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16,682 results for “Lung.”
Discovery proteomics by mass spectrometry comparing secreted proteins from young and old mouse lung mesenchymal stromal cells
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High prevalence of lipopolysaccharide mutants and R2-Pyocin susceptible variants in Pseudomonas aeruginosa populations sourced from cystic fibrosis lung infections
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Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
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Data from: Why is our roe deer short of breath? – Prevalence and promotive factors of lung parasites in roe deer (Capreolus capreolus) in southeast Germany
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Fecal microbiota transplants (FMT) of three distinct human communities to germ-free mice exacerbated inflammation and decreased lung function in their offspring
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Tumor growth kinetics of subcutaneously implanted Lewis Lung carcinoma cells
<p><strong>Please cite</strong><br> Benzekry, S., Lamont, C., Beheshti, A., Tracz, A., Ebos, J. M. L., Hlatky, L., & Hahnfeldt, P. (2014). Classical mathematical models for description and prediction of experimental tumor growth. <em>PLoS Computational Biology</em>, <em>10</em>(8), e1003800. http://doi.org/10.1371/journal.pcbi.1003800</p> <p><strong>Cell culture</strong><br> Murine Lewis lung carcinoma (LLC) cells, originally derived from a spontaneous tumor in a C57BL/6 mouse [1], were obtained from American Type Culture Collection (Manassas, VA). </p> <p><strong>Tumor injections</strong><br> For the subcutaneous mouse syngeneic lung tumor model, C57BL/6 male mice with an average lifespan of 878 days were used [2]. At time of injection mice were 6 to 8 weeks old (Jackson Laboratory, Bar Harbor, Maine). Subcutaneous injections of 10<sup>6</sup> LLC cells in 0.2 ml phosphate-buffered saline (PBS) were performed on the caudal half of the back in anesthetized mice.</p> <p><strong>Tumor measurements</strong><br> Tumor size was measured regularly with calipers to a maximum of 1.5 cm<sup>3</sup> for the lung data set. Largest (L) and smallest (w) diameters were measured subcutaneously using calipers and the formula V = <span class="math-tex">\(\frac{\pi}{6}w^2 L\)</span> was then used to compute the volume (ellipsoid). Volumes ranged 14–1492 mm<sup>3</sup> over time spans from 4 to 22 days for the lung tumor model (two experiments of 10 animals each).</p> <p>[1] Bertram JS, Janik P (1980) Establishment of a cloned line of Lewis Lung Carcinoma cells adapted to cell culture. Cancer Lett 11: 63–73. Available: http://www.ncbi.nlm.nih.gov/pubmed/7226139. Accessed 9 July 2013.</p> <p>[2] Kunstyr I, Leuenberger HG (1975) Gerontological data of C57BL/6J mice. I. Sex differences in survival curves. J Gerontol 30: 157–162. Available: http:// www.ncbi.nlm.nih.gov/pubmed/1123533. Accessed 9 July 2013.</p>
COVID-19 CT Lung and Infection Segmentation Dataset
<p>This dataset contains 20 labeled COVID-19 CT scans. Left lung, right lung, and infections are labeled by two radiologists and verified by an experienced radiologist. <br> To promote the studies of annotation-efficient deep learning methods, we set up three segmentation benchmark tasks based on this dataset <a href="https://gitee.com/junma11/COVID-19-CT-Seg-Benchmark">https://gitee.com/junma11/COVID-19-CT-Seg-Benchmark</a>.</p> <p>In particular, we focus on learning to segment left lung, right lung, and infections using</p> <ul> <li>pure but limited COVID-19 CT scans;</li> <li>existing labeled lung CT dataset from other non-COVID-19 lung diseases;</li> <li>heterogeneous datasets include both COVID-19 and non-COVID-19 CT scans.</li> </ul>
3d Virtual Patho-Histology of Lung Tissue from Covid19 Patients based on Phase Contrast X-ray Tomography
<p>X-ray phase contrast tomographys datasets of lung tissue from 6 Covid-19 patients (paraffin embedded unstained tissue), and one control tissue (healthy lung, in fixative solution). The data has been recorded as part of the Covid-19 Call for Proposals at DESY April 2020 at the GINIX instrument, beamline P10 of the PETRAIII storage ring at 8keV. Three different datasets are included in a single tar archive for each sample: (i) overview scan (up to 4mm cross section ) from stitching different tomograms, (ii) 1mm cylindrical punch, and (iii) cone-beam zoom tomogram recorded with waveguide illumination. </p> <p>voxel sizes: (i) 1.3µm, (ii) 650nm, (iii) 167nm. </p> <p>3 datasets per sample, raw format, voxel numbers given in Filename, single (32bit real)</p> <p> </p>
Data from: Exposure effects beyond the epithelial barrier: trans-epithelial induction of oxidative stress by diesel exhaust particulates in lung fibroblasts in an organotypic human airway model
<p><i>In vitro</i> bronchial epithelial monoculture models have been pivotal in defining the adverse effects of inhaled toxicant exposures; however, they are only representative of one cellular compartment and may not accurately reflect the effects of exposures on other cell types. Lung fibroblasts exist immediately beneath the bronchial epithelial barrier and play a central role in lung structure and function, as well as disease development and progression. We tested the hypothesis that <i>in vitro</i> exposure of a human bronchial epithelial cell barrier to the model oxidant diesel exhaust particulates caused trans-epithelial oxidative stress in the underlying lung fibroblasts using a human bronchial epithelial cell and lung fibroblast co-culture model. We observed that diesel exhaust particulates caused trans-epithelial oxidative stress in underlying lung fibroblasts as indicated by intracellular accumulation of the reactive oxygen species hydrogen peroxide, oxidation of the cellular antioxidant glutathione, activation of NRF2, and induction of oxidative stress responsive genes. Further, targeted antioxidant treatment of lung fibroblasts partially mitigated the oxidative stress response gene expression in adjacent human bronchial epithelial cells during diesel exhaust particulate exposure. This indicates that exposure induced oxidative stress in the airway extends beyond the bronchial epithelial barrier and that lung fibroblasts are both a target and a mediator of the adverse effects of inhaled chemical exposures despite a lack of direct exposure to the inhaled material. These findings illustrate the value of co-culture models and suggest that trans-epithelial exposure effects should be considered in inhalation toxicology research and testing.</p>
Epigenome-Wide Association Study of DNA Methylation and Adult Asthma in the Agricultural Lung Health Study
<p>In an epigenome-wide association study of blood DNA methylation in adults conducted in the Agricultural Lung Health Study, 524 differentially methylated CpG sites were associated with non-atopic asthma (FDR<0.05) and 1,086 differentially methylated CpGs were associated with atopic asthma. No CpG sites were differentially methylated in relation to atopy alone. </p>
Confronting assumptions about prey selection by lunge-feeding whales using a process-based model
<ol> <li class="CH3AbstractCxSpFirst"><span>The relative energetic benefits of foraging on one type of prey rather than another are not easily measured, particularly for large free-ranging predators. Nonetheless, assumptions about preferred and alternative prey are frequently made when predicting how a predator may impact its environment, adapt to environmental change, or interact with human activities.</span></li> <li class="CH3AbstractCxSpMiddle"><span>We developed and implemented a process-based model to investigate the potential energetic benefit (PEB) of <i>in situ</i> foraging opportunities in rorqual whales. The model integrates and evaluates the energetic importance of measured prey patch characteristics (prey distribution, energy content and predator avoidance) and predator characteristics (morphometrics, foraging tactics and feeding rates). We applied the model to test the assumption that hatchery-released juvenile salmon are an "easy meal" for humpback whales compared to more common prey, herring and krill. </span></li> <li class="CH3AbstractCxSpMiddle"><span>In eleven out of the thirteen foraging situations considered, whales were found to be feeding in a manner where net energy gain was greater than the energetic costs of non-foraging swimming. Humpback whale PEB for hatchery-released juvenile salmon fell within the range of the PEB for krill and herring but varied by species, from relatively high PEB for chum salmon to relatively low for coho salmon. Our model provides behavioral insight as well, indicating that shallow feeding may be more important for reducing energy expenditure through slower lunge speeds than for increasing prey capture. The model also provides a means of identifying prey patch characteristics, with prey aggregation playing the largest role in determining PEB despite being a poor overall proxy for PEB, supporting the use of the complex model framework. </span></li> <li class="CH3AbstractCxSpLast"><span>Modeling approaches are especially valuable where they can use reasonable assumptions to substitute for lack of reliable observations, thereby integrating a range of interacting factors into a single framework. Additionally, because process-based models can make predictions outside the range of previously observed conditions, they will be increasingly useful in a changing climate.</span></li> </ol>
Neutrophil extracellular traps are present in the airways of ENaC-overexpressing mice with cystic fibrosis-like lung disease
<p>Background: Neutrophils are key components of the exacerbated inflammation and tissue damage in cystic fibrosis (CF) airways. Neutrophil extracellular traps (NETs) trap and kill extracellular pathogens. While NETs are abundant in the airways of CF patients and have been hypothesized to contribute to lung damage in CF, the in vivo role of NETs remains controversial, partially due to lack of appropriate animal models. The goal of this study was to detect NETs and to further characterize neutrophilmediated inflammation in the airways of mice overexpressing the epithelial sodium channel (βENaC-Tg mice on C57BL/6 background) in their lung with CF-like airway disease, in the absence of any apparent bacterial infections.</p> <p>Methods: Histology scoring of lung tissues, flow cytometry, multiplex ELISA, immunohistochemistry and immunofluorescence were used to characterize NETs and the airway environment in uninfected, βENaC-Tg mice at 6 and 8 weeks of age, the most chronic time points so far studied in this model.</p> <p>Results: Excessive neutrophilic infiltration characterized the lungs of uninfected, βENaC-Tg mice at 6 and 8 weeks of age. The bronchoalveolar lavage fluid (BALF) of βENaC-Tg mice contains increased levels of CF-associated cytokines and chemokines: KC, MIP-1α/β, MCP-1, G-CSF, IL-5, and IL-6. The BALF of βENaC-Tg mice contain MPO-DNA complexes, indicative of the presence of NETs. Immunofluorescence and flow cytometry of BALF neutrophils and lung tissues demonstrated increased histone citrullination, a NET-specific marker, in βENaC-Tg mice.</p> <p>Conclusions: NETs are detected in the airways of βENaC-Tg mice, in the absence of bacterial infections. These data demonstrate the usefulness of the βENaC-Tg mouse to serve as a model for studying the role of NETs in chronic CF airway inflammation.</p> <p>Keywords Cystic fibrosis; neutrophil extracellular traps; NET; ENaC, neutrophil.</p>
Data from: Assessment of lung function in successfully treated Tuberculosis reveals high burden of ventilatory defects and COPD
<p>Background: Burden, phenotype and risk-factors of lung function defects in successfully treated tuberculosis cases are unclear. Methods: We performed spirometry with bronchodilators in new drug-sensitive adult (>18 years) pulmonary tuberculosis cases during the 12 months following successful treatment in India. Airflow obstruction was defined as pre-bronchodilator FEV1/FVC<5th percentile of Global Lung Initiative mixed-ethnicity reference (lower limit of normal [LLN]). Chronic obstructive pulmonary disease (COPD) was defined as post-bronchodilator FEV1/FVC</p> <p>Methods: We performed spirometry with bronchodilators in new drug-sensitive adult (≥18 years) pulmonary tuberculosis cases during the 12 months following successful treatment in India. Airflow obstruction was defined as pre-bronchodilator FEV1/FVC<5<sup>th</sup> percentile of Global Lung Initiative mixed-ethnicity reference (lower limit of normal [LLN]). Chronic obstructive pulmonary disease (COPD) was defined as post-bronchodilator FEV1/FVC<LLN among participants with obstruction. Restrictive spirometry pattern was defined as FVC<LLN among participants without obstruction. Multivariable logistic and linear regression was used to identify risk-factors for obstruction, restriction and low lung function despite successful treatment.</p> <p>Results: Of the 172 participants included in the analysis, 82 (48%) were female, 22 (13%) had diabetes and 34 (20%) ever-smoked with a median (IQR) exposure of 3.5 (0.2–9.9) pack-years. Median (IQR) age and body-mass index (BMI) at enrollment was 32 (23–39) years and 18.1 (16.0–20.5) kg/m<sup>2</sup> respectively. Airflow obstruction was detected in 42 (24%) participants; of whom 9 (21%) responded to short-acting bronchodilators and 25 (56%) had COPD; and was associated with duration of illness prior to treatment (aOR = 1.32 per 30-days, 95%CI 1.04–1.68, p = 0.02). A restrictive spirometry pattern was detected in 89 (52%) participants and was associated with female sex (aOR = 3.73, 95%CI 1.51–9.17, p = 0.004) and diabetes (aOR = 4.06, 95%CI 1.14–14.42, p = 0.03). Higher HbA1c at treatment initiation was associated with greater odds of a restrictive spirometry pattern (aOR = 1.29 per unit higher HbA1c, 95%CI 1.04 to 1.60, p = 0.02).</p> <p>We found a high burden of lung function defects and COPD in tuberculosis cases who successfully completed treatment. Screening for chronic lung diseases following treatment and linkage to respiratory health clinics should be included in the routine management plan of all tuberculosis cases in India, regardless of conventional COPD risk-factors such as older age and smoking.</p>
Data from: Early mechanistic events induced by low molecular weight polycyclic aromatic hydrocarbons in mouse lung epithelial cells: a role for eicosanoid signaling
Low molecular weight polycyclic aromatic hydrocarbons (LMW PAHs; <206.3 g/mol) are under regulated environmental contaminants (e.g., secondhand smoke) that lead to gap junction dysregulation, p38 MAPK activation, and increased mRNA production of inflammatory mediators, such as cytokines and cyclooxygenase (COX2), in lung epithelial cells. However, the early mechanisms involving lipid signaling through the arachidonic acid pathway and subsequent eicosanoid production leading to these downstream events are not known. Common human exposures are to mixtures of LMW PAH's, thus C10 cells (a mouse lung epithelial cell line) were exposed to a representative binary PAH mixture, 1-methylanthracene (1-MeA) and fluoranthene (Flthn), for 30 min – 24 h with and without p38 and cytosolic phospholipase A2 (cPLA2) inhibitors. cPLA2 inhibition reversed PAH-induced phospho-p38 MAPK activation and gap junction dysregulation at 30 min. A significant biphasic increase of cPLA2 protein was observed at 30 min, 2, & 4 h, as well as COX2 protein at 2 & 8 h. Untargeted metabolomics demonstrated a similar trend with significantly changing metabolites at 30 min & 4 h of exposure relative to 1 h; a "cPLA2-like" subset of metabolites within the biphasic response were predominately phospholipids. argeted metabolomics showed several eicosanoids (e.g., prostaglandin D2 (PGD2), PGE2α) were significantly increased at 4, 8, and 12 h following exposure to the binary PAH mixture and this effect was p38-dependent. Lastly, PAH metabolism was not observed until after 8 h. These results indicate an early lipid signaling mechanism of PAH toxicity in lung epithelial cells due to parent PAH compounds.
Data from: Early treatment response in non-small cell lung cancer patients using diffusion-weighted imaging and functional diffusion maps - a feasibility study
Objective: The aim of this study was to prospectively evaluate the feasibility of monitoring treatment response to chemotherapy in patients with non-small cell lung carcinoma using functional diffusion maps (fDMs). Materials and Methods: This study was approved by the Cantonal Research Ethics Committee and informed written consent was obtained from all patients. Nine patients (mean age = 66 years; range = 53–76 years, 5 females, 4 males) with overall 13 lesions were included. Imaging was performed within two weeks before initiation of chemotherapy and at one, two, and six weeks after initiation of chemotherapy. Imaging included a respiratory-triggered diffusion-weighted sequence including three b-factors (100, 600, and 800 s/mm2). Treatment response was defined by change in tumor diameter on computed tomography (CT) after two cycles of chemotherapy. Changes in the apparent diffusion coefficient (ADC) on a per-lesion basis and the percentages of voxel with significantly increased or decreased ADCs on fDMs were analyzed using repeated measures analysis of variance (ANOVA). Changes in tumor size were used as covariate to examine the ability of ADCs and fDM parameters to predict treatment response. Results: Repeated measures ANOVA revealed that the percentage of voxels with increased ADCs on fDMs (p = 0.002) as well as the mean ADC increase (p = 0.011) were significantly higher in good responders with a large reduction in tumor size on CT. Conclusion: Our results indicate that the percentage of voxels with significantly increased ADCs on fDMs seems to be a promising biomarker for early prediction of treatment response in patients with non-small cell lung carcinoma. Contrary to averaged values, this approach allows the spatial heterogeneity of treatment response to be resolved.
Lung250M-4B: A Combined 3D Dataset for CT- and Point Cloud-Based Intra-Patient Lung Registration
<p>Point Cloud Data from the Lung250M-4B dataset.</p><p>Visit https://github.com/multimodallearning/Lung250M-4B for image data and associated code.</p>
MIHIC: A multiplex IHC histopathological image classification dataset for lung cancer immune microenvironment quantification
<p>A cohort of 47 TMA sections from 114 patients was collected from Liaoning cancer hospital \& Institute, where each TMA section has the size of 188,416$\times$110,080 pixels (i.e., 42660.87um$\times$24924.15um) at 40$\times$ magnification. TMA sections contain different number of tissue cores, ranging from 28 to 48. After excluding poor quality TMA sections with tissue folding, missing or contamination, there are totally 114 patients. Each patient has tissue cores with 12 different IHC stains, including CD3, CD20, CD34, CD38, CD68, CDK4, cyclin-D1, D2-40, FAP, Ki67, P53, and SMA. Two pathologists have manually labeled clear tissue regions (i.e., without controversy) in TMA sections based on visual examination via Qupath software, where six tissue types including Alveoli, Immune cells, Nerosis, Other, Stroma, Tumor were annotated. Besides the annotated six tissue types, we added one more Background type.</p> <p>To build histological classification models, we split 309,698 image patches in MIHIC dataset into three sets: training, validation and test. Note that image patches extracted from the same annotated tissue region are distributed into the same set, which avoids data leakage during classification model optimization. According to the number of extracted ROIs, train, val and test accounted for 64\%, 16\% and 20\%.</p> <h1>if you use this dataset, please cite:</h1> <pre>@article{wang2024mihic, title={MIHIC: a multiplex IHC histopathological image classification dataset for lung cancer immune microenvironment quantification}, author={Wang, Ranran and Qiu, Yusong and Wang, Tong and Wang, Mingkang and Jin, Shan and Cong, Fengyu and Zhang, Yong and Xu, Hongming}, journal={Frontiers in Immunology}, volume={15}, year={2024}, publisher={Frontiers Media SA} }</pre>
Awareness of Lung Cancer Risk Factors and Symptoms in Syria: An Online Cross-Sectional Study
<p><strong>Background:</strong> Globally, lung cancer is the leading cause of cancer fatalities and the second most frequent cancer. Population knowledge of the features of lung cancer is a crucial strategy for early diagnosis and decreasing the mortality rate of lung cancer patients. In this study, we aim to assess the Syrian population's knowledge of lung cancer and its risk factors and to measure awareness of symptoms related to lung cancer. <strong>Methods:</strong> This national cross-sectional study was conducted between October 12 to November 21, 2022 in Syria. We included Syrian people above 18 years from all Syrian governorates. The questionnaire consisted of three categories of questions: sociodemographic information, awareness of lung cancer symptoms, and awareness of lung cancer risk factors. <strong>Results:</strong> Overall, 2251 participants were involved in this research; almost half of them (47.3%) were aged between 21-30 years, and 30.9% indicated they are smoking cigarettes. The overall mean score of knowledge regarding closed questions about risk factors of lung cancer was 4.29; however, the mean score of knowledge regarding open questions about symptoms of lung cancer was 1.52. About half of the study sample (51.3%) indicated that unexplained weight loss is a possible symptom of lung cancer. Our findings showed that cigarette smokers have a lower probability of having adequate knowledge toward lung cancer risk factors than a non-smoker (AOR=0.73, COR=0.68, P-value<0.05). We also defined that females have higher statistically significant odds (AOR=1.3, COR=1.38, P-value<0.05) for being knowledgeable about the symptoms of lung cancer compared to the male sample study. Conclusion: According to our findings, there is inadequate knowledge toward lung cancer risk factors and moderate knowledge of lung cancer symptoms. Along with educational programs to raise public knowledge of the dangers of smoking and other LC risk factors, effective tobacco control policy execution is crucial. </p>
SAMPLER representations of FFPE TCGA-lung WSIs using tile-level features of the MMIL-Transformer model
<p>Here we provide single-scale SAMPLER representations of the FFPE TCGA-lung (LUAD and LUSC) WSIs using tile-level features provided in https://github.com/hustvl/MMIL-Transformer. To learn more about SAMPLER please visit https://github.com/TheJacksonLaboratory/SAMPLER.</p><p>The SAMPLER representations are provided as a single python pickle file. This pickle file contains a dictionary where each key is a WSI ID and each entry is the SAMPLER representation of the WSI.</p>
Genomic features of lung cancer patients in Indonesia's National Cancer Center
<p><strong>Introduction:</strong> Advances in molecular biology bring advantages to lung cancer management. Moreover, high-throughput molecular tests are currently useful for revealing genetic variations among lung cancer patients. We investigated the genomics profile of the lung cancer patients at the National Cancer Centre of Indonesia.</p> <p><strong>Methods:</strong> A retrospective study enrolled 627 tissue biopsy samples using real time polymerase chain reaction (RT-PCR) and 80 circulating tumour DNA (ctDNA) liquid biopsy samples using next-generation sequencing (NGS) from lung cancer patients admitted to the Dharmais Cancer Hospital from January 2018 to December 2022. Data were obtained from medical records. Data statistically analysed with p<0.05 is considered significant.</p> <p><strong>Result:</strong> The <em>EGFR</em> test results revealed by RT-PCR were wild type (51.5%), single variant (38.8%), double variant (8.3%), and triple variant (1.4%), with 18.66% L85R, 18.22% Ex19del, and 11.08% L861Q variant. Liquid biopsy ctDNA using NGS showed only 2.5% <em>EGFR</em> wild type, 62.5% single variant and 35% co-variant, with <em>EGFR/TP53</em> and <em>EGFR/PIK3CA</em> as the highest.</p> <p><strong>Conclusion:</strong> EGFR variants are the most found in our centre. Liquid biopsy with ctDNA using NGS examination could detect broad variants and co-variants that will influence the treatment planning.</p>
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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.