Computational framework to understand the clinical stages of COVID-19 and visualization of time course for various treatment strategies.

Coronavirus disease 2019 is known to be regulated by multiple factors such as delayed immune response, impaired T cell activation, and elevated levels of proinflammatory cytokines. Clinical management of the disease remains challenging due to interplay of various factors as drug candidates may elicit different responses depending on the staging of the disease. In this context, we propose a computational framework which provides insights into the interaction between viral infection and immune response in lung epithelial cells, with an aim of predicting optimal treatment strategies based on infection severity. First, we formulate the model for visualizing the nonlinear dynamics during the disease progression considering the role of T cells, macrophages and proinflammatory cytokines. Here, we show that the model is capable of emulating the dynamic and static data trends of viral load, T cell, macrophage levels, interleukin (IL)-6 and TNF-α levels. Second, we demonstrate the ability of the framework to capture the dynamics corresponding to mild, moderate, severe, and critical condition. Our result shows that, at late phase (>15 days), severity of disease is directly proportional to pro-inflammatory cytokine IL6 and tumor necrosis factor (TNF)-α levels and inversely proportional to the number of T cells. Finally, the simulation framework was used to assess the effect of drug administration time as well as efficacy of single or multiple drugs on patients. The major contribution of the proposed framework is to utilize the infection progression model for clinical management and administration of drugs inhibiting virus replication and cytokine levels as well as immunosuppressant drugs at various stages of the disease.

An ML prediction model based on clinical parameters and automated CT scan features for COVID-19 patients.

Outcome prediction for individual patient groups is of paramount importance in terms of selection of appropriate therapeutic options, risk communication to patients and families, and allocating resource through optimum triage. This has become even more necessary in the context of the current COVID-19 pandemic. Widening the spectrum of predictor variables by including radiological parameters alongside the usually utilized demographic, clinical and biochemical ones can facilitate building a comprehensive prediction model. Automation has the potential to build such models with applications to time-critical environments so that a clinician will be able to utilize the model outcomes in real-time decision making at bedside. We show that amalgamation of computed tomogram (CT) data with clinical parameters (CP) in generating a Machine Learning model from 302 COVID-19 patients presenting to an acute care hospital in India could prognosticate the need for invasive mechanical ventilation. Models developed from CP alone, CP and radiologist derived CT severity score and CP with automated lesion-to-lung ratio had AUC of 0.87 (95% CI 0.85-0.88), 0.89 (95% CI 0.87-0.91), and 0.91 (95% CI 0.89-0.93), respectively. We show that an operating point on the ROC can be chosen to aid clinicians in risk characterization according to the resource availability and ethical considerations. This approach can be deployed in more general settings, with appropriate calibrations, to predict outcomes of severe COVID-19 patients effectively.

Analytics Pipeline for Visualization of Single Cell RNA Sequencing Data from Brochoaveolar Fluid in COVID-19 Patients: Assessment of Neuro Fuzzy-C-Means and HDBSCAN.

Since the mutation in SARS-COV2 poses new challenges in designing vaccines, it is imperative to develop advanced tools for visualizing the genetic information. Specially, it remains challenging to address the patient-to-patient variability and identify the signature for severe/critical conditions. In this endeavor we analyze the large-scale RNA-sequencing data collected from broncho-alveolar fluid. In this work, we have used PCA and tSNE for the dimension-reduction. The novelty of the current work is to depict a detailed comparison of k-means, HDBSAN and neuro-fuzzy method in visualization of high-dimension data on gene expression. Clinical Relevance- The subpopulation profiling can be used to study the patient-to patient variability when infected by SARS-COV-2 and its variants. The distribution of cell types can be relevant in designing new drugs that are targeted to control the distribution of epithelial cells T cells and macrophages.

Automated Quantification of Inflamed Lung Regions in Chest CT by UNet++ and SegCaps: A Comparative Analysis in COVID-19 Cases.

During the current COVID-19 pandemic, a high volume of lung imaging has been generated in the aid of the treating clinician. Importantly, lung inflammation severity, associated with the disease outcome, needs to be precisely quantified. Producing consistent and accurate reporting in high-demand scenarios can be a challenge that can compromise patient care with significant inter- or intra-observer variability in quantifying lung inflammation in a chest CT scan. In this backdrop, automated segmentation has recently been attempted using UNet++, a convolutional neural network (CNN), and results comparable to manual methods have been reported. In this paper, we hypothesize that the desired task can be performed with comparable efficiency using capsule networks with fewer parameters that make use of an advanced vector representation of information and dynamic routing. In this paper, we validate this hypothesis using SegCaps, a capsule network, by direct comparison, individual comparison with CT severity score, and comparing the relative effect on a ML(machine learning)-based prognosis model developed elsewhere. We further provide a scenario, where a combination of UNet++ and SegCaps achieves improved performance compared to individual models.

FDA approved L-type channel blocker Nifedipine reduces cell death in hypoxic A549 cells through modulation of mitochondrial calcium and superoxide generation.

As hypoxia is a major driver for the pathophysiology of COVID-19, it is crucial to characterize the hypoxic response at the cellular and molecular levels. In order to augment drug repurposing with the identification of appropriate molecular targets, investigations on therapeutics preventing hypoxic cell damage is required. In this work, we propose a hypoxia model based on alveolar lung epithelial cells line using chemical inducer, CoCl2 that can be used for testing calcium channel blockers (CCBs). Since recent studies suggested that CCBs may reduce the infectivity of SARS-Cov-2, we specifically select FDA approved calcium channel blocker, nifedipine for the study. First, we examined hypoxia-induced cell morphology and found a significant increase in cytosolic calcium levels, mitochondrial calcium overload as well as ROS production in hypoxic A549 cells. Secondly, we demonstrate the protective behaviour of nifedipine for cells that are already subjected to hypoxia through measurement of cell viability as well as 4D imaging of cellular morphology and nuclear condensation. Thirdly, we show that the protective effect of nifedipine is achieved through the reduction of cytosolic calcium, mitochondrial calcium, and ROS generation. Overall, we outline a framework for quantitative analysis of mitochondrial calcium and ROS using 3D imaging in laser scanning confocal microscopy and the open-source image analysis platform ImageJ. The proposed pipeline was used to visualize mitochondrial calcium and ROS level in individual cells that provide an understanding of molecular targets. Our findings suggest that the therapeutic value of nifedipine may potentially be evaluated in the context of COVID-19 therapeutic trials.

Performance of intensive care unit severity scoring systems across different ethnicities in the USA: a retrospective observational study.

BACKGROUND: Despite wide use of severity scoring systems for case-mix determination and benchmarking in the intensive care unit (ICU), the possibility of scoring bias across ethnicities has not been examined. Guidelines on the use of illness severity scores to inform triage decisions for allocation of scarce resources, such as mechanical ventilation, during the current COVID-19 pandemic warrant examination for possible bias in these models. We investigated the performance of the severity scoring systems Acute Physiology and Chronic Health Evaluation IVa (APACHE IVa), Oxford Acute Severity of Illness Score (OASIS), and Sequential Organ Failure Assessment (SOFA) across four ethnicities in two large ICU databases to identify possible ethnicity-based bias. METHODS: Data from the electronic ICU Collaborative Research Database (eICU-CRD) and the Medical Information Mart for Intensive Care III (MIMIC-III) database, built from patient episodes in the USA from 2014-15 and 2001-12, respectively, were analysed for score performance in Asian, Black, Hispanic, and White people after appropriate exclusions. Hospital mortality was the outcome of interest. Discrimination and calibration were determined for all three scoring systems in all four groups, using area under receiver operating characteristic (AUROC) curve for different ethnicities to assess discrimination, and standardised mortality ratio (SMR) or proxy measures to assess calibration. FINDINGS: We analysed 166 751 participants (122 919 eICU-CRD and 43 832 MIMIC-III). Although measurements of discrimination were significantly different among the groups (AUROC ranging from 0·86 to 0·89 [p=0·016] with APACHE IVa and from 0·75 to 0·77 [p=0·85] with OASIS), they did not display any discernible systematic patterns of bias. However, measurements of calibration indicated persistent, and in some cases statistically significant, patterns of difference between Hispanic people (SMR 0·73 with APACHE IVa and 0·64 with OASIS) and Black people (0·67 and 0·68) versus Asian people (0·77 and 0·95) and White people (0·76 and 0·81). Although calibrations were imperfect for all groups, the scores consistently showed a pattern of overpredicting mortality for Black people and Hispanic people. Similar results were seen using SOFA scores across the two databases. INTERPRETATION: The systematic differences in calibration across ethnicities suggest that illness severity scores reflect statistical bias in their predictions of mortality. FUNDING: There was no specific funding for this study.