Protein contact map prediction using multi-stage hybrid intelligence inference systems

AbstractProteins are one of the most important molecules in organisms. Protein function can be inferred from its 3D structure. The gap between the number of discovered protein sequences and the number of structures determined by the experimental methods is increasing. Accurate prediction of protein contact map is an important step toward the reconstruction of the protein’s 3D structure. In spite of continuous progress in developing contact map predictors, highly accurate prediction is still unresolved problem. In this paper, we introduce a new predictor, JUSTcon, which consists of multiple parallel stages that are based on adaptive neuro-fuzzy inference System (ANFIS) and K nearest neighbors (KNNs) classifier. A smart filtering operation is performed on the final outputs to ensure normal connectivity behaviors of amino acids pairs. The window size of the filter is selected by a simple expert system. The dataset was divided into testing dataset of 50 proteins and training dataset of 450 proteins. The system produced an average accuracy of 45.2% for the sequence separation of six amino acids. In addition, JUSTcon outperformed SVMcon and PROFcon predictors in the cases of large separation distances. JUSTcon produced an average accuracy of 15% for the sequence separation of 24 amino acids after applying it on CASP9 targets

Stress Hyperglycemia Ratio as a Prognostic Marker in Diabetic Patients Hospitalized with COVID-19

Evidence is conflicting about the diabetes characteristics associated with worse outcome among hospitalized COVID-19 patients. We aimed to assess the role of stress hyperglycemia ratio (SHR) as a prognostic marker among them. In our retrospective cohort study, patients were stratified according to SHR, admission glucose, and glycated hemoglobin tertiles. The primary outcome was a composite endpoint of invasive mechanical ventilation, intensive care unit admission, and in-hospital mortality. The study included 395 patients with a mean age of 59 years, and 50.1% were males. Patients in the third tertile of SHR developed more primary events, and the difference was significant compared to the first tertile (p = 0.038) and close to significance compared to the second tertile (p = 0.054). There was no significant difference in the outcomes across admission glucose and glycated hemoglobin tertiles. A higher SHR tertile was an independent risk factor for the primary outcome (OR, 1.364; 95% CI: 1.014–1.836; p = 0.040) after adjustment for other covariables. In hospitalized COVID-19 diabetic patients, SHR third tertile was significantly associated with worse outcome and death. SHR can be a better prognostic marker compared to admission glucose and glycated hemoglobin. A higher SHR was an independent risk factor for worse outcome and in-hospital mortality

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background: Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods: The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results: NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion: As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population