The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic human coronaviruses (CoVs). Anti-CoVs mAbs and vaccines may be effective, but the emergence of neutralization escape variants is inevitable. Angiotensin-converting enzyme 2 and dipeptidyl peptidase 4 enzyme are the getaway receptors for SARS-CoV-2 and MERS-CoV, respectively. Thus, we reformatted these receptors as Fc-fusion decoy receptors. Then, we tested them in parallel with anti-SARS-CoV (ab1-IgG) and anti-MERS-CoV (M336-IgG) mAbs against several variants using pseudovirus neutralization assay. The generated Fc-based decoy receptors exhibited a strong inhibitory effect against all pseudotyped CoVs. Results showed that although mAbs can be effective antiviral drugs, they might rapidly lose their efficacy against highly mutated viruses. We suggest that receptor traps can be engineered as Fc-fusion proteins for highly mutating viruses with known entry receptors, for a faster and effective therapeutic response even against virus harboring antibodies escape mutations.

Cellular molecules interact with one another in a structured manner, defining a regulatory network topology that describes cellular mechanisms. Genetic mutations alter these networks’ pathways, generating complex disorders such as autism spectrum disorder (ASD). Boolean models have assisted in understanding biological system dynamics since Kauffman’s 1969 discovery, and various analytical tools for regulatory networks have been developed. This study examined the protein–protein interaction network created in our previous publication of four ASD patients using the SPIDDOR R package, a Boolean model-based method. The aim is to examine how patients’ genetic variations in INTS6L, USP9X, RSK4, FGF5, FLNA, SUMF1, and IDS affect mTOR and Wnt cell signaling convergence. The Boolean network analysis revealed abnormal activation levels of essential proteins such as β-catenin, MTORC1, RPS6, eIF4E, Cadherin, and SMAD. These proteins affect gene expression, translation, cell adhesion, shape, and migration. Patients 1 and 2 showed consistent patterns of increased β-catenin activity and decreased MTORC1, RPS6, and eIF4E activity. However, patient 2 had an independent decrease in Cadherin and SMAD activity due to the FLNA mutation. Patients 3 and 4 have an abnormal activation of the mTOR pathway, which includes the MTORC1, RPS6, and eIF4E genes. The shared mTOR pathway behavior in these patients is explained by a shared mutation in two closely related proteins (SUMF1 and IDS). Diverse activities in β-catenin, MTORC1, RPS6, eIF4E, Cadherin, and SMAD contributed to the reported phenotype in these individuals. Furthermore, it unveiled the potential therapeutic options that could be suggested to these individuals.

Variations in the genetic code for proteins are considered to confer traits and underlying disease. Identifying the functional consequences of these genetic variants is a challenging endeavor. There are online databases that contain variant information. Many publications also have described variants in detail. Furthermore, there are tools that allow for the prediction of the pathogenicity of variants. However, navigating these disparate sources is time-consuming and sometimes complex. Finally, text mining and large language models offer promising approaches to understanding the textual form of this knowledge. This review discusses these challenges and the online resources and tools available to facilitate this process. Furthermore, a computational framework is suggested to accelerate and facilitate the process of identifying the phenotype caused by a particular genetic variant. This framework demonstrates a way to gather and understand the knowledge about variants more efficiently and effectively.

Text mining methods are being developed to assimilate the volume of biomedical textual materials that are continually expanding. Understanding protein–protein interaction (PPI) deficits would assist in explaining the genesis of diseases. In this study, we designed an automated system to extract PPIs from the biomedical literature that uses a deep learning sentence classification model, a pretrained word embedding, and a BiLSTM recurrent neural network with additional layers, a conditional random field (CRF) named entity recognition (NER) model, and shortest-dependency path (SDP) model using the SpaCy library in Python. The automated system ensures that it targets sentences that contain PPIs and not just these proteins mentioned in the framework of disease discovery or other context. Our first model achieved 13% greater precision on the Aimed/BioInfr benchmark corpus than the previous state-of-the-art BiLSTM neural network models. The NER model presented in this study achieved 98% precision on the Aimed/BioInfr corpus over previous models. In order to facilitate the production of an accurate representation of the PPI network, the processes were developed to systematically map the protein interactions in the texts. Overall, evaluating our system through the use of 6027 abstracts pertaining to seven proteins associated with Autism Spectrum Disorder completed the manually curated PPI network for these proteins. When it comes to complicated diseases, these networks would assist in understanding how PPI deficits contribute to disease development while also emphasizing the influence of interactions on protein function and biological processes.

Background/Objectives: Transmission electron microscopy (TEM) is an essential tool for diagnosing renal diseases. It produces high-resolution visualization of glomerular and mesangial ultrastructural features. However, manual interpretation of TEM images is labor-intensive and prone to interobserver variability. In this study, we introduced and evaluated deep learning architectures based on YOLOv8-OBB for automated detection of six ultrastructural features in kidney biopsy TEM images: glomerular basement membrane, mesangial folds, mesangial deposits, normal podocytes, podocytopathy, and subepithelial deposits. Methods: Building on our previous work, we propose a modified YOLOv8-OBB architecture that incorporates three major refinements: a grayscale input channel, a high-resolution P2 feature pyramid with refinement blocks (FPRbl), and a four-branch oriented detection head designed to detect small-to-large structures at multiple image scales (feature-map strides of 4, 8, 16, and 32 pixels). We compared two pretrained variants: our previous YOLOv8-OBB model developed with a grayscale input channel (GSch) and four additional feature-extraction layers (4FExL) (Pretrained + GSch + 4FExL) and the newly developed (Pretrained + FPRbl). Results: Quantitative assessment showed that our previously developed model (Pretrained + GSch + 4FExL) achieved an F1-score of 0.93 and mAP@0.5 of 0.953, while the (Pretrained + FPRbl) model developed in this study achieved an F1-score of 0.92 and mAP@0.5 of 0.941, demonstrating strong and clinically meaningful performance for both approaches. Qualitative assessment based on expert visual inspection of predicted bounding boxes revealed complementary strengths: (Pretrained + GSch + 4FExL) exhibited higher recall for subtle or infrequent findings, whereas (Pretrained + FPRbl) produced cleaner bounding boxes with higher-confidence predictions. Conclusions: This study presents how targeted architectural refinements in YOLOv8-OBB can enhance the detection of small, low-contrast, and variably oriented ultrastructural features in renal TEM images. Evaluating these refinements and translating them into a web-based platform (Renal-AI) showed the clinical applicability of deep learning-based tools for improving diagnostic efficiency and reducing interpretive variability in kidney pathology.