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16,682 results for “Lung.”
Lung MRI Raw Data Acquired with 3D UTE Radial Trajectory
<p>This repository contains the raw data for the second lung MRI result in <a href="https://arxiv.org/abs/1909.13482">Extreme MRI: Large-Scale Volumetric Dynamic Imaging from Continuous Non-Gated Acquisitions</a>. The data is stored as numpy arrays, containing k-space data (ksp.npy), coordinates (coord.npy), and density compensation factors (dcf.npy). Code to process and reconstruct the data is available here: <a href="https://github.com/mikgroup/extreme_mri">https://github.com/mikgroup/extreme_mri</a></p> <p>For more information about how the data is acquired, please see the linked paper.</p>
Targeted Disruption of Mouse Dip2B Leads to Abnormal Lung Development and Prenatal Lethality
<p>Supplementary Figures</p> <p><strong>Figure S1</strong>. Picro-sirius red stained sections of lung at E18.5.</p> <p><strong>Figure S2</strong>. Cell apoptosis assay by TUNEL staining. A. Immunofluorescent TUNEL staining of E18.5 lungs. Scale bar: 66.2μm. B. Quantitative analysis by counting of multiple sections from 3 independent samples per group. NS= not significant by student’s t- test.</p> <p><strong>Table S1</strong>. Summary of RNA-Seq mapping results. The raw reads were mapped to the Mus Musculus genome (GRCm38) using TopHat2.</p> <p><strong>Table S2</strong>. List of DEG (Differentially Expressed Gene) from RNA-Seq analysis results. Differentail expression analysis was carried out using DESeq2.</p> <p><strong>Table S3</strong>. List of DEGs annotated under Gene Ontology (GO) terms cell cycle and immune system process.</p> <p><strong>Table S4</strong>. List of DEGs annotated under KEGG Pathway oxidative phosphorylation and hematopoietic cell lineage pathways. </p>
Corrected super-resolution microscopy enables nanoscale imaging of auto-fluorescent lung macrophages
<p>Observing the cell surface and underlying cytoskeleton at nanoscale resolution using super-resolution microscopy has enabled many insights into cell signalling and function. However, the nanoscale dynamics of tissue-specific immune cells have been relatively little studied. Tissue macrophages, for example, are highly auto-fluorescent, severely limiting the utility of light microscopy. Here, we report a correction technique to remove auto-fluorescent noise from Stochastic Optical Reconstruction Microscopy (STORM) datasets. Simulations identified a moving median filter as an accurate and robust correction technique. Using this, we were able to visualise lung macrophages activated through Fc receptors by antibody-coated glass slides. Accurate, nanoscale quantification of macrophage morphology revealed that activation induced the formation of cellular protrusions tipped with MHC class I protein. These data are consistent with a role for lung macrophage protrusions in antigen presentation. We further show that the tetraspanin and extracellular vesicle (EV) marker CD81 appears in ring-shaped structures (mean diameter 93 ± 50 nm) at the surface of activated lung macrophages, likely marking the secretion of extracellular vesicles. Moreover, this correction method for super-resolution microscopy is widely applicable to other challenging biological samples.</p>
Additional data for "Air leaks: stapling affects porcine lungs biomechanics"
<p>This document is an extension of the Air leaks: stapling affects porcine lungs biomechanics publication and provide guidelines to analyze the experimental data of the publication. It contains the experimental data acquired by the pressure sensor and the microcontroller for the volume in a text file that can be analyzed with the Matlab code attached. It also has the data used to create the comparative table of the publication as well as an extract of the digital image correlation data for a specimen in CSV files. These data are analyzable with the Python code linked in the article. In addition, a video abstract is available as well as a video of the resection procedure used in the methodology.</p>
Semi-Siamese U-Net for separation of lung and heart bioimpedance images: a simulation study of thorax EIT
<p><span>Electrical impedance tomography (EIT) is widely used for bedside monitoring of lung ventilation status. Its goal is to reflect the internal conductivity changes and estimate the electrical properties of the tissues in the thorax. However, poor spatial resolution affects EIT image reconstruction to the extent that the heart and lung-related impedance images are barely <a name="_Hlk56106607">distinguishable</a>. Several studies have attempted to tackle this problem, and approaches based on decomposition of EIT images using linear transformations have been developed, and recently, U-Net has become a prominent architecture for semantic segmentation. In this paper, we propose a novel semi-Siamese U-Net specifically tailored for EIT application. It is <a name="_Hlk48748756">based on the state-of-the-art U-Net</a>, whose structure is modified and extended, forming shared encoder with parallel decoders and has multi-task weighted losses added to adapt to the individual separation tasks. The trained semi-Siamese U-Net model was evaluated with a test dataset, and the results were compared with those of the classical U-Net in terms of Dice similarity coefficient and mean absolute error. </span></p> <p><span>Results showed that compared with the classical U-Net, semi-Siamese U-Net exhibited performance improvements of 11.37% and 3.2% in Dice similarity coefficient, and 3.16% and 5.54% in mean absolute error, in terms of heart and lung-impedance image separation, respectively.</span></p>
Figure 1. from: Acoustic biomarkers of Chronic Obstructive Lung Disease - Research Ideas and Outcomes 2: e9173 (11 May 2016) https://doi.org/10.3897/rio.2.e9173
Figure 1. - Poster as it was presented at the conference. Please see text for details.
Cross-disease integration of single-cell RNA sequencing data from lung myeloid cells reveals TAM signature in in vitro model
<p>Single cells from a 3D human cell-based model comprising tumor cell line-derived spheroids, cancer-associated fibroblasts and primary monocytes were dissociated and analyzed using scRNAseq. 4 monocyte donors were used in the 3D model, and 3 monocyte donors were used for 2D differentiation of macrophages.</p>
Deciphering genomic evolution of metastatic organotropism with 535 paired primary lung cancers and metastases
<p>Scripts and processed data used in the analyses of the manuscript:</p> <p><em>Deciphering genomic evolution of metastatic organotropism with 535 paired primary lung cancers and metastases.</em></p>
Commonly asked questions for lung cancer screening
<p class="MsoNormal"><strong>Introduction.</strong> Lung cancer screening (LCS) can reduce lung cancer mortality; however, poor understanding of results may impact patient experience and follow-up. We sought to determine whether an informational handout accompanying LCS results can improve patient-reported outcomes and adherence to follow-up.</p> <p class="MsoNormal"><strong>Study Design.</strong> This was a prospective alternating intervention pilot trial of a handout to accompany LCS results delivery.</p> <p class="MsoNormal"><strong>Setting/Participants.</strong> Patients undergoing LCS in a multisite program over a 6-month period received a mailing containing either: 1) a standardized form letter of LCS results (control) or 2) the LCS results letter and the handout (intervention).</p> <p class="MsoNormal"><strong>Intervention.</strong> A two-sided informational handout on commonly asked questions after LCS was created through iterative mixed-methods evaluation with both LCS patients and providers.</p> <p class="MsoNormal"><strong>Outcome Measures.</strong> The primary outcomes of 1)patient understanding of LCS results, 2)correct identification of next steps in screening, and 3)patient distress were measured through survey. Adherence to recommended follow-up after LCS was determined through chart review. Outcomes were compared between the intervention and control group using generalized estimating equations.</p> <p class="MsoNormal"><strong>Results.</strong> 389 patients were eligible and enrolled with survey responses from 230 participants (59% response rate). We found no differences in understanding of results, identification of next steps in follow-up or distress but did find higher levels of knowledge and understanding on questions assessing individual components of LCS in the intervention group. Follow-up adherence was overall similar between the two arms, though was higher in the intervention group among those with positive findings (p=0.007).</p> <p class="MsoNormal"><strong>Conclusions.</strong> There were no differences in self-reported outcomes between the groups or overall follow-up adherence. Those receiving the intervention did report greater understanding and knowledge of key LCS components, and those with positive results had a higher rate of follow-up. This may represent a feasible component of a multi-level intervention to address knowledge and follow-up for LCS.</p>
Multi-breath 4DCT images of lung cancer patients
<p><strong>Multi-breath 4DCT images of six non-small cell lung cancer (NSCLC) patients.</strong></p><p>Breathing motion has been transferred across longitudinal imaging to generate new 4DCT images sampling five consecutive breaths.</p><p>This dataset is the result of processing six subjects selected from the 4D-Lung dataset published in The Cancer Imaging Archive: <a href="https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE">https://doi.org/10.7937/K9/TCIA.2016.ELN8YGLE </a>Hugo et al. (2016).</p><p>Data generated within the project "New concept for adaptive real time tumour tracking" funded by the Swiss National Science Foundation (SNSF) under grant agreement 200021_185082: <a href="https://data.snf.ch/grants/grant/185082">https://data.snf.ch/grants/grant/185082</a> </p><p> </p>
SHEEP SHEARING 2023 IN RGYAB LUNG (JIALONG) COMMUNITY, RTA NAG MA (HEIMAHE) TOWNSHIP TOWN, GSER CHEN (GONGHE) COUNTY, MTSHO LHO (HAINAN) TIBETAN AUTONOMOUS PREFECTURE, MTSHO SNGON (QINGHAI) PROVINCE, PR CHINA by Sgrol ma yag སྒྲོལ་མ་ཡག
<p>SHEEP SHEARING 2023 IN RGYAB LUNG (JIALONG) COMMUNITY, RTA NAG MA (HEIMAHE) TOWNSHIP TOWN, GSER CHEN (GONGHE) COUNTY, MTSHO LHO (HAINAN) TIBETAN AUTONOMOUS PREFECTURE, MTSHO SNGON (QINGHAI) PROVINCE, PR CHINA</p><p>Sgrol ma yag སྒྲོལ་མ་ཡག</p><p>May-June is sheep-shearing time in my home area of Rgyab lung (Jialong) Community, Rta nag ma (Heimahe) Township Town, Gser chen (Gonghe) County,<a href="#_ftn1">[1]</a> Mtsho lho (Hainan) Tibetan Autonomous Prefecture, Mtsho sngon (Qinghai) Province, PR China. My family stopped shearing sheep in about 2007. I filmed the first time I participated in sheep shearing since then, helping five local families shear sheep. There have been many changes in sheep-shearing including what families do with the sheared wool and tools used to shear. Most families have around ten people to help.</p><p>Father (b. 1970) said that if we don't shear at this time, the sheep will be uncomfortable and scratch against walls, rocks, and ditches, and might roll over, be unable to stand, and die. </p><p>At around 5PM, my cousin's family arrived with their sheep, brought from the summer pasture to the spring pasture. After the family drove the sheep into the sheep enclosure, the son slaughtered a sheep, and his parents went to the township town by motorcycle and bought various beverages, fruit, biscuits, and other items. Father helped the son take care of the meat. </p><p>Early the next morning, the family got up at four and began shearing after a simple breakfast. Later, helpers came one after another.</p><p>Before they start shearing, men sharpen the <i>bal he</i> 'shearing scissors,' and two or three women of the family cook, prepare milk tea, and cook meat and noodles. Each man has ten <i>bkyig tigs</i> 'strings', indicating each is to catch ten sheep and shear them. This is <i>bkyigs thabs gcig</i> 'one round.' If it is a shearer's first time to shear, other men help him. </p><p>When I was a child, each man had his own strings, and most were made of wool. They colored their strings to differentiate them from others. Father's strings were wool and colored red on top. Every time he finished shearing, I was responsible for collecting the strings. At that time men twisted their strings around their waists and pulled one when they caught a sheep and tied its legs with it. </p><p>Most men who participated in the sheep shearing this year had few wool strings. Instead, they bought cloth from the market and tore the cloth into strips. </p><p>During shearing, two or three women were responsible for marking the sheared sheep with <i>lcags rtsi</i> 'paint'. Each family had a distinctive paint color and marked the sheep differently. For instance, the first family I helped, used green on the neck and blue on the rump. Other women or children were responsible for collecting <i>bal rdul</i> 'pieces of wool that had broken off during shearing'. When I was a child, we children were responsible for collecting <i>bal rdul</i> and preventing the sheep from escaping as elders were catching them. I did the same during the sheep shearing this year. </p><p>After one round finished, the men collected their strings and took a short break. Some resharpened their scissors, and the family offered beverages and snacks. </p><p>One element of fun in sheep shearing is young men competing to see who is the fastest. They joke with each other. One of my cousins was the funniest person that day. He teased young men that if they didn't shear the wool well, they would not find good wives. The young men also verbally sparred with each other. One of my cousins and his friend had a contest of to see who could shear the fastest. My cousin lost several times, so his friends and cousins teased him that he might not find a good wife. They also teasingly suggested that he needed to join more sheep shearing events to practice his ability. </p><p>Father said when he was young, they were happy to join the sheep-shearing events of local families. Once, one of his cousins and he participated in a sheep shearing. There were many young men there to help the family and they competed to see who was the fastest. Father laughingly said that one young man had shaved the edge of his robe that day. Everybody laughed at him and teased him that day. </p><p>Jokes and laughing release tiredness. </p><p>During the shearing, some families medicate the sheep, because they won't have to catch the sheep again with few family members. For instance, one family brought anthrax vaccine of anthrax provided by the local government. </p><p>One family takes care of the wool traditionally. Women scatter the sheared wool on the ground in a line near the sheep enclosure and spread other wool on the scattered wool. A woman puts a stick on the scattered wool and twists it. Another woman helps her to twist the scattered wool to make the wool easier to twist. They make the line of twisted wool into a round shape after twisting it tightly. </p><p>Two or three women spin several pieces of wool to make a long strip men use to bind the <i>bal dos</i> 'rounded wool' with a <i>yog thag</i> 'spun strip'. This process is locally called <i>bal gcu sdom byed pa</i> and it is the final process. Men put the <i>bal dos</i> in the family's storage room. </p><p>Very few families take care of the wool in traditional ways. The shorn wool is simply placed into plastic bags, which doesn't involve arduous labor, such as what the last family event that I joined. They made long strips, scattered the wool on the ground, and so forth. </p><p>Finally, the family offers water for the men to wash their hands. The housewife and the husband or other family members ask others to sit. They offer tea and then meat, noodles, bread, snacks, and various beverages. Family members repeatedly urge guests and helpers to eat and drink more. If some are unfamiliar with the guests, they don't eat much, pretending that they are full after a small amount of food. </p><p>I did the same in one family where I met some guests for the first time. The family leader is a relative of my father and has no son. He is in his seventies, so Father helps him every year during their sheep-shearing. </p><p>This was my first time to participate in this family's sheep-shearing. The day before the shearing, the family head phoned Father and asked if he could come help. He said that it was fine if he could not because of Father's back pain. Father said he would help and added that he would bring me with him. The man was grateful for Father's generous help. </p><p>Father is famous for his sheep-shearing ability. Locals said Father was the best shearer in our community when he was young. </p><p>Except for the last family, Father didn't join the sheep-shearing of other families that I joined. There were many helpers and they said it was fine that he didn't help because they knew about his back pain. Some helpers said that the work would be easier if Father was there. </p><p>Father said when he was young, sheep-shearing took place in the summer pasture, because there were few families, few livestock, enough grass for the animals, and locals moved to summer pasture earlier. So, they packed the <i>bal dos </i>onyaks to the spring pasture where they could store the <i>bal dos</i> as long as they wanted. </p><p>TIBETAN TERMS</p><p>bal dos བལ་དོས།</p><p>bal gcu sdom byed pa བལ་གཅུ་སྡོམ་བྱེད་པ།</p><p>bal he བལ་ཧེ།</p><p>bal rdul བལ་རྡུལ།</p><p>bkyig thag བཀྱིག་ཐག</p><p>bkyigs thabs gcig བཀྱིགས་ཐབས་གཅིག</p><p>gser chenགསེར་ཆེན།</p><p>lcags rtsi ལྕགས་རྩི།</p><p>mtsho lho མཚོ་ལྷོ།</p><p>mtsho sngon མཚོ་སྔོན།</p><p>rgyab lung རྒྱབ་ལུང་།</p><p>rta nag ma རྟ་ནག་མ།</p><p>sgrol ma yag སྒྲོལ་མ་ཡག</p><p>yog thag ཡོག་ཐག</p><p> </p><p>CHINESE TERMS</p><p> </p><p>Jialong 加隆</p><p>Heimahe 黑马河</p><p>Hainan 海南</p><p>Gonghe 共和</p><p><a href="#_ftnref1">[1]</a> In 2021, Gser chen County included seven towns, four townships, ninety-nine administrative communitys, and a total population of 133,409. The county had twenty-two ethnic minorities (seventy percent of the total population) including Tibetans, Han (34,364), Hui (8,844), and Mongolian (2,140). The county had 18,761,600 <i>mu</i> of usable grassland, 457,600 <i>mu</i> of arable land, and an average altitude of 3,200 <a href="https://bit.ly/3Gw2RfS">https://bit.ly/3Gw2RfS</a> 20 November 2022). Heimahe's (township town) population was 4,000 with Tibetans accounting for ninety percent of the total. The township town is 1,000 square kilometers in area with jurisdiction over Rgyab lung (Jialong), Brag mchog (Zhiheqv), Bum pa (Wenba), and Ra 'khyog (Ranheqv) <a href="https://bit.ly/3GuaDXK">https://bit.ly/3GuaDXK</a> 20 November 2022). </p><p>The 2011 population of Mtsho lho Prefecture was 437,800, including 269,100 Tibetans (sixty-three percent) https://bit.ly/2OAGwll 25 July 2020. </p>
Molecular dynamics dataset for pharmacological repositioning in the treatment of non-small-cell lung cancer
<p><span>Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK<sup>+</sup>. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK<sup>+ </sup>NSCLC patients.</span> <span>However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an <em>in silico</em> approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling to obtain a structural model of cdALK<sup>+</sup> protein and then performed molecular docking and molecular dynamics of the complex cdALK<sup>+</sup>-iALKs to generate the pharmacophore model. The pharmacophore was used to identify potential iALKs from FDA-approved drugs library by ligand-based virtual screening. Four pharmacophores with different atomistic characteristics were generated, resulting in six drugs that satisfied the proposed atomistic positions</span> <span>and coupled at the ATP-binding site. Mitoxantrone, riboflavin and abacavir exhibit the best interaction energies with 228.29, 165.40 and 133.48 kjoul/mol respectively. In addition, the special literature proposed these drugs for other types of diseases due to pharmacological repositioning. This study proposes FDA-approved drugs with ALK inhibitory characteristics. Moreover, we identified pharmacophores sites that can be tested with other pharmacological libraries</span><span>.</span></p>
Dataset of "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy"
<p>Dataset for the article entitled "Optical Signatures of Thermal Damage on ex-vivo Brain, Lung and Heart Tissues using Time-Domain Diffuse Optical Spectroscopy" </p> <p> </p> <p>Abstract:</p> <p> </p> <p>Thermal Therapies treat tumors by means of heat, greatly reducing pain, post-operation complications, and cost as compared to traditional methods. Yet, effective tools to avoid under- or over-treatment are mostly needed, to guide surgeons in laparoscopic interventions.<br>In this work, we investigated the temperature-dependent optical signatures of ex-vivo calf brain, lung, and heart tissues, based on the reduced scattering and absorption coefficients in the near-infrared spectral range (657 to 1107 nm). These spectra were measured by time domain diffuse optics, applying a step-like spatially homogeneous thermal treatment at 43 °C, 60 °C, and 80 °C.<br>We found three main increases in scattering spectra, possibly due to the denaturation of collagen, myosin, and proteins secondary structure.<br>After 75 °C, we found the rise of two new peaks at 770 and 830 nm in the absorption spectra due to the formation of a new chromophore, possibly related to hemoglobin or myoglobin.<br>This research marks a significant step forward in controlling thermal therapies with diffuse optical techniques by identifying several key markers of thermal damage. This could enhance the ability to monitor and adjust treatment in real-time, promising improved outcomes in tumor therapy.</p> <p> </p> <p> </p> <p>Authors:</p> <p>ALESSANDRO BOSSI , LEONARDO BIANCHI , PAOLA SACCOMANDI , AND ANTONIO PIFFERI<br>Politecnico di Milano</p> <p> </p> <p> </p> <p><a href="https://opg.optica.org/boe/fulltext.cfm?uri=boe-15-4-2481&id=548108" target="_blank" rel="noopener">Link to the article</a></p>
Data from: Use of the lung flute ECO to assist in sputum collection for tuberculosis testing: a randomized crossover trial
<p>The Lung Flute ECO, a self-powered, low cost, oscillatory positive expiratory pressure (OPEP) device, assisted people with presumptive tuberculosis to produce an adequate sputum volume for diagnostic testing and was well-tolerated.</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS lung injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of lung (indicated poumon) from HbSS mice injected or not with heme are presented here . </p> <p>The results of lung (indicated poumon) from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10965912</p> <p>Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA lung injected or not with heme
<div> <div> <p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of lung (indicated poumon) from HbAA mice injected or not with heme are presented here . </p> <p>The results of lung (indicated poumon) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10966094</p> <p>Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p> </div> </div>
CT dataset for "Integrated multiomics signatures to optimize the accurate diagnosis of lung cancer" Part-I
<p>To develop and validate a radiomics-based method for lung cancer detection, chest CT images of patients with pulmonary nodules from clinical 5 centers were collected. Due to size limit of zenodo.org, we split the whole dataset into 2 parts, and this is the Part 1.</p> <p>We hope this large-scale dataset could facilitate both clinical research for automatic lung cancer detection and diagnoses, and engineering research for 3D detection, segmentation and classification. This dataset is a research effort of thousands of hours by experienced thoracic surgeons, and radiologists. We kindly ask you to respect our effort by appropriate citation and keeping data license.</p> <p> </p>
LungMAP Azimuth Reference - Human Adult Lung scRNA-Seq
<p>The LungMAP scRNA-Seq reference associated with the Lung CellCards resource. The initial reference integrated 259k cells from 72 donors from five published (PMIDs: 32726565, 32427931, 30554520, 32832599, 32832598) and one unpublished single cell RNA-seq cohort. Non-diseased adult and pediatric healthy lung single-cell 10x Genomics captures (3’ v2 and v3). Cells from different donors were integrated using Batchlor. Preliminary cell types were called based on Leiden clustering analysis and expression patterns of LungMAP cell card markers. UMAP embeddings were generated using monocle3. This reference, along with a corresponding single-nucleus specific version of this atlas, is under active construction. We expect to release the beta version of the reference in November 2021. Conforms to<strong> </strong>Azimuth reference data structure described at <a href="https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format">https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format</a>.</p>
A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 12
<p>We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 12 contains stitched image montages of thin sections (selected areas) through the lung of patients C04 and C07 which were acquired by scanning electron microscopy. The images show alveolae with various degree of epithelial damage.</p>
A detailed ultrastructural examination of lung cryobiopsy samples from a COVID-19 patient case series – Data set 11
<p>We investigated six cryobiopsy samples from six deceased patients (patients C03 to C08 from Barisione et al. 2020 <a href="https://doi.org/10.1007/s00428-020-02934-1">doi.org/10.1007/s00428-020-02934-1</a>) by using thin section electron microscopy (Cortese et al. 2022 <a href="http://doi.org/10.1007/s00428-022-03308-5">doi.org/10.1007/s00428-022-03308-5</a>). A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 11 contains a stitched image montage of a thin section (selected area) through the lung of patient C05 which was acquired by scanning electron microscopy. The image shows a lung area with a dissolved alveolar architecture and a massive type-2-cell hyperplasia.</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.