Find research datasets worth reusing

opencc-by-4.0Jan 2021View details →

Silver Nanoparticles Alter Cell Viability Ex Vivo and in Vitro and Induce Proinflammatory Effects in Human Lung Fibroblasts

Dataset for data generated and presented in following article by Löfdahl et al in Nanomaterials 2020, 10, 1868. doi:10.3390/nano10091868

opencc-by-4.0Jun 2021View details →

4DMRI moving lung meshes

Moving lung meshes extracted from 4DMRIs The newest version of the dataset and the documentation can be found on <a href="http://gitlab.psi.ch/duetschler_a/4DMRI_moving_lung_meshes">https://gitlab.psi.ch/duetschler_a/4DMRI_moving_lung_meshes</a>. The moving lung meshes can for example be used to generate synthetic 4DCT(MRI)s. The code for generating 4DCT(MRI)s using a reference CT and the moving lung mesh data can be found on <a href="http://gitlab.psi.ch/duetschler_a/4DMRI_moving_lung_meshes">https://gitlab.psi.ch/duetschler_a/4DCT-MRI</a>. Please cite the following publication when using the data: Duetschler, A., Bauman, G., Bieri, O., Cattin, P.C., Ehrbar, S., Engin-Deniz, G., Giger, A., Josipovic, M., Jud, C., Krieger, M., Nguyen, D., Persson, G.F., Salomir, R., Weber, D.C., Lomax, A.J. and Zhang, Y. (2022), Synthetic 4DCT(MRI) lung phantom generation for 4D radiotherapy and image guidance investigations. Med. Phys.. <a href="https://doi.org/10.1002/mp.15591">https://doi.org/10.1002/mp.15591</a>

opencc-zeroApr 2016View details →

MicroRNA Panel Predicts Lung Adenocarcinoma in Patients Presenting with Ground-Glass Nodules

MicroRNA (miRNA) expression is correlated with tumor histology, differentiation, invasiveness and treatment outcome. We aimed to identify miRNAs whose differential expression might enable early diagnosis of lung adenocarcinoma in patients presenting with ground-glass nodules (GGNs). To identify potential miRNAs of interest, we analyzed the miRNA expression profile of tumor and adjacent non para-tumor tissue in 3 participants by next-generation sequencing (NGS). We then assessed the expression levels of the miRNAs of interest in 73 lung adenocarcinoma presenting with GGNs with matched adjacent non-tumor tissue by quantitative real-time polymerase chain reaction (qRT-PCR). Target genes of our selected miRNA panel were predicted using Miranda with default parameters. Twenty-three miRNAs showed differential expression between tumor and adjacent non-tumor tissue by NGS. Five miRNAs exhibited higher expression in tumor tissue compared to adjacent non-tumor tissue (P＜0.05), eighteen miRNAs demonstrated lower expression in tumor tissue versus adjacent non-tumor tissue (P＜0.05). When qRT-PCR was performed for the 23 miRNAs identified by NGS in the pilot stage, seven were found to have statistically significant expression in tumor versus adjacent non-tumor tissue (P＜0.05). The predicted targets of our miRNAs of interest are frequently associated with cancer signaling pathways. We developed a miRNA panel that could potential predict the presence of lung adenocarcinoma in patients presenting with GGNs.

opencc-zeroMay 2016View details →

Optimization of SPECT/CT based lung dose calculation for Holmium-166 hepatic radioembolization

Background: Quantitative SPECT of the lungs after intra-arterial hepatic radioembolization using Holmium-166 (166Ho)microspheres is essential to assess therapy safety. A SPECT estimated lung absorbed dose resulting from radioembolization of more than 30 Gy is a contra-indication for therapy. Earlier we showed the superiority of Monte Carlo-based iterative reconstructions over conventional reconstructions due to its quantitative nature, required for dosimetry, at the cost of substantial computation times. In clinical routine, however, the limited available time between scout imaging and therapy constrains its application. To reduce computation times, we investigated the minimum number of iterations required to guarantee a clinical acceptable accuracy in lung dose estimation using patient and phantom data. Methods: 166Ho scout SPECT data (range: 222-283 MBq) were used from 9 patients. SPECT images were Monte Carlo-based OSEM reconstructed (iterations: 30, subsets: 8). Additionally, the 4D XCAT anthropomorphic phantom was used to mimic SPECT studies with an injected scout activity of 250 MBq and with varying lung doses ranging from 0 to 15.6 mGy/MBq. These studies were reconstructed in the same way as the patient data. Results: In all patients the lung absorbed dose upon OSEM convergence ranged from 0 to 0.025 mGy/MBq, and ranged from 0.002 to 0.078 mGy/MBq after five iterations, still well below the allowed 30 Gy in case treatment was proceeded. In the phantom data, the estimated lung dose ranged from 0.004 to 15 mGy/MBq upon convergence and from 0.03 to 13.9 mGy/MBq after five iterations, simulating situations well below and above an estimated treatment lung dose of 30 Gy. Importantly, the lung absorbed dose upon OSEM convergence was underestimated by 15% as compared to the actual simulated lung dose, and the dose after five OSEM iterations was underestimated by 9% as compared to the dose upon convergence. Both underestimations were irrespective of the magnitude of the lung dose and thus can be easily corrected for. Conclusions: The number of OSEM iterations necessary for a quantitative estimate of the lung dose can be reduced from 30 to 5. The resulting six fold reduction in calculation time enables data processing of the scout images before therapy administration.

opencc-by-4.0Oct 2023View details →

Dataset related to the manuscript entitled "Inhalation with Vitamin D3 Metabolites - A Novel Strategy to Restore Vitamin D3 Deficiencies in Lung Tissue"

The dataset contains the results presented in the manuscript entitled "Inhalation with Vitamin D3 Metabolites - A Novel Strategy to Restore Vitamin D3 Deficiencies in Lung Tissue" Appl. Sci. 2023, 13, 10672.  The presented dataset contains the results of the implementation of the following research project: Project title: "Assessment of the possibility of using vitamin D3 in the prevention and treatment of pulmonary fibrosis in the course of hypersensitivity pneumonitis - in vivo studies"Founder: National Scientific Center, PolandProject number: UMO-2020/38/E/NZ7/00366Principal Investigator: Marta Kinga LemieszekMain investigators: Michał Chojnacki, Jakub Anisiewicz, Ilona LeśniowskaPlace of project implementation: Department of Medical Biology, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland

opencc-by-4.0Nov 2023View details →

Metabolomics Analysis for the Identification of Biomarkers in Small Cell Lung Cancer

Small cell lung cancer (SCLC), a highly aggressive malignancy with a poor prognosis is usually detected at the extensive stage of the disease. The demand for early diagnostic methods and reliable biomarkers is increasing, although a number of tumor markers such as NSE and NCAM have already been utilized in clinics. Here, we conducted untargeted metabolomics in 54 plasma samples from 34 patients with SCLC and 20 healthy controls.

opencc-by-4.0Nov 2023View details →

Simulation of smFISH experiments on mouse lung tissue with simTissue

Simulations of smFISH experiments on mouse lung tissue simulated with the package simTissue (https://github.com/tdefa/SimTissue)These simulations are generated from scRNA-seq data and smFISH experemient from: Curras-Alonso, S., Soulier, J., Defard, T. et al. An interactive murine single-cell atlas of the lung responses to radiation injury. Nat Commun 14, 2445 (2023). https://doi.org/10.1038/s41467-023-38134-zthe folder 'df_spots' contains the spot coordinates of each image: - The pixel scale zxy is [300, 0.108, 0.108]the column cell is the cell_id of the corresponding cell in the nucleus mask and cytoplasm mask.the folder 'cytoplasm' contains the cytoplasm masks. - some cells are simulated without a nucleus to better mimic smFISH tissue experimentthe folder 'nuclei' contains the nucleus segmentation. Not all cells have a nucleusthe folder 'dict_centroid' contains the coordinate of the centroid of each nucleus.the folder df_cell_type contains the ground truth cell type name of each cellContact  : thomas.defard@mines-paristech.fr

FIG. 5. — A in Aristotle on the anatomy of the heart and lungs (HA 1.17): new insights from a multidisciplinary approach

FIG. 5. — A, Fresh lungs of a pig. The colour of the lungs is deep red, as is the case for the lungs in mammals; B, lungs of a chicken. Notice the pale pink colour of the lungs, which coincides with most anatomical descriptions of a chicken's lungs. This image is magnified for viewing purposes. Credits: A, Oleksandr Lyt- vynenko; B, E-Iona; taken and modified from https://www.shutterstock.com/, last consultation on 4 December 2023.

FIG. 3 in Aristotle on the anatomy of the heart and lungs (HA 1.17): new insights from a multidisciplinary approach

FIG. 3. — The process of breathing for gas exchange and the pressure change in the pleural cavity: A, during inspiration, air enters the lungs (light blue arrow), the negative pressure inside of the pleural cavity (black arrowhead) decreases and the thoracic cavity expands (orange arrows), while the lungs increase in volume;B, in exhalation, as air comes out of the lungs (light blue arrow) the pressure inside the pleural cavity (black arrowhead) increases, the thoracic cavity contracts (orange arrows), and the volume of the lungs reduces. Credit: image by Mariana Ruiz Villareal [LadyofHats], modified and taken from https://commons.wikimedia.org/, last consultation on 4 December 2023.

FIG. 1 in Aristotle on the anatomy of the heart and lungs (HA 1.17): new insights from a multidisciplinary approach

FIG. 1. — Dissection of the thoracic cavity of a dog positioned dorsally (on its back or upper side). The heart (H) can be seen located above the lungs (L) and slightly towards the right side. The lungs have collapsed to the sides of the thoracic cavity, which is limited laterally by the ribs and intercostal muscles (R-IcM). The heart is surrounded by the pericardium (Pc), partially cut to create a window, while the diaphragm (D) lies below. Credit: image by ATLOMY.

FIG. 2 in Aristotle on the anatomy of the heart and lungs (HA 1.17): new insights from a multidisciplinary approach

FIG. 2. — The position of the heart in mammalian animals: A, the human heart (white arrowhead) is positioned in the midline of the thoracic cavity, tilted to the left and surrounded by the lungs; B, the heart of a dog (white arrowhead) is also located in the thoracic cavity where it is surrounded by the lungs, as is the case in four-legged animals. Credits: images by A, Matis75; B, SciePro, taken and modified from https://www.shutterstock.com, last consultation on 4 December 2023.

FIG. 4. — A in Aristotle on the anatomy of the heart and lungs (HA 1.17): new insights from a multidisciplinary approach

FIG. 4. — A, Lateral view of the left lung of a dog. The organ is deep red in colour, as the animal has not been exsanguinated with the modern-day technique applied in slaughterhouses; B, lateral view of the lung of a pig in a slaughterhouse. The pale pink colour is a result of exsanguination, applied as part of the slaughterhouse method. Notice a lesion compatible with Enzootic Pneumonia in the middle lobe of the lung (white circle) and the heart behind it. Credits: A, image taken and modified from Singh 2018: 201; B, image taken and modified from Bonicelli et al. 2021.

opencc-by-4.0Jan 2024View details →

Single-cell RNA-seq profiles of lung adenocarcinoma patients and tumor-bearing mice

single-cell RNA sequencing (scRNA-seq) profiles from eight patients with lung adenocarcinoma (LUAD) and four samples of tumor tissues from tumor bearing mice were performed. By integrating other scRNA-seq data and clinical information, we identified activated adaptive immune responses in older patients, reflected by enriched dysfunctional T cell signature scores and immune checkpoint molecules. Our study shows increased efficacy of immune checkpoint blockade therapy in older patients, addressing the prominent role of age when considering immunotherapy.

opencc-by-4.0Apr 2024View details →

RNA sequencing of macrophages co-cultured with MSCs and RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCs

RNA sequencing of macrophages co-cultured with MSCS Table 5 RNA sequencing of alveolar macrophages from mice with lung injury treated with MSCS Table 8

opencc-by-4.0Nov 2024View details →

PERFORMANCE OF MACHINE LEARNING ALGORITHMS FOR LUNG CANCER PREDICTION: A COMPARATIVE STUDY

This study compares the performance of five machine learning algorithms—logistic regression, support vector machines, random forests, gradient boosting, and neural networks—for lung cancer prediction using demographic, lifestyle, and medical data from the UCI Machine Learning Repository. Gradient boosting and random forests achieved the highest accuracy (89% and 87%, respectively) and AUC-ROC scores (0.93 and 0.92), while neural networks reached 90% accuracy but presented interpretability limitations. Key predictors included smoking history, chronic disease, and respiratory symptoms, aligning with established risk factors. Ensemble methods, particularly gradient boosting and random forests, provided an optimal balance of accuracy and interpretability, highlighting their potential for clinical applications in early lung cancer detection.

dryad40/100

Data from: The impact of long-term azithromycin on antibiotic resistance in HIV-associated chronic lung disease

Background: Selection for resistance to azithromycin (AZM) and other antibiotics such as tetracyclines and lincosamides remains a concern with long-term AZM use for treatment of chronic lung diseases (CLD). We investigated the impact of 48 weeks of AZM on the carriage and antibiotic resistance of common respiratory bacteria among children with HIV-associated CLD. Methods: Nasopharyngeal (NP) swabs and sputa were collected at baseline, 48 and 72 weeks from participants with HIV-associated CLD randomised to receive weekly AZM or placebo for 48 weeks and followed post-intervention until 72 weeks. The primary outcomes were prevalence and antibiotic resistance of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) at these timepoints. Mixed-effects logistic regression and Fisher's exact test were used to compare carriage and resistance respectively. Results: Of 347 (174 AZM, 173 placebo) participants (median age 15 years [IQR =13–18], females 49%),NP carriage was significantly lower in the AZM (n=159) compared to placebo (n=153) arm for SP (18% vs 41%, p<0.001), HI (7% vs 16%, p=0.01), and MC (4% vs 11%, p=0.02); SP resistance to AZM (62% [18/29] vs 13%[8/63], p<0.0001) or tetracycline (60%[18/29] vs 21%[13/63], p<0.0001) were higher in the AZM arm. Carriage of SA resistant to AZM (91% [31/34] vs 3% [1/31], p<0.0001), tetracycline (35% [12/34] vs 13% [4/31], p= 0.05) and clindamycin (79% [27/34] vs 3% [1/31], p<0.0001) was also significantly higher in the AZM arm and persisted at 72 weeks. Similar findings were observed for sputa. Conclusions: The persistence of antibiotic resistance and its clinical relevance for future infectious episodes requiring treatment needs further investigation.

opencc-zeroNov 2021View details →

Research data and code for Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants

# Research data repository ## Introduction This repository contains the research data, scripts and codes to process the simulation and generate the figures in research article:   "Numerical investigation of the influence of the source and detector position for optical measurement of lung volume and oxygen content in preterm infants" This work uses the discrete 3D mesh of the thorax of a newborn that is available at: http://doi.org/10.5281/zenodo.4916863 This article has been submitted and publied in Journal of Biophotonics: - DOI: 10.1002/jbio.202200041 - Link: <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041">https://onlinelibrary.wiley.com/doi/abs/10.1002/jbio.202200041</a> ## Article status  [X] Submitted    [X] Under review    [X] Corrections    [X] Published   ## Content - Folder "data": This folder needs to be unzipped and contains the raw data from the simulation, as well as some processed data needed to generate the figures. This folder contains all the data necessary to generate the figures. However some intermediate data files (the Photon Hitting Density values interpolated on the elements of the mesh) are not given here because the files are too big. These can be created using the convertPHD2element script. - Folder "function": This folder needs to be unzipped and contains some functions that are used by the scripts to process data or generate the figures - Matlab .m files: The .m files are scripts that are used to generate the figures (generateFigX.m) or to process the data computeYYY.m. The description of each script and function is given in the comment section at the beginning of each file. ## Licence This data is published under the creative common CC-BY licence. You are free to use this data as long as you cite this dataset and the article (when DOI available) ## Digital Object Identifier DOI: 10.5281/zenodo.5996855 ## Authors Simulation: Andrea Pacheco Article writing: Andrea Pacheco Data processing and figure generation: Andrea Pacheco and Baptiste Jayet Conceptualisation, investigation, review and editing: Emilie Krite Svanberg, Hamid Dehghani and Eugene Dempsey Project supervision: Stefan Andersson-Engels ## Funding The research leading to these results was funded by Science Fundation Ireland project no. SFI/15/RP/2828

Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice

Data repository for the paper: Galaris A., Fanidis D. et al. Obesity reshapes the microbial population structure along the gut-liver-lung axis in mice. 2021 For further data requests and questions please contact the corresponding author of the respective publication. All fastq files have been processed to remove human and mouse sequences.

Bevacizumab plus erlotinib versus erlotinib alone as first line treatment of patients with EGFR-mutated advanced nonsquamous non-small cell lung cancer. BEVacizumab plus ERLotinib studY (BEVERLY): an academic, multicenter, randomised phase III trial.

Background. Adding bevacizumab to erlotinib prolonged PFS of patients with EGFR-mutated advanced NSCLC in the Japanese NEJ026 trial, but limited data were available in non-Asian patients. BEVERLY is an Italian, multicenter, randomized phase III trial of bevacizumab plus erlotinib versus erlotinib alone as first-line treatment of advanced EGFR-mutated NSCLC. Methods. Eligible patients were randomized 1:1 to erlotinib (150mg daily) plus bevacizumab (15mg/kg iv q3w) or erlotinib alone, until disease progression or unacceptable toxicity. Center, ECOG PS and type of mutation (ex19 deletion vs ex21 L858R vs others) were stratification variables. Investigator-assessed PFS (IA-PFS) and blinded-independent centrally-reviewed PFS (BICR-PFS) were co-primary endpoints. With 80% power in detecting a 0·60 HR and 2–sided α error 0·05, 126 events out of 160 patients were needed. The trial was registered as NCT02633189 and EudraCT 2015-002235-17. Findings. From Apr 11, 2016 to Feb 27, 2019, 160 pts were randomized to erlotinib pus bevacizumab (80) or erlotinib alone (80). Baseline characteristics were balanced between arms; 34 (42·5%) patients in erlotinib plus bevacizumab arm and 43 (53·8%) in erlotinib arm were former or current smokers. At a median follow-up of 36·3 months, 140 PFS events (87·5%) were reported, 68 with erlotinib plus bevacizumab and 72 with erlotinib. Median IA-PFS was 15·4 months (95% CI 12·2–18·6) with erlotinib plus bevacizumab and 9·6 months (95% CI 8·2–10·6) with erlotinib (HR 0·66; 95%CI: 0·47–0·92). BICR-PFS analysis confirmed this result. A significant interaction with treatment effect was found for smoking habit (P=0·0323): former or current smokers receiving erlotinib plus bevacizumab had a longer PFS (16·9 months [95% CI 10·2–21·8] versus 8·8 months [95% CI 5·6–9·6]) than those receiving erlotinib alone. Hypertension (grade≥3: 24% vs 5%), skin rash (grade≥3: 31% vs 14%), thromboembolic events (any grade: 11% vs 4%), and proteinuria (any grade: 23% vs 6%) were more frequent with the combination treatment. Interpretation. The addition of bevacizumab to first-line erlotinib significantly prolonged PFS in Italian patients with EGFR-mutated NSCLC, without unexpected safety issues.

Raw Data for the article: Donor Preconditioning with Inhaled Sevoflurane Mitigates the Effects of Ischemia-Reperfusion Injury in a Swine Model of Lung Transplantation

Primary graft dysfunction (PGD) and ischemia-reperfusion injury (IRI) occur in up to 30% of patients undergoing lung transplantation and may impact on the clinical outcome. Several strategies for the prevention and treatment of PGD have been proposed, but with limited use in clinical practice. In this study, we investigate the potential application of sevoflurane (SEV) preconditioning to mitigate IRI after lung transplantation. The study included two groups of swines (preconditioned and not preconditioned with SEV) undergoing left lung transplantation after 24-hour of cold ischemia. Recipients' data was collected for 6 hours after reperfusion. Outcome analysis included assessment of ventilatory, hemodynamic, and hemogasanalytic parameters, evaluation of cellularity and cytokines in BAL samples, and histological analysis of tissue samples. Hemogasanalytic, hemodynamic, and respiratory parameters were significantly favorable, and the histological score showed less inflammatory and fibrotic injury in animals receiving SEV treatment. BAL cellular and cytokine profiling showed an anti-inflammatory pattern in animals receiving SEV compared to controls. In a swine model of lung transplantation after prolonged cold ischemia, SEV showed to mitigate the adverse effects of ischemia/reperfusion and to improve animal survival. Given the low cost and easy applicability, the administration of SEV in lung donors may be more extensively explored in clinical practice.