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Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation. Thus, we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential and implications for understanding COVID-19 complications. We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively. Our findings illuminate COVID-19 pathogenesis and highlight the importance of considering autoimmune potential when developing therapeutic interventions to reduce adverse reactions. 

This paper illustrates the application of machine learning algorithms in predictive analytics for local governments using administrative data. The developed and tested machine learning predictive algorithm overcomes known limitations of the conventional ordinary least squares method. Such limitations include but not limited to imposed linearity, presumed causality with independent variables as presumed causes and dependent variables as presume result, likely high multicollinearity among features, and spatial autocorrelation. The study applies the algorithms to 311 non-emergency service requests in the context of Miami-Dade County. The algorithms are applied to predict the volume of 311 service requests and the community characteristics affecting the volume across Census tract neighborhoods. Four common families of algorithms and an ensemble of them are applied. They are random forest, support vector machines, lasso and elastic-net regularized generalized linear models, and extreme gradient boosting. Two feature selection methods, namely Boruta and fscaret, are applied to identify the significant community characteristics. The results show that the machine learning algorithms capture spatial autocorrelation and clustering. The features generated by fscaret algorithms are parsimonious in predicting the 311 service request volume. 

The main purpose of this paper is to illustrate the application of causal inference method to administrative data and the challenges of such application. We illustrate by applying Bayesian networks method to 311 data from Miami-Dade County, Florida (USA). The 311 centers provide non-emergency services to residents. The 311 data are large and granular. We aim to explore the equity issues and biases that might exist in this particular type of service requests. As a case study, the relationship between population characteristics (independent variables) and request volume and completion time (dependent variables) is examined to identify the disparities, if any, from the observational data. The empirical analysis shows that there are no biases in services provided to any specific demographic, socioeconomic, or geographical groups. However, the administrative data do have various challenges for inferring causality due to missing or impure data, inadequacy, and latent confounders. The precautions of applying causal techniques to analyzing administrative data like 311 are discussed. 

Background: Long non-coding RNA plays a vital role in changing the expression profiles of various target genes that lead to cancer development. Thus, identifying prognostic lncRNAs related to different cancers might help in developing cancer therapy. Method: To discover the critical lncRNAs that can identify the origin of different cancers, we propose the use of the state-of-the-art deep learning algorithm concrete autoencoder (CAE) in an unsupervised setting, which efficiently identifies a subset of the most informative features. However, CAE does not identify reproducible features in different runs due to its stochastic nature. We thus propose a multi-run CAE (mrCAE) to identify a stable set of features to address this issue. The assumption is that a feature appearing in multiple runs carries more meaningful information about the data under consideration. The genome-wide lncRNA expression profiles of 12 different types of cancers, with a total of 4768 samples available in The Cancer Genome Atlas (TCGA), were analyzed to discover the key lncRNAs. The lncRNAs identified by multiple runs of CAE were added to a final list of key lncRNAs that are capable of identifying 12 different cancers. Results: Our results showed that mrCAE performs better in feature selection than single-run CAE, standard autoencoder (AE), and other state-of-the-art feature selection techniques. This study revealed a set of top-ranking 128 lncRNAs that could identify the origin of 12 different cancers with an accuracy of 95%. Survival analysis showed that 76 of 128 lncRNAs have the prognostic capability to differentiate high- and low-risk groups of patients with different cancers. Conclusion: The proposed mrCAE, which selects actual features, outperformed the AE even though it selects the latent or pseudo-features. By selecting actual features instead of pseudo-features, mrCAE can be valuable for precision medicine. The identified prognostic lncRNAs can be further studied to develop therapies for different cancers.