DTAmetasa: An R shiny application for meta-analysis of diagnostic test accuracy and sensitivity analysis of publication bias.

Meta-analysis of diagnostic test accuracy (DTA) is a powerful statistical method for synthesizing and evaluating the diagnostic capacity of medical tests and has been extensively used by clinical physicians and healthcare decision-makers. However, publication bias (PB) threatens the validity of meta-analysis of DTA. Some statistical methods have been developed to deal with PB in meta-analysis of DTA, but implementing these methods requires high-level statistical knowledge and programming skill.

The Efficacy of Golimumab Against Non-Infectious Uveitis: A PRISMA-Compliant Systematic Review and Meta-Analysis.

Purpose: In this PRISMA-compliant systematic review and meta-analysis, we aimed to assess the efficacy of golimumab (GOL) against non-infectious uveitis (NIU).

Methods: We included eight articles in the meta-analysis. The primary outcome was inflammation remission.

Safety, efficacy, and cost-effectiveness of insulin degludec U100 versus insulin glargine U300 in adults with type 1 diabetes: a systematic review and indirect treatment comparison.

Background: Clinical differences between degludec U100 (Deg-100) and glargine U300 (Gla-300) in type 1 diabetes (T1D) were unknown.

Aim: To indirectly compare the safety, efficacy, and cost-effectiveness between Deg-100 and Gla-300 in T1D adults via systematic review.

Method: Medline, the Cochrane Library, ClinicalTrials.

Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation.

The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2. The receptor binding domain (RBD) of the S-protein has been considered critical for this interaction and acts as the target of numerous neutralizing antibodies and antiviral peptides. This study used the fragment molecular orbital method to analyze the interactions between the RBD and antibodies/peptides and extracted crucial residues that can be used as epitopes.

MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny.

Background: Even though R is one of the most commonly used statistical computing environments, it lacks a graphical user interface (GUI) that appeals to students, researchers, lecturers, and practitioners in medicine and pharmacy for conducting standard data analytics. Current GUIs built on top of R, such as EZR and R-Commander, aim to facilitate R coding and visualization, but most of the functionalities are still accessed through a command-line interface (CLI). To assist practitioners of medicine and pharmacy and researchers to run most routines in fundamental statistical analysis, we developed an interactive GUI; i.

Vonoprazan vs proton pump inhibitors in treating post-endoscopic submucosal dissection ulcers and preventing bleeding: A meta-analysis of randomized controlled trials and observational studies.

Background: Vonoprazan is a potassium-competitive acid blocker (P-CAB) that is frequently used in Japan for Helicobacter pylori (H. pylori) eradication, treatment of gastroesophageal reflux disease, and treatment of post endoscopic submucosal dissection (ESD) complications. We sought to determine if vonoprazan was superior to proton pump inhibitors (PPIs) for treating ESD-induced ulcers (as assessed by ulcer healing and shrinkage ratios) and preventing delayed bleeding over various treatment durations (2, 4, and 8 weeks).

Three-Dimensional Classification Structure-Activity Relationship Analysis Using Convolutional Neural Network.

Quantitative structure-activity relationship (QSAR) techniques, especially those that possess three-dimensional attributes, such as the comparative molecular field analysis (CoMFA), are frequently used in modern-day drug design and other related research domains. However, the requirement for accurate alignment of compounds in CoMFA increases the difficulties encountered in its use. This has led to the development of several techniques-such as VolSurf, Grid-independent descriptors (GRIND), and Anchor-GRIND-which do not require such an alignment.

Vonoprazan versus proton pump inhibitors in treating post-endoscopic submucosal dissection ulcers and preventing bleeding: Protocol for meta-analysis of randomized controlled trials and observational studies.

Background: Vonoprazan is a potassium-competitive acid blocker (P-CAB). It is often used in Japan for Helicobacter pylori (H pylori) eradication, gastroesophageal reflux disease, and endoscopic submucosal dissection (ESD) ulcers and bleeding. This meta-analysis aims to evaluate whether vonoprazan has better therapeutic effect on ESD-induced ulcers and bleeding than proton pump inhibitors (PPIs) at different length of treatment periods (2, 4, and 8 weeks).

Dengue Virus and Its Inhibitors: A Brief Review.

The global occurrence of viral infectious diseases poses a significant threat to human health. Dengue virus (DENV) infection is one of the most noteworthy of these infections. According to a WHO survey, approximately 400 million people are infected annually; symptoms deteriorate in approximately one percent of cases.

Mordred: a molecular descriptor calculator.

Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints.

Novel Concepts for Drug Hypersensitivity Based on the Use of Long-Time Scale Molecular Dynamic Simulation.

The discovery that several drug hypersensitivity reactions (DHRs) are associated with specific human leukocyte antigen (HLA) alleles has attracted increasing research interest. However, the underlying mechanisms of these HLA-induced DHRs remain unclear, especially for drug-induced immediate activation of T-cell clones (TCCs). Recently, a novel hypothesis involving partial detachment between self-peptide(s) and the HLA molecule (altered peptide-HLA (pHLA) model) has been proposed to explain these phenomena.

In silico analysis of enantioselective binding of immunomodulatory imide drugs to cereblon.

Background: Thalidomide and its analogs, lenalidomide and pomalidomide (referred to as immunomodulatory imide drugs or IMiDs) have been known to treat multiple myeloma and other hematologic malignancies as well as to cause teratogenicity. Recently the protein cereblon was identified as the primary target of IMiDs, and crystallographic studies of the cereblon-IMiDs complex showed strong enantioselective binding for the (S)-enantiomer of IMiDs.

Results: Using the structures of cereblon and IMiDs [both (S)-enantiomers and (R)-enantiomers] we performed docking simulations in order to replicate this enantiomeric selectivity and to identify the region(s) contributing to this selectivity.

Pharmacophore Modeling and Molecular Docking Studies of potential inhibitors to E6 PBM-PDZ from Human Papilloma Virus (HPV).

High-risk human papillomaviruses (HPVs) are known to cause cervical cancer. Vaccines are now available to prevent HPV infection. However, a clinically approved drug is yet not available to treat HPV.

Discovery of novel low-molecular-weight HIV-1 inhibitors interacting with cyclophilin A using in silico screening and biological evaluations.

Cyclophilin A has attracted attention recently as a new target of anti-human immunodeficiency virus type 1 (HIV-1) drugs. However, so far no drug against HIV-1 infection exhibiting this mechanism of action has been approved. To identify new potent candidates for inhibitors, we performed in silico screening of a commercial database of more than 1,300 drug-like compounds by using receptor-based docking studies.

Design and evaluation of antiretroviral peptides corresponding to the C-terminal heptad repeat region (C-HR) of human immunodeficiency virus type 1 envelope glycoprotein gp41.

Two alpha-helical heptad repeats, N-HR and C-HR, located in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp41, play an important role in membrane fusion by forming a 6-helix bundle. C34, a peptide mimicking C-HR, inhibits the formation of the 6-helix bundle; thus, it has potential as a novel antiretroviral compound. In order to improve the inhibitory effect of C34 on HIV-1 replication, we designed new C34-derived peptides based on computational analysis of the stable conformation of the 6-helix bundle.