cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification

Background\ud Pediatric cardiomyopathies are a rare, yet heterogeneous group of pathologies of the myocardium that are routinely examined clinically using Cardiovascular Magnetic Resonance Imaging (cMRI). This gold standard powerful non-invasive tool yields high resolution temporal images that characterize myocardial tissue. The complexities associated with the annotation of images and extraction of markers, necessitate the development of efficient workflows to acquire, manage and transform this data into actionable knowledge for patient care to reduce mortality and morbidity.\ud \ud Methods\ud We develop and test a novel informatics framework called cMRI-BED for biomarker extraction and discovery from such complex pediatric cMRI data that includes the use of a suite of tools for image processing, marker extraction and predictive modeling. We applied our workflow to obtain and analyze a dataset of 83 de-identified cases and controls containing cMRI-derived biomarkers for classifying positive versus negative findings of cardiomyopathy in children. Bayesian rule learning (BRL) methods were applied to derive understandable models in the form of propositional rules with posterior probabilities pertaining to their validity. Popular machine learning methods in the WEKA data mining toolkit were applied using default parameters to assess cross-validation performance of this dataset using accuracy and percentage area under ROC curve (AUC) measures.\ud \ud Results\ud The best 10-fold cross validation predictive performance obtained on this cMRI-derived biomarker dataset was 80.72% accuracy and 79.6% AUC by a BRL decision tree model, which is promising from this type of rare data. Moreover, we were able to verify that mycocardial delayed enhancement (MDE) status, which is known to be an important qualitative factor in the classification of cardiomyopathies, is picked up by our rule models as an important variable for prediction.\ud \ud Conclusions\ud Preliminary results show the feasibility of our framework for processing such data while also yielding actionable predictive classification rules that can augment knowledge conveyed in cardiac radiology outcome reports. Interactions between MDE status and other cMRI parameters that are depicted in our rules warrant further investigation and validation. Predictive rules learned from cMRI data to classify positive and negative findings of cardiomyopathy can enhance scientific understanding of the underlying interactions among imaging-derived parameters

Subject-Specific Calculation of Left Atrial Appendage Blood-Borne Particle Residence Time Distribution in Atrial Fibrillation

Atrial fibrillation (AF) is the most common arrhythmia that leads to thrombus formation, mostly in the left atrial appendage (LAA). The current standard of stratifying stroke risk, based on the CHA2DS2-VASc score, does not consider LAA morphology, and the clinically accepted LAA morphology-based classification is highly subjective. The aim of this study was to determine whether LAA blood-borne particle residence time distribution and the proposed quantitative index of LAA 3D geometry can add independent information to the CHA2DS2-VASc score. Data were collected from 16 AF subjects. Subject-specific measurements included left atrial (LA) and LAA 3D geometry obtained by cardiac computed tomography, cardiac output, and heart rate.We quantified 3D LAA appearance in terms of a novel LAA appearance complexity index (LAA-ACI). We employed computational fluid dynamics analysis and a systems-based approach to quantify residence time distribution and associated calculated variable (LAA mean residence time, tm) in each subject. The LAA-ACI captured the subject-specific LAA 3D geometry in terms of a single number. LAA tm varied significantly within a given LAA morphology as defined by the current subjectivemethod and it was not simply a reflection of LAA geometry/appearance. In addition, LAA-ACI and LAA tm varied significantly for a given CHA2DS2-VASc score, indicating that these two indices of stasis are not simply a reflection of the subjects’ clinical status. We conclude that LAA-ACI and LAA tm add independent information to the CHA2DS2-VASc score about stasis risk and thereby can potentially enhance its ability to stratify stroke risk in AF patients

A method for the identification of COVID-19 biomarkers in human breath using Proton Transfer Reaction Time-of-Flight Mass Spectrometry

Background: COVID-19 has caused a worldwide pandemic, making the early detection of the virus crucial. We present an approach for the determination of COVID-19 infection based on breath analysis. Methods: A high sensitivity mass spectrometer was combined with artificial intelligence and used to develop a method for the identification of COVID-19 in human breath within seconds. A set of 1137 positive and negative subjects from different age groups, collected in two periods from two hospitals in the USA, from 26 August, 2020 until 15 September, 2020 and from 11 September, 2020 until 11 November, 2020, was used for the method development. The subjects exhaled in a Tedlar bag, and the exhaled breath samples were subsequently analyzed using a Proton Transfer Reaction Time-of-Flight Mass Spectrometer (PTR-ToF-MS). The produced mass spectra were introduced to a series of machine learning models. 70% of the data was used for these sub-models\u27 training and 30% was used for testing. Findings: A set of 340 samples, 95 positives and 245 negatives, was used for the testing. The combined models successfully predicted 77 out of the 95 samples as positives and 199 out of the 245 samples as negatives. The overall accuracy of the model was 81.2%. Since over 50% of the total positive samples belonged to the age group of over 55 years old, the performance of the model in this category was also separately evaluated on 339 subjects (170 negative and 169 positive). The model correctly identified 166 out of the 170 negatives and 164 out of the 169 positives. The model accuracy in this case was 97.3%. Interpretation: The results showed that this method for the identification of COVID-19 infection is a promising tool, which can give fast and accurate results