>6. FigS5_SDA_internal control.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values of N-WT shown in <em>Supplementary figure 5B</em>.</p> <p><strong>7. FigS6_SDA_induction timepoints.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values and median of expression detected by flow cytometry reported in <em>Supplementary Figure 6</em>.</p>
Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye
<p>Pattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the <em>Drosophila</em> eye into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye epithelium. Here, we find that the templating mechanism is instead, mechanical in origin; newly born columns of ommatidia serve as a template to spatially pattern cell flows that move the cells in the epithelium into position to form each new column of ommatidia. Cell flow is generated by a pressure gradient that is caused by a narrow zone of cell dilation precisely positioned behind the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.</p>
Long-term adaptation of lymphoma cell lines to hypoxia is mediated by diverse molecular mechanisms that are targetable with specific inhibitors - Supplemental Data Tables
<p><strong>Supplemental Data Table - Metabolome.xlsx</strong> - a complete list of measured metabolites for Ramos and HBL2 cell lines. Peak area values for normoxic and hypoxia-adapted cells in triplicates. Mean log 2 fold change and adjusted P values are provided for all metabolites except those under the limits of detection.</p> <p><strong>Supplemental Data Table - Transcriptome Differential Expression.xlsx</strong> - the tables of all transcripts detected in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls. Fold change and log 2 fold change, log 2 CPM, F statistic, P value and False Discovery Rate (FDR) were calculated using EdgeR package. Last column shows if a transcript was significantly <em>up</em>- or <em>down</em>regulated or not (<em>ns</em>).</p> <p><strong>Supplemental Data Table - Transcriptome Gene Set Analysis.xlsx</strong> - the tables of the gene set enrichment analysis of Reactome pathways in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Proteome Differential Expression.xlsx</strong> - the tables of proteins detected and differentially expressed in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Cell lines SNV characterization.xlsx</strong> - the tables of mutations (single nucleotide variations and short indels) detected in four tested lymphpoma cell lines and corresponding primary tumor (PT) samples. AF_CTRL - allelic frequency (0..1) in healthy control DNA from the patient, AF_PT - allelic frequency in primary tumor, AF_PDCL - allelic frequency in patient-derived cell line. DP - total sequence depth, TLOD - Log odds that the variant is present in the tumor sample relative to the expected noise. Gencode and HGNC annotation columns are output of the Funcotator analysis. SNVs were detected using Mutect2 as a part of GATK 4.6.0.0 somatic variat calling pipeline.</p>
Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity
<p>1- workflow for data analysis and figures generation</p>
Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data
<p>Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data</p>
Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data
<p>Anti-cytokine storm activity of fraxin and quercetin, alone and in combination, and their possible molecular mechanisms via TLR4 and PPARγ signaling pathways in LPS-induced RAW 264.7 cell line article data</p>
Mechanical manipulation of cancer cell tumorigenicity via heat shock protein signaling
<p><span>Biophysical cues of rigid tumor matrix play a critical role in cancer cell malignancy. Herein, we report that stiffly confined cancer cells exhibit robust growth of spheroids in the stiff hydrogel that exerts substantial confining stress on the cells. The stressed condition activated Hsp (heat shock protein)-STAT3 signaling via the TRPV4-PI3K/Akt axis, thereby upregulating the expression of the stemness-related markers in cancer cells, whereas these signaling activities were suppressed in cancer cells cultured in softer hydrogels or stiff hydrogels with stress relief or Hsp70 knockdown/inhibition. This mechanopriming based on 3D culture enhanced cancer cell tumorigenicity and metastasis in animal models upon transplantation, and pharmaceutically inhibiting Hsp70 improved the anticancer efficacy of chemotherapy. Mechanistically, our study reveals the crucial role of Hsp70 in regulating cancer cell malignancy under mechanically stressed conditions and its impacts on cancer prognosis-related molecular pathways for cancer treatments. </span></p>
Salivary chemical barrier proteins in Oral Squamous Cell Carcinoma – Alterations in the defense mechanism of the oral cavity
<p>Oral squamous cell carcinoma (OSCC) is one of the most frequent type of head and neck cancers. Despite the genetic and environmental risk factors, OSCC is also associated with microbial infections and/or dysbiosis. The secreted saliva serves as the chemical barrier of the oral cavity and since OSCC can alter the protein composition of saliva, our aim was to analyze the effect of OSCC on the salivary chemical barrier proteins. Publicly available datasets regarding the analysis of salivary proteins from patients with OSCC and controls were collected and examined in order to identify differentially expressed chemical barrier proteins. The network analysis and gene onthology (GO) classification of the differentially expressed chemical barrier proteins were performed, as well. 127 proteins showing different expression pattern between the OSCC and control groups were found. The protein-protein interaction network of up- and down-regulated proteins were constructed and analyzed. The main hub proteins (IL-6, IL-1B, IL-8, TNF, APOA1, APOA2, APOB, APOC3, APOE, and HP) were identified and the enriched GO terms were examined. Our study highlighted the importance of the chemical barrier of saliva in the development of OSCC.</p>
The Role of CD4+ T Cell Subsets in the Mechanism of Action of Vedolizumab in Ulcerative Colitis
ClinicalTrials.gov study NCT02721719. IPD Sharing: NO. Countries: 1. Publications: 31.
Study of the Biological Mechanisms Associated With the Immunogenicity in Anaplastic Large Cell Lymphoma ( ALCL ) ALK +
ClinicalTrials.gov study NCT02902874. IPD Sharing: NO. Countries: 1. Publications: 0.
Characteristics and Mechanism of Denosumab-treated Giant Cell Tumor of Bone
ClinicalTrials.gov study NCT03259152. IPD Sharing: NO. Countries: 1. Publications: 3.
Immunological Mechanisms of Hematopoietic Stem Cell Transplantation in Multiple Sclerosis
ClinicalTrials.gov study NCT00342134. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Mitochondrial Dysfunction of Alveolar and Circulating Immune Cells During Acute Respiratory Distress Syndrome: Impact of Infectious Aggression and Alveolar Stretching as a Result of Mechanical Ventila
ClinicalTrials.gov study NCT03955887. IPD Sharing: Not stated. Countries: 1. Publications: 2.
White Blood Cell Signaling and Defense Mechanisms in Patients With Diabetes Mellitus Type 2 and Periodontitis
ClinicalTrials.gov study NCT01848379. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Mechanisms of Cell Death in Spinal Muscular Atrophy
ClinicalTrials.gov study NCT01754441. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Single-Cell Insights Into Diabetic Retinopathy Mechanisms
ClinicalTrials.gov study NCT06497608. IPD Sharing: UNDECIDED. Countries: 0. Publications: 5.
Immunogenic Cell Death as a Novel Mechanism of Mitomycin C Activity in Bladder Cancer
ClinicalTrials.gov study NCT04256616. IPD Sharing: NO. Countries: 1. Publications: 1.
Defining the Molecular and Physiological Mechanisms of Pancreatic Islet Cell Dysfunction Which Lead to Type 2 Diabetes
ClinicalTrials.gov study NCT02505308. IPD Sharing: NO. Countries: 1. Publications: 2.
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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.