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3,750 results for “fibrosis”
Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis "
<table> <tbody> <tr> <td> <p>Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix (ECM) deposition. Current IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive ECM production in IPF. Here we report that fibrotic AT2 cells regulate production and crosslinking of ECM via the co-transcriptional activator YAP. YAP leads to increase expression of Lysyloxidase (LOX) and subsequent LOX mediated crosslinking by fibrotic AT2 cells. Pharmacological YAP inhibition reverses fibrotic AT2 cell reprogramming and LOX expression in experimental lung fibrosis <span>in vivo</span><span> and in human fibrotic </span><span>tissue ex vivo</span><span>. We thus identify YAP-TEAD/LOX inhibition in AT2 cells as a promising potential new therapy for IPF patients.<span> </span></span></p> <p><span><span>In</span></span></p> </td> </tr> </tbody> </table>
Supplementary Data - MORTALITY RATE DUE TO PULMONERY FIBROSIS ASSOCIATED WITH SARS- COV-2 INFECTION: SCOPE OF BEST FIT REGRESSION
<p>The dataset contains number of infected pateints - Death Frquencies - Mortality rate globally due to pulmonary fibrosis associated with SARS-COV-2 infection with effect from 21st Jan to 28 th April ,2020 . Data analysis report by best fit regression software Curve Expert V.1.4 supported with Spreadsheet ( Excel , Office 2007 ) are included for computation of statistical significance .</p>
Impedance Reconstruction of Non-transmural Cardiac Fibrosis
<div>In this dataset we can find geometrical setups that served as an input to carry simulations with openCARP and EIDORS. The setup consists of a Lasso with point electrodes placed on patch of tissue and embedded in a box of blood. The tissue simulates a myocardium that can be either fully healthy, fully scarred, or healthy with a 8-mm width line of scar tissue.</div> <div>In addition, the voltage and local impedance maps obtained as results are included.</div> <div>Two kinds of simulations were performed: reconstruction the forward injection of a 5µA current at 14.6kHz with EIDORS, and the electrical wave propagation with openCARP.</div> <div>For the impedance reconstruction, a four electrode circuit was always used, meaning that two electrodes were part of the injecting pattern and a potential difference was measured between another two. The stimulating pair were sequentially changed among all pairs of neighbouring electrodes, whereas the rest of them contributed to the measurement.</div> <div>The voltage maps were computed taking the recovered EGMs from the electrode positions.</div> <div> </div> <h2>Data structure</h2> <div> <ul> <li>inputGeometries: 24 vtk files representing the input setup for simulations. The file names are of the form imageXX_append_cleanToGrid_LOCATION, where XX is a number among 06, 11, 52, and 55, and LOCATION refers to the position in z-axis (transmural, endo-, midmyo-, epicardio).</li> </ul> </div> <div> <ul> <li>results: <ul> <li>BidomainSimulations: the extracellular potentials of each electrical propagation simulation using the Courtemanche model are saved in each of the 16 folders. All the corresponding outputs from a pseudobidomain openCARP simulation are located in each folder. <ul> <li>2023-04-16_image06_endo_00</li> <li>2023-04-16_image06_epi_00</li> <li>2023-04-16_image06_mid_00</li> <li>2023-04-16_image06_transmural_00</li> <li>2023-04-16_image11_endo_00</li> <li>2023-04-16_image11_epi_00</li> <li>2023-04-16_image11_mid_00</li> <li>2023-04-16_image11_transmural_00</li> <li>2023-04-16_image52_endo_00</li> <li>2023-04-16_image52_epi_00</li> <li>2023-04-16_image52_mid_00</li> <li>2023-04-16_image52_transmural_00</li> <li>2023-04-16_image55_endo_00</li> <li>2023-04-16_image55_epi_00</li> <li>2023-04-16_image55_mid_00</li> <li>2023-04-16_image55_transmural_00</li> </ul> </li> <li>ImpedanceSimulations: mat and vtk files corresponding to either local electrical impedance reconstruction simulation. The file names are of the form imageXX_append_cleanToGrid_LOCATION, where XX is a number among 06, 11, 52, and 55, and LOCATION refers to the position in z-axis (transmural, endo-, midmyo-, epicardio). </li> </ul> </li> </ul> </div>
Data set for the publication entitled "Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis"
<p>Set of files containing data used for microbiota analysis by 16S rRNA amplicon sequencing.</p> <p>The study cohort included patients with idiopathic pulmonary fibrosis from four centres in Switzerland, treated with azithromycin or placebo, sampled sequentially by oropharyngeal swab.</p> <p>This work is available in medRxiv and has been submitted</p>
Personalized in silico model for radiation-induced pulmonary fibrosis | (source code, simulation input+output data)
<p>This repository concerns the supplementary material data of the research article entitled "<em>Personalised in silico model for radiation-induced pulmonary fibrosis</em>" that is published in the Royal Society Interface journal (rsif.royalsocietypublishing.org). More specifically, the repository contains the source code of the radiation-induced pulmonary fibrosis simulator, the results produced from the medical image analysis of this study (CT scans and RT dosage maps) for each patient case, the input files necessary to run the simulator and the corresponding output produced respectively. Each patient ID corresponds to each case documented in the research article.</p>
Single cell RNA-seq Data - Dissecting the functional reprogramming of the microenvironment in bone marrow fibrosis at the single cell level
<p>We provide results regarding the bioinformatic analysis of scRNA-seq from distinct bone marrow fibrosis mouse models and human samples.</p> <p> </p> <p>These include:</p> <p>Robjects&Markdown - R markdown and R objects with QC statistics, UMAP and final scRNA-seq data sets.</p> <p>Markers - Excel tables with cluster specific marker genes.</p> <p>DE Genes - Excel table with DE genes when comparing cells in control vs. disease condition per cluster.</p> <p>GO Analysis - Gene enrichment analysis of either DE genes. These are divided by either UP or down regulated genes.</p>
Metabolic and lipidomic data of patients with idiopathic pulmonary fibrosis and healthy volunteers
<p>The metabolomic / lipidomic datasets used in the manuscript draft entiteld: </p> <p>"Changes in Serum Metabolomics in Idiopathic Pulmonary Fibrosis and effect of approved antifibrotic medication"</p> <p>by</p> <p>Benjamin Seeliger, Alfonso Carleo, Pedro David Wendel-Garcia, Jan Fuge, Ana Montes Worboys, Sven Schuchardt, Maria Molina-Molina and Antje Prasse</p> <p>Data is untransformed and missing data were imputated. All values are in µmol/L.</p>
Global Functional Genomics Reveals GRK5 as a Therapeutic Target for Cystic Fibrosis
<p>Cystic Fibrosis (CF) is a life-shortening disease affecting >90,000 individuals worldwide predominantly with respiratory symptoms. About 80% of individuals with CF have the F508del mutation that causes the CF transmembrane conductance regulator (CFTR) protein to misfold and be targeted for premature degradation by the endoplasmic reticulum (ER) quality control (ERQC), thus preventing its plasma membrane (PM) traffic. Despite the recent approval of a ‘highly effective’ drug rescuing F508del-CFTR, maximal lung function improvement is ~14% and the drug-targeted genes remain unknown.</p> <p>To identify global modulators of F508del traffic, we performed a high-content siRNA microscopy-based screen of >9,000 genes and monitored F508del-CFTR PM rescue in human airway cells. This primary screen identified 227 F508del-CFTR traffic regulators, of which 35 could be validated by additional siRNAs. Subsequent mechanistic studies established GRK5 as a robust regulator whose inhibition rescues F508del-CFTR PM traffic, thus emerging as a novel potential drug target for CF.</p>
High-resolution AI image dataset for diagnosing oral submucous fibrosis and squamous cell carcinoma
<p>This deposition contains only training dataset of ORCHID database. The validation and test dataset related to the same study can be found at DOI: <strong>10.5281/zenodo.12646943.</strong></p>
Figure 1 in Antioxidant extract of black rice prevents renal dysfunction and renal fibrosis caused by ethanol-induced toxicity
Figure 1. Histopathological changes of kidney sections of 1) NC (Normal Control group) Control section of kidney showing cortical parenchyma to consist of dense rounded structures, the glomeruli (G), surrounded by narrow Bowman's capsular spaces (BCS); 2) PC (Positive Control group) showing glomeruli with mild mesangial proliferation (G), moderate degree of chronic interstitial inflammatory infiltrate and tubular epithelial cells focal degeneration, Cloudy swelling tubular cells with narrow (arrow) or obliterated (yellow arrow); 3) 100 mg/kg bw BREE showing mild interstitial inflammation in the interstitium (arrow); 4) 200 mg/kg bw BREE showing normal appearance of glomerular capillary tuft (G) and Bowman's capsule basement membrane (BCS) and a clear improvement in the general shape of tubes and cells. H&E (Mag. X400).
Figure 2 in Antioxidant extract of black rice prevents renal dysfunction and renal fibrosis caused by ethanol-induced toxicity
Figure 2. Histopathology of nephropathy in 1) NC (Normal Control group) showing minimal amount of collagen around renal tubules, capillary tuft and Bowman's capsules of glomerulus; 2) PC (Positive Control group) showing an increase of the collagen fibers around Bowman's capsule, capillary loops and convoluted tubules of glomerulus and both necrotic and apoptotic changes in the renal tubules; 3) 100 mg/kg bw BREE showing mild to moderate increased collagen fibres; 4) 200 mg/kg bw BREE.Showing a little amount of collagen similar or close to NC. (Masson's Trichrome × 400).
Dihydrosphingolipids are associated with steatosis and increased fibrosis damage in human and animal models of non-alcoholic fatty liver disease
<p>Data sets used for the article entitled: "Accumulation of dihydrosphingolipids and neutral lipids is related to steatosis and fibrosis damage in human and animal models of non-alcoholic fatty liver disease"</p> <p>- Patient data: DATA Patients JLR.xlsx</p> <p>- Mouse data: DATA Mice.xlsx</p>
Dynamic analysis of pathogenesis and a suppression function of TREM2-dependent macrophages in skin fibrosis
<p>Systemic sclerosis (SSc) is a chronic and incurable autoimmune disease with high mortality rates, and fibrosis is the distinguishing hallmark in the pathogenesis. Identification of the precise, time dependent composition of stromal and immune cells may provide clues for the establishment of new biomarkers and therapeutic approaches targeting SSc fibrosis. Here, the temporal dynamics of pathological process in a mouse model of skin fibrosis is investigated using single-cell RNA-sequencing (scRNA-seq). we collected skin single cell suspensions for transcriptome profiling by scRNA-seq from four time points after BLM-treatment (day 3, 7, 14, and 28) and untreated control skin (day 0) with on average three replicate mice per time point, and repeated once at each time point.{mouse_SSc_scRNAseq_day0_sample1_B1_1, mouse_SSc_scRNAseq_day3_sample1_B2_1, mouse_SSc_scRNAseq_day3_sample2_B2_2, mouse_SSc_scRNAseq_day7_sample1_B3_1, mouse_SSc_scRNAseq_day7_sample2_B3_2, mouse_SSc_scRNAseq_day14_sample1_B4_1, mouse_SSc_scRNAseq_day14_sample2_B4_2, mouse_SSc_scRNAseq_day28_sample1_B5_1, mouse_SSc_scRNAseq_day28_sample2_B5_2}</p>
Knockout of liver fluke granulin, Ov-grn-1, impedes malignant transformation during chronic infection with Opisthorchis viverrini: BrdU staining and fibrosis
<p>Knockout of liver fluke granulin, Ov-grn-1, impedes malignant transformation during chronic infection with Opisthorchis viverrini:</p> <p>1. BrdU stained images for the detection of proliferation with manual counting of brown stained cell proportion. Each group in a seperate file BRDUxxx</p> <p>2. Fibrosis local images stained with Sirius red with automated analysis with imageJ. Grouped into one zip file</p> <p>3. Global analysis of liver fibrosis pathogenesis (Ishak scores) performed by 2 blinded pathologists. Grouped into one zip file</p> <p>Methods in associated publication. Briefly 3 groups of 15 hamsters were infected with 100 NEJ flukes that had been gene edited with CRISPR/Cas9 plasmids targeting either Ov-grn-1, Ov-tsp-2, or a scrambled sequence as the control group. Images in these files are the micrographs from these three groups of hamsters. Numbered 1-15 representing the hamster and left/middle/right representing the liver lobe the section was taken from.</p> <p> </p> <p>Knockout of liver fluke granulin, Ov-grn-1, impedes malignant transformation during chronic infection with Opisthorchis viverrini</p> <p>ABSTRACT: Infection with the food-borne liver fluke <em>Opisthorchis viverrini</em> is the principal risk factor for cholangiocarcinoma (CCA) in the Mekong Basin countries of Thailand, Lao PDR, Vietnam, Myanmar and Cambodia. Using a novel model of CCA, involving infection with gene-edited liver flukes in the hamster during concurrent exposure to dietary nitrosamine, we explored the role of the fluke granulin-like growth factor <em>Ov</em>-GRN-1 in malignancy. We derived RNA-guided gene knockout flukes (<em>ΔOv-grn-1)</em> using CRISPR/Cas9/gRNA materials delivered by electroporation. Genome sequencing confirmed programmed Cas9-catalyzed mutations of the targeted genes, which was accompanied by rapid depletion of transcripts and the proteins they encode. Gene-edited parasites colonized the biliary tract of hamsters and developed into adult flukes. However, less hepatobiliary tract disease manifested during chronic infection with <em>ΔOv-grn-1</em> worms in comparison to hamsters infected with control gene-edited and mock-edited parasites. Specifically, immuno- and colorimetric-histochemical analysis of livers revealed markedly less periductal fibrosis surrounding the flukes and less fibrosis globally within the hepatobiliary tract during infection with <em>ΔOv-grn-1</em> genotype worms, minimal biliary epithelial cell proliferation, and significantly fewer mutations of <em>TP53</em> in biliary epithelial cells. Moreover, fewer hamsters developed high-grade CCA compared to controls. The clinically relevant, pathophysiological phenotype of the hepatobiliary tract confirmed a role for this secreted growth factor in malignancy and morbidity during opisthorchiasis.</p>
Global burden of non-tuberculous mycobacteria in the cystic fibrosis population: A systematic review and meta-analysis
<p><span><strong>Background</strong>:</span><span> People living with cystic fibrosis have an increased risk of lung infection with non-tuberculous mycobacteria (NTM), which is reportedly increasing. We conducted a systematic review of the literature to estimate the burden (prevalence and incidence) of non-tuberculous mycobacteria in the cystic fibrosis population. </span></p> <p><span><strong>Methods</strong>: Electronic databases, registries, and grey literature sources were searched for cohort and cross-sectional studies reporting epidemiological measures (incidence and prevalence) of NTM infection or NTM pulmonary disease (NTM-PD) in cystic fibrosis. The last search was conducted in September 2021; we included reports since database creation and registry reports published since 2010. The methodological quality of studies was appraised with the Joanna Briggs Institute tool. A random-effects meta-analysis was conducted to summarize the prevalence of NTM infection, and the remaining results are presented in a narrative synthesis. </span></p> <p><span><strong>Results</strong>: Ninety-five studies were included in this review. All 95 studies reported on NTM infection, and 14 of these also reported on NTM-PD. The pooled estimate for the point prevalence of NTM infection was 7.9% (CI 95%, 5.1–12.0%). In meta-regression, sample size and geographical location of the study modified the estimate. Longitudinal analysis of registry reports showed an increasing trend in NTM infection prevalence between 2010 and 2019. </span></p> <p><span><strong>Conclusions</strong>: The overall prevalence of NTM infection in CF is 7.9% and is increasing over time based on international registry reports. Future studies should report screening frequency, microbial identification methods, and incidence rates of progression from NTM infection to pulmonary disease.</span></p>
Whole blood RNA-seq demonstrates an increased host immune response in individuals with cystic fibrosis who develop nontuberculous mycobacterial pulmonary disease
<p><strong>Background </strong></p> <p>Individuals with cystic fibrosis have an elevated lifetime risk of colonization, infection, and disease caused by nontuberculous mycobacteria. A prior study involving non-cystic fibrosis individuals reported a gene expression signature associated with susceptibility to nontuberculous mycobacteria pulmonary disease (NTM-PD). In this study, we determined whether people living with cystic fibrosis who progress to NTM-PD have a gene expression pattern similar to the one seen in the non-cystic fibrosis population. <strong> </strong></p> <p><strong>Methods</strong></p> <p>We evaluated whole blood transcriptomics using bulk RNA-seq in a cohort of cystic fibrosis patients with samples collected closest in timing to the first isolation of nontuberculous mycobacteria. The study population included patients who did (n = 12) and did not (n = 30) develop NTM-PD following the first mycobacterial growth. Progression to NTM-PD was defined by a consensus of two expert clinicians based on reviewing clinical, microbiological, and radiological information. Differential gene expression was determined by DESeq2.</p> <p><strong>Results</strong></p> <p>No differences in demographics or composition of white blood cell populations between groups were identified at baseline. Out of 213 genes associated with NTM-PD in the non-CF population, only two were significantly different in our cystic fibrosis NTM-PD cohort. Gene set enrichment analysis of the differential expression results showed that CF individuals who developed NTM-PD had higher expression levels of genes involved in the interferon (α and γ), tumor necrosis factor, and IL6-STAT3-JAK pathways. <strong> </strong></p> <p><strong>Conclusion</strong></p> <p>In contrast to the non-cystic fibrosis population, the gene expression signature of patients with cystic fibrosis who develop NTM-PD is characterized by increased innate immune responses.</p>
Bright Light Therapy for Depression Symptoms in Adults With Cystic Fibrosis (CF) and COPD
ClinicalTrials.gov study NCT04921332. IPD Sharing: YES. Countries: 1. Publications: 3.
Evaluation of Lung Clearance Index in Cystic Fibrosis (CF) Patients, Infected With P.Aeruginosa
ClinicalTrials.gov study NCT02248922. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Study of Safety, Tolerability, and Efficacy of a Combination Treatment of LJN452 and CVC in Adult Patients With NASH and Liver Fibrosis
ClinicalTrials.gov study NCT03517540. IPD Sharing: UNDECIDED. Countries: 17. Publications: 2.
Study to Evaluate the Safety & Tolerability of MRT5005 Administered by Nebulization in Adults With Cystic Fibrosis
ClinicalTrials.gov study NCT03375047. IPD Sharing: YES. Countries: 1. Publications: 1.
ScienceDex guides
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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.