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2,015 results for “Pneumonia”
Viral Pneumonia Classification Using Machine and Transfer Learning Techniques
<p>Pneumonia is considered a deadly and harmful disease throughout the world. Pneumonia can be lethal if not treated promptly with antibiotics. As a result, early detection of pneumonia increases the likelihood of recovery and lowers mortality. X-rays are one of the most important diagnostic tools for pneumonia. Because of its lower diagnostic costs, the chest X-ray is routinely used to diagnose various lung illnesses. Indeed, diagnosis can be subjective for various reasons, including disease presentation, which might be confusing in chest X-ray images or misdiagnosed as another condition. As a result, the employment of chest X-rays for the diagnoses of pneumonia disease is considered a way forward to fight the challenges being faced with during the examination process and expert readings of results. The dataset comprises 1,067 Pneumonia Chest X-ray images that were curated from the Hopskin Diagnostic Center Nigeria for Research Purposes. This was used to classify Pneumonia disease for pneumonia class encoding. The result yield Pneumonia Disease with High Accuracy, precision and Recall. </p>
Dataset for the paper "Prolonged prothrombin time as an early prognostic indicator of severe acute respiratory distress syndrome in patients with COVID-19 related pneumonia"
<p>The dataset contains the data on ICU-transferred (N=100) and Stable (N=131) patients with COVID-19 (N=156) and Non-COVID-19 viral pneumonia (N=75). Among COVID-19 patients of this study, 82 patients developed Refractory Respiratory Failure (RRF) or Severe Acute Respiratory Distress Syndrome (SARDS) and were transferred to Intensive Care Unit (ICU), 74 patients had a Stable course of disease and were not transferred to ICU. Collected data are presented as a table with columns:<br> - Gender;<br> - Age (years);<br> - SARS-CoV-2 RT-PCR testing results;<br> - Time between the disease onset and admission to the hospital (days);<br> - Time between admission to the hospital and transfer to ICU (days);<br> - Artificial lung ventilation in ICU needed;<br> - C-reactive protein (CRP) upon admission (mg/L);<br> - International Normalized Ratio (INR) upon admission;<br> - Prothrombin Time (PT) upon admission (sec.);<br> - Fibrinogen upon admission (mg/L);<br> - Chest Computed Tomography (CT) upon admission: lung tissue affected (%);<br> - Platelet count upon admission (10^9/L);<br> - Chest CT, 1 week after admission: lung tissue affected (%);<br> - CRP, 1 week after admission (mg/L);<br> - Platelet count, 1 week after admission (10^9/L).</p>
Characterization of cefiderocol resistant spontaneous mutant variants of Klebsiella pneumoniae producing NDM-5 with single mutation in cirA
<p>Cefiderocol (CFDC) is a siderophore-cephalosporin antibiotic designed to combat highly resistant Gram-negative bacterial infections. Its mechanism involves a strong affinity for iron and active transport into bacterial cells, providing an alternative against strains resistant to common antibiotics. However, the emergence of CFDC resistance in Klebsiella is a growing concern. Recent reports highlight increasing CFDC resistance in K. pneumoniae, particularly associated with mutations in the cirA gene, responsible for encoding a siderophore receptor. Co-localization of blaNDM-like gene and cirA mutations correlates with higher CFDC resistance. The study focuses on a carbapenem-resistant K. pneumoniae strain (Kp-1) with carbapenemases blaNDM-5 and blaOXA-181, recovered from a post-surgery patient. The strain exhibited resistance to all tested antibiotics but susceptibility to CFDC. Heteroresistant populations with the halo on inhibition of CFDC were observed. Genomic analysis identified a novel mutation (W123*) in the cirA gene associated with CFDC resistance. Additionally, increased blaNDM-5 expression in Kp-1 IHC (intra-halo colony) compared to Kp-1 was noted. The coexistence of blaNDM-like and cirA variants, along with high blaNDM-5 expression, explains the observed 21-fold increase in Minimum Inhibition Concentration (MIC) in Kp-1 IHC. The study contributes to understanding the molecular mechanisms driving the emergence of cefiderocol resistance, emphasizing the significance of coexisting mutations in cirA and blaNDM-like genes.</p>
Genomic Typing, Antimicrobial Resistance Gene, Virulence Factor and Plasmid Replicon Dataset for the Important Pathogenic Bacteria Klebsiella pneumoniae
<p>The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called 'the clones of high risk' often drive the spread of resistance within particular species. </p> <p>Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. </p> <p>In this dataset, we present the results of a genomic epidemiology analysis of 61,857 genomes of a dangerous bacterial pathogen <em>Klebsiella pneumoniae</em> obtained from NCBI Genbank database. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), capsular (KL) and oligosaccharide (OL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to clonal groups (CG). The presence of antimicrobial resistance and virulence genes, as well as plasmid replicons, within the genomes is also reported. </p> <p>These data will be useful for researchers in the field of <em>K. pneumoniae</em> genomic epidemiology, resistance analysis and prevention measure development.</p>
Compressed Database of Klebsiella pneumoniae for WhatsGNU
<p>WhatsGNU_Kp_Ortholog.zip: <em>Klebsiella pneumoniae</em> Version-04/28/2020 (compressed 46,072,343 proteins in 8752 genomes to 1,466,934 protein variants). Updated File to fix issue with download.</p>
Under5-Children-Pneumonia-CXR-Nigerian-Dataset
<p>This dataset comprises <strong>190 chest radiographs</strong> of under-5 children, collected from the University College Hospital and Rainbow Scans Diagnostic Center in Ibadan, Nigeria. The dataset includes <strong>97 radiographs showing pneumonia</strong> and <strong>93 normal radiographs</strong>, evaluated and confirmed by experienced radiologists. The dataset is designed to support AI-based diagnostic research, particularly for pneumonia detection in low-resource settings. Personal identifiers have been removed to ensure patient privacy.</p>
Data from : Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B12-Producing Strain from Indonesian Tempeh
<p>Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin B<sub>12</sub>-producing strain that exhibited a different genetic profile from pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3, which may provide insights on the nature of fermentation, nutrition, and immunological function of Indonesian tempeh.</p>
Figure 2 in Peptidoglycan from Immunobiotic Lactobacillus rhamnosus Improves Resistance of Infant Mice to Respiratory Syncytial Viral Infection and Secondary Pneumococcal Pneumonia
Figure 2. – Photography of a juvenile lemon shark identified as Negaprion acutidens with an estimated total length of 70 cm (Photo MI).
Figure 1 in Peptidoglycan from Immunobiotic Lactobacillus rhamnosus Improves Resistance of Infant Mice to Respiratory Syncytial Viral Infection and Secondary Pneumococcal Pneumonia
Figure 1. – The Chesterfield islands (A) lie in the Coral Sea with New Caledonia (NC) to the east and Australia (AUS) to the west. The atoll structure of the Chesterfield (B) includes a V shaped barrier reef in the South (C) where the juvenile lemon sharks were observed (arrow).
Ivercori Dataset and dictionary. Ivermectin impact in COVID-19 pneumonia mortality and need of respiratory support
<p>Dataset of IVERCORI and variables dictionary. IVERCORI is a propensity matched score retrospective study that analyses the impact of ivermectin in COVID-19 pneumonia in-hospital mortality and need of respiratory support:</p>
Decreased community-acquired pneumonia coincided with rising awareness of precautions before governmental containment policy in Japan
<p>Google community mobility data provides regional-level movement trends by location type (retail and recreation, grocery and pharmacy, parks, transit stations, workplaces, and residential) as a relative change from the day-of-the-week-wise average from January 3 through February 6, 2020. We obtained the daily national average of Google mobility in Japan in all location types but residential to measure the contact behavior of individuals outside the home.</p>
Input data for running a GWAS on penicillin resistance in Streptococcus pneumoniae
<p>Results from running the pyseer tutorial at https://pyseer.readthedocs.io/en/master/tutorial.html</p>
Swab Testing to Optimize Pneumonia Treatment with Empiric Vancomycin
ClinicalTrials.gov study NCT06272994. IPD Sharing: YES. Countries: 1. Publications: 24.
Study of Efficacy and Safety of DV890 in Patients With COVID-19 Pneumonia
ClinicalTrials.gov study NCT04382053. IPD Sharing: YES. Countries: 12. Publications: 1.
Study of Efficacy and Safety of Canakinumab Treatment for CRS in Participants With COVID-19-induced Pneumonia
ClinicalTrials.gov study NCT04362813. IPD Sharing: UNDECIDED. Countries: 6. Publications: 2.
Dataset - PONE-D-20-09507 - Usefulness of circulating miR-146a and miR-16-5p microRNAs as prognostic biomarkers in community-acquired pneumonia
<p>This dataset shows a prospective observational study performed in a cohort of 153 patients admitted to hospital with CAP.</p> <p>Clinical and analytical variables were collected, and the main outcome variable was 30-day mortality.</p> <p>Small RNA was purified from patients´ plasma samples by column-based protocol, and retrotranscribed to cDNA (Exiqon's miRCURY ™ series kits), adding synthetic RNA controls (spike-in). The quality of the process was evaluated (QC control) and only 117 samples passed the test.</p> <p>FIRST STEP: Eight samples paired by age and gender were selected (4 patients who had suffered a cardiovascular event or death during follow-up and 4 who had not) and a panel of 752 human miRNAs was tested (miRCURY LNA ™ Universal - Ready-to-Use Human Panel , Exiqon), in order to determine a preliminary pattern of differential miRNA expression between patients with different CAP evolution.</p> <p>SECOND STEP: According to the preliminary data obtained, 25 candidate miRNAs were selected: 5 intended to be used as normalizers, 5 selected by statistical criteria (univariate association with mortality) and 15 selected from an exhaustive bibliographic search on miRNAs, sepsis, inflammation and / or cardiovascular disease, prioritizing those that appeared in a greater number of publications and those related to respiratory diseases. RT-PCR was carried out by hybridization with double-stranded flurochrome (ExiLENT SYBR® Green Master Mix) using the C1000 Touch CFX384 thermocycler (Bio-Rad).</p> <p>The relative amount of each miRNA was calculated with ∆Ct = CtmiRNA - CtUniSp2, and it was later normalized using the GeNorm algorithm. The final data was calculated with the formula 2<sup>-∆Ct</sup> and the values were expressed as the fold change (FC) of each miRNA with respect to UniSP2<em>.</em></p>
Short and Long Read Sequences from VIM-1 producing (Klebsiella pneumoniae test-dataset)
<p>Creation of a downsized version of the long and short reads data of VIM-1 producing <i>Klebsiella pneumoniae</i>. Samples were obtained from the Hospital Infanta Cristina (Badajoz, Spain) on October 11th, 2019. </p><p>- Long read data: Oxford Nanopore Technology (A1403KPN.fastq.gz).</p><p>- Short read data : Illumina (A1403KPN_R2_filtered.fastq.gz && A1403KPN_R2_filtered.fastq.gz)</p>
Emerging Resistance to Novel b-Lactam b-Lactamase Inhibitor Combinations in Klebsiella pneumoniae bearing KPC Variants
<p><em><span><span>Klebsiella pneumoniae</span></span></em><span><span> carbapenemase (KPC) variants, predominantly KPC-2 and KPC-3, are a significant global resistance mechanism in <em><span>K. pneumoniae</span></em>. KPC-2 and KPC-3 confer resistance to a broad range of β-lactams, including carbapenems, while remaining susceptible to ceftazidime-avibactam (CZA). Lately, new KPC variants have emerged and developed resistance to CZA, often through mutations, insertions, or deletions in key regions such as the Omega loop, the 237–243 loop, and the 266–275 loop. In the present work we aim to understand the role of these mutations in KPC in the emergence of cross-resistance to last-resort antibiotics like cefiderocol (FDC) and cefepime/zidebactam (FPZ). Fifteen clinical isolates of KPC-producing <em><span>Klebsiella</span></em> spp. were analyzed, representing 15 distinct KPC variants. CZA resistance was confirmed in 12 of the 15 KPC variants tested. Cross-resistance to FDC was observed in eight isolates, with five of these exhibiting spontaneous resistant subpopulations, including one originally categorized as FDC-susceptible. Six FDC-resistant strains carried mutations in the 266–275 loop. Cross-resistance to FPZ was observed in five KPC variants, particularly those with mutations in the 266–275 loop, although many omega loop and 237–243 loop mutants remained susceptible to FPZ. WGS of FDC-resistant subpopulations revealed additional mutations in genes such as <em><span>ompC</span></em>, <em><span>rpoC</span></em>, <em><span>dksA</span></em>, and <em><span>cirA</span></em>.<br>This study demonstrates that KPC variants show resistance to both CZA and FDC, with cross-resistance to FPZ observed to a lesser degree. The emergence of cross-resistance in strains that had not been exposed to these antibiotics raises concerns about the spread of resistance. The identification of mutations in <em><span>bla</span></em><sub>KPC</sub>, <em><span>cirA</span></em>, and other novel genes highlights the importance of understanding the molecular mechanisms driving resistance to develop effective therapeutic strategies. </span></span></p>
X-ray database: pneumonia and norm
<p>X-rays result of patients with pneumonia and normal chest radiographs. X-rays were taken in frontal and lateral projections using Apollo DRF (VILLA SISTEMI MEDICALI).</p>
Raw Data for the article: A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome
<p>In this work, we assessed and characterized the epidemiological scenario of carbapenem-resistant Klebsiella pneumoniae strains (CR-Kp) at IRCCS-ISMETT, a transplantation hospital in Palermo, Italy, from 2008 to 2017. A total of 288 K. pneumoniae clinical isolates were selected based on their resistance to carbapenems. Molecular characterization was also done in terms of the presence of virulence and resistance genes. All patients were inpatients from our facility and clinical isolates were collected from several sources, either from infection or colonization cases. We observed that, in agreement with the Italian epidemiological scenario, initially only ST258 and ST512 clade II (but not from clade I) were identified from 2008 to 2011. From 2012 onwards, other STs have been observed, including the clinically relevant ST101 and ST307, but also others not previously observed in other Italian health settings, such as ST220 and ST753. The presence of genes involved in resistance and virulence was confirmed, and a heterogeneous genetic resistance profile throughout the years was observed. Our work highlights that resistance genes are rapidly disseminating between different and novel K. pneumoniae clones which, combined with resistance to multiple antibiotics, can derive into more aggressive and pathogenic multidrug-resistant strains of clinical importance. Our results stress the importance of continuous surveillance of CR Enterobacterales in health facilities so that novel STs carrying resistance and virulence genes that may become increasingly pathogenic can be identified and adequate therapies to adopted to avoid their dissemination and derived pathologies.</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.