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16,682 results for “Lung.”
Multi-omics with dynamic network biomarker algorithm prefigures organ-specific metastasis of lung adenocarcinoma
<p><span>Efficacious strategies for early detection of lung cancer metastasis are of significance for improving the survival of lung cancer patients. Utilizing two clinical cohorts of four major types of lung cancer distant metastases, with single-cell RNA sequencing (scRNA-seq) of primary lesions and liquid chromatography mass spectrometry data of sera, we identified the marker genes and serum secretome foreshadowing the lung cancer site-specific metastasis through dynamic network biomarker (DNB)</span> <span>algorithm. Also, we located the intermediate status of cancer cells, along with its gene signatures, in each metastatic state trajectory that cancer cells at this stage still had no specific organotropism. Furthermore, an integrated neural network model based on the filtered scRNA-seq data was successfully constructed and validated to predict the metastatic state trajectory of cancer cells. Overall, our study provided a new insight to locate the pre-metastasis status of lung cancer and primarily examined its clinical application value, contributing to the early detection of lung cancer metastasis in a more feasible and efficacious way.</span></p>
Supplementary tables for the paper: "Comprehensive computational analysis via Adverse Outcome Pathways and Aggregate Exposure Pathways in exploring synergistic effects from radon and tobacco smoke on lung cancer."
<p><strong>Authors</strong>:<br>Thomas Jaylet, Vinita Chauhan, Laura Mezquita, <em>Nadia Boroumand</em><em>, </em>Olivier Laurent, <em>Karine Elihn</em><em>, Lovisa Lundholm</em><em>, </em>Olivier Armant, Karine Audouze</p>
Spatially resolved single-cell atlas unveils A distinct cellular signature of fatal lung COVID-19 in a Malawian population
<p>Postmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTD) including Covid19, but there is minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. We used histology and high-dimensional imaging to characterise fatal lung disease in Malawian adults with (n=9) and without (n=7) Covid19, and generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved Covid19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in USA, European and Asian cohorts by type I/III interferon responses, particularly in blood-derived monocytes, in the Malawi cohort, by response to interferon-gamma (IFN-γ) in lung-resident macrophages. HIV status had minimal impact on histology or immunopathology. Our study provides a data resource and highlights the importance of studying the cellular mechanisms of disease in underrepresented populations, indicating shared and distinct targets for treatment. </p> <p>Here, there are scripts containing pre-processing, image denoise, cell segmentation, single-cell and spatial statistics analysis as well as visualisation plots for the Imaging Mass Cytometry of the post-mortem lung sections. </p> <p>Check out the interactive single cell atlas hosted on the cellxgeneVIP platform hosted by the University of Glasgow, by clicking on <a href="https://cellatlas-cxg.mvls.gla.ac.uk/COSMIC/view/COSMIC_IMC_Lung.h5ad/" rel="nofollow">https://cellatlas-cxg.mvls.gla.ac.uk/COSMIC/view/COSMIC_IMC_Lung.h5ad/</a></p>
Lung ECs scRNA-seq: Gene Expression and Metadata
<p>Normalized gene expression and cell metadata derived from a Seurat object.</p>
Immunotherapy-mediated thyroid dysfunction: genetic risk and impact on outcomes with PD-1 blockade in non-small cell lung cancer
<p>Polygenic risk score weights derived using LDpred for hypothyroidism and thyroid medication use.</p>
Dataset for Subnormothermic ex vivo lung perfusion attenuates ischemia reperfusion injury from donation after circulatory death donors
<p>Use of normothermic <i>ex vivo</i> lung perfusion (EVLP) was adopted in clinical practice to assess the quality of marginal donor lungs. Subnormothermic perfusion temperatures are in use among other solid organs to improve biochemical, clinical and immunological parameters. In a rat EVLP model of donation after circulatory death (DCD) lung donors, we tested the effect of four subnormothermic EVLP temperatures that could further improve organ preservation. Warm ischemic time was of 2 hours. EVLP time was of 4 hours. Lung physiological data were recorded and metabolic parameters were assessed. Lung oxygenation at 21°C and 24°C were significantly improved whereas pulmonary vascular resistance and edema formation at 21°C EVLP were significantly worsened when compared to 37°C EVLP. The perfusate concentrations of potassium ions and lactate exiting the lungs with 28°C EVLP were significantly lower whereas sodium and chlorine ions with 32°C EVLP were significantly higher when compared to 37°C EVLP. Also compared to 37°C EVLP, the pro-inflammatory chemokines MIP2, MIP-1α, GRO-α, the cytokine IL-6 were significantly lower with 21°C, 24°C and 28°C EVLP, the IL-18 was significantly lower but only with 21°C EVLP and IL-1β was significantly lower at 21°C and 24°C EVLP. Compared to the 37°C EVLP, the lung tissue ATP content after 21°C, 24°C and 28°C EVLP were significantly higher, the carbonylated protein content after 28°C EVLP was significantly lower and we measured significantly higher myeloperoxidase activities in lung tissues with 21°C, 24°C and 32°C. The 28°C EVLP demonstrated acceptable physiological variables, significantly higher lung tissue ATP content and decreased tissue carbonylated proteins with reduced release of pro-inflammatory cytokines. In conclusion, the 28°C EVLP is a non inferior setting in comparison to the clinically approved 37°C EVLP and significantly improve biochemical, clinical and immunological parameters and may reduce I/R injuries of DCD lung donors.</p>
Preliminary Report on Computed Tomography Radiomics Features as biomarkers to Immunotherapy selection in Lung Adenocarcinoma Patients
<p>We uploaded all radiomics metrics extracted for 88 patients enrolled in the study: Preliminary Report on Computed Tomography Radiomics Features as biomarkers to Immunotherapy selection in Lung Adenocarcinoma Patients.</p> <p>Each radiomic feature is described in the Appendix of the manuscript.</p> <p>Moreover Overall survival (OS) and Progression free survival (PFS) for each patient is provided.</p>
CarcSeq measurement of lung cancer driver mutations predicts mouse strain- and sex-related incidence of spontaneous lung neoplasia
<p>The data contained herein are the fastq files collected for individual mouse lung DNA samples. Ten samples each of male and female, B6C3F1 and CD-1 mouse lung DNA were analyzed using the CarcSeq method for error-corrected next-generation sequencing as previously described [Harris, KL, Walia, V, Gong, B, et al. Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq. <i>Environ Mol Mutagen</i>. 2020; 61: 872– 889. <a href="https://doi.org/10.1002/em.22409">https://doi.org/10.1002/em.22409</a> and Karen L McKim, Meagan B Myers, Kelly L Harris, Binsheng Gong, Joshua Xu, Barbara L Parsons, CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia, <em>Toxicological Sciences</em>, 2021;, kfab040, <a href="https://doi.org/10.1093/toxsci/kfab040">https://doi.org/10.1093/toxsci/kfab040</a>]. A readme text file provides the key to which sample numbers correspond with which mouse strain and sex. All the fastq files within a given folder were used to construct single strand consensus sequences, which were then subject to downstream analyses as reported in the associated publication.</p>
Effect of emodin on lung inflammation and intestinal microbes in Chronic Obstructive Pulmonary Disease
<p><strong>Effect of emodin on lung inflammation and intestinal microbes in Chronic Obstructive Pulmonary Disease</strong></p>
Deep learning to estimate durable clinical benefit and prognosis from patients with non-small cell lung cancer treated with PD-1/PD-L1 blockade
<p>Different biomarkers based on genomics variants have been used to predict the response of patients treated with PD-1/programmed death receptor 1 ligand (PD-L1) blockade. We aimed to use deep-learning algorithm to estimate clinical benefit in patients with non-small-cell lung cancer (NSCLC) before immunotherapy. Peripheral blood samples or tumor tissues of 915 patients from three independent centers were profiled by whole-exome sequencing or next-generation sequencing. Based on convolutional neural network (CNN) and three conventional machine learning (cML) methods, we used multi-panels to train the models for predicting the durable clinical benefit (DCB) and combined them to develop a nomogram model for predicting prognosis. In the three cohorts, the CNN achieved the highest area under the curve of predicting DCB among cML, PD-L1 expression, and tumor mutational burden (area under the curve [AUC] = 0.965, 95% confidence interval [CI]: 0.949–0.978, <em>P</em> < 0.001; AUC =0.965, 95% CI: 0.940–0.989, <em>P</em> < 0.001; AUC = 0.959, 95% CI: 0.942–0.976, <em>P</em> < 0.001, respectively). Patients with CNN-high had longer progression-free survival (PFS) and overall survival (OS) than patients with CNN-low in the three cohorts. Subgroup analysis confirmed the efficient predictive ability of CNN. Combining three cML methods (CNN, SVM, and RF) yielded a robust comprehensive nomogram for predicting PFS and OS in the three cohorts (each <em>P</em> < 0.001). The proposed deep-learning method based on mutational genes revealed the potential value of clinical benefit prediction in patients with NSCLC and provides novel insights for combined machine learning in PD-1/PD-L1 blockade.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONROL CASE 2 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a non-COVID-19-related pneumonia donor (CONTROL CASE 2 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 3 FOV1
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (CONTROL CASE 3 FOV1)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 4 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 4 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - PROLONGED CASE 5 FOV2
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (PROLONGED CASE 5 FOV2)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Multiplexed histology of COVID-19 post-mortem lung samples - ACUTE CASE 2 FOV4
<p><strong>Image-based data set of a post-mortem lung sample from a COVID-19 donor (ACUTE CASE 2 FOV4)</strong></p> <p>Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.</p>
Hysterectomy: effects on the lungs of near full-term newborn pigs
<p>Supplementary Tables S1-S4 for the manuscript (Title: Hysterectomy: effects on the lungs of near full-term newborn pigs; corresponding author: Jing Sun ,email: sunjing85026@163.com)</p>
Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung
<p>Code and data for the preprint "Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung". </p> <p><strong>Metagenomic analysis</strong> </p> <p>- uses `<a href="https://github.com/ropensci/targets">targets</a>` (workflow manager) and `<a href="https://github.com/rstudio/renv">renv</a>` (environment manager) R packages. </p> <p>- calling `targets::tar_make()`, once the environment is configured using renv and a separate project has been created (with the exact file structure including the data), should run the entire pipeline, creating a _targets folder with all the .rds files </p> <p>- independent objects can be explored using `targets::tar_load(obj)` or `targets::tar_read(plot)` </p> <p><a href="https://books.ropensci.org/targets/">Targets user manual </a>for more information. Preprocessing/QC scripts can be provided upon reasonable request. </p> <p> </p>
Unintegrated lung cell atlas
<p>Dataset from the Lung cell atlas study:</p> <p>https://www.biorxiv.org/content/10.1101/2022.03.10.483747v1</p> <p>Extracted from</p> <p>https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293</p> <p> </p> <p>The file is zstd compressed, as explained in</p> <p>https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_h5ad.html</p>
A molecular cell atlas of the human lung from single cell RNA sequencing
<p>https://cellxgene.cziscience.com/collections/5d445965-6f1a-4b68-ba3a-b8f765155d3a</p> <p>https://www.nature.com/articles/s41586-020-2922-4</p>
Chemically prepared dog lung being inflated.
<p>md5:da9d52154f62a2c7b59b80c275fac4ef (d60 SC)- Dog´s lung prepared with curing salt solution, conserved for 60 days, and inflated with great malleability.</p> <p>md5:7e158348c687364b89d5f684229fc28b (d60 alcool) - Dog´s lung prepared with curing salt solution and alcohol, conserved for 60 days, and inflated with great malleability.</p> <p>md5:51acf953c9f5107b977dd8d7fc3d376d (d120 sc) - Dog´s lung prepared with curing salt solution, conserved for 120 days ,and inflated with great malleability.</p> <p>md5:70801260b0d82e1c8fbd9c4201826770 (d120alcool)- Dog´s lung prepared with curing salt solution and alcohol, conserved for 120 days, and inflated with great malleability.</p>
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.