Immunosuppressive domain (ISD) is a conserved region of transmembrane proteins (TM) in envelope gene (env) of retroviruses. in vitro and vivo, a synthetic peptide (CKS-17) that shows homology to ISD inhibits immune function. Evidence has shown that ISD suppresses lymphocyte proliferation and allows escape from immune effectors of the innate and adaptive arms in mouse immune system. Previously, we have developed a tool ISDTool 1.0 to identify ISD of human endogenous retrovirus (HERV). However, several other important retroviruses exist and no method is devoted to ISD prediction of them so far. In the paper, a computational model is proposed to identify ISD of six typical retroviruses from three species. The model combines the minimum Redundancy Maximum Relevance (mRMR) feature selection criterion with weighted extreme learning machine (WELM) to achieve high identification accuracies of 98.95%, 96.34% and 96.87% using self-consistency, 5-fold and 10-fold cross-validation, respectively. A software tool named ISDTool 2.0 has been developed to facilitate the application of the model and a large number of new putative ISDs of the six retroviruses were predicted. In addition, motifs of ISD in these retroviruses were analyzed and the evolutionary relationship was discussed. Datasets and the software involved in the paper are available at http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/.
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http://dx.doi.org/10.1016/j.jtbi.2014.06.033 | DOI Listing |
Eur J Med Res
January 2025
Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou Branch, No. 5, Fu-Shing St., GuiShan, Taoyuan, Taiwan.
Background: This study compared the ventilatory variables and computed tomography (CT) features of patients with coronavirus disease 2019 (COVID-19) versus those of patients with pulmonary non-COVID-19-related acute respiratory distress syndrome (ARDS) during the early phase of ARDS.
Methods: This prospective, observational cohort study of ARDS patients in Taiwan was performed between February 2017 and June 2018 as well as between October 2020 and January 2024. Analysis was performed on clinical characteristics, including consecutive ventilatory variables during the first week after ARDS diagnosis.
J Cheminform
January 2025
Department of Intelligent Electronics and Computer Engineering, Chonnam National University, Gwangju, Republic of Korea.
The human ether-a-go-go-related gene (hERG) channel plays a critical role in the electrical activity of the heart, and its blockers can cause serious cardiotoxic effects. Thus, screening for hERG channel blockers is a crucial step in the drug development process. Many in silico models have been developed to predict hERG blockers, which can efficiently save time and resources.
View Article and Find Full Text PDFItal J Pediatr
January 2025
High Institute of Public Health, Alexandria University, Alexandria, Egypt.
Background: Attention-Deficit Hyperactivity Disorder (ADHD) is a complex disease that negatively impacts the social and academic/occupational activities of children and is more common in boys than in girls.
Methods: This case-control study aimed to assess the association between some environmental risk factors and ADHD among children in Alexandria, Egypt. It was carried out at the outpatient clinics of El Shatby Pediatric University Hospital in Alexandria, Egypt, with 252 children (126 cases and 126 controls).
Background: Drivers of COVID-19 severity are multifactorial and include multidimensional and potentially interacting factors encompassing viral determinants and host-related factors (i.e., demographics, pre-existing conditions and/or genetics), thus complicating the prediction of clinical outcomes for different severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants.
View Article and Find Full Text PDFBMC Med
January 2025
Department of Nuclear Medicine, West China Hospital, Sichuan University, Guoxue Alley, Address: No.37, Chengdu City, Sichuan, 610041, China.
Background: This study aimed to construct a radiomics-based imaging biomarker for the non-invasive identification of transformed follicular lymphoma (t-FL) using PET/CT images.
Methods: A total of 784 follicular lymphoma (FL), diffuse large B-cell lymphoma, and t-FL patients from 5 independent medical centers were included. The unsupervised EMFusion method was applied to fuse PET and CT images.
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