Computational Prediction of Multiple Antigen Epitopes.

MOTIVATION: Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable. RESULTS: Here, we introduce the antigen epitope prediction program ISPIPab that combines information from two feature-based methods and a docking-based method. We demonstrate that ISPIPab outperforms each of its individual classifiers as well as other state-of-the-art methods, including those designed specifically for epitope prediction. By combining the prediction algorithm with hierarchical clustering, we show that we can effectively capture epitopes that align with available experimental data while also revealing additional novel targets for future experimental investigations. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computational Prediction of Multiple Antigen Epitopes.

Motivation: Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable. Results: Here, we introduce the antigen epitope prediction program ISPIPab that combines information from two feature-based methods and a docking-based method. We demonstrate that ISPIPab outperforms each of its individual classifiers as well as other state-of-the-art methods, including those designed specifically for epitope prediction. By combining the prediction algorithm with hierarchical clustering, we show that we can effectively capture epitopes that align with available experimental data while also revealing additional novel targets for future experimental investigations. Contact: raji@yu.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

Relationship between kalemia and intensive care unit admission or death in hospitalized COVID-19 patients: A cohort study.

BACKGROUND: SARS-CoV-2 uses Angiotensin-Converting Enzyme 2 as a viral gateway to the cell and could interact with the renin-angiotensin-aldosterone system. Other studies have shown kalemia abnormalities in patients with severe forms of coronavirus disease 2019. Our goal was to assess the prognosis value of kalemia within ten days of symptom offset in the COVID-19 hospitalized population. METHODS: We analyzed data from a prospective cohort that included 65 patients with COVID-19, admitted between March 15, 2020, and March 21, 2020. The study aimed at determining the relationship between baseline kalemia and the admission to an intensive care unit (ICU) or death. RESULTS: The median age of the patients was 65 [54-79] years old, and 66.2% of the patients were men. Baseline kalemia under 3.8mmol/l occurred in 31 patients (48%), including 11 patients (35.5%) who were admitted to an ICU and one patient (3.2%) who died before ICU admission. In the primary end-point analysis, the adjusted hazard ratios for admission to an ICU or death were 3.52 [95% confidence interval (CI), 1.12 to 11.04] among patients with low baseline kalemia. CONCLUSION: Our study suggests that low kalemia levels within ten days of the first symptom onset might be associated with an increased risk of intensive care unit admission or death. The future perspective should be to better understand this relationship.

[Actual use of direct oral anticoagulants in venous thromboembolic disease]. / Place actuelle des anticoagulants oraux directs dans la maladie thromboembolique veineuse.

Direct oral anticoagulants recently became the first-line choice for anticoagulation in venous thromboembolic disease. Many studies have shown its non-inferiority regarding the risk of thromboembolic recurrence compared to anti-vitamin K without increasing the risk of bleeding in the general population. However, specific populations such as patients with cancer, patients with kidney failure, patients with constitutional thrombophilia, elderly patients, or patients with extreme weight are at risk of intolerance to the use of direct oral anticoagulants. Precautions in use may be necessary as discussed in recently published guidelines about antiphospholipid syndrome. This review aims to list the main clinical trials investigating direct oral anticoagulants in venous thromboembolic disease in the general population and populations at risk, as well as to provide an update on current international and French guidelines.