Genetics

Crisis averted: a world united against the menace of multiple drug-resistant superbugs -pioneering anti-AMR vaccines, RNA interference, nanomedicine, CRISPR-based antimicrobials, bacteriophage therapies, and clinical artificial intelligence strategies to safeguard global antimicrobial arsenal.

The efficacy of antibiotics and other antimicrobial agents in combating bacterial infections faces a grave peril in the form of antimicrobial resistance (AMR), an exceedingly pressing global health issue. The emergence and dissemination of drug-resistant bacteria can be attributed to the rampant overuse and misuse of antibiotics, leading to dire consequences such as organ failure and sepsis. Beyon...

Identifying unique exposure-specific transgenerational differentially DNA methylated region epimutations in the genome using hybrid deep learning prediction models.

Exposure to environmental toxicants can lead to epimutations in the genome and an increase in differential DNA methylated regions (DMRs) that have been linked to increased susceptibility to various diseases. However, the unique effect of particular toxicants on the genome in terms of leading to unique DMRs for the toxicants has been less studied. One hurdle to such studies is the low number of obs...

Circulating tumor DNA for monitoring classic Hodgkin lymphoma patients: Correlation with FDG-PET/CT.

The value of circulating tumor DNA (ctDNA) as a biomarker of disease activity in classic Hodgkin lymphoma (cHL) patients has not yet been well establi...

Identifying Explainable Machine Learning Models and a Novel SFRP2 Fibroblast Signature as Predictors for Precision Medicine in Ovarian Cancer.

Ovarian cancer (OC) is a type of malignant tumor with a consistently high mortality rate. The diagnosis of early-stage OC and identification of functi...

Quantitative Modeling of Stemness in Single-Cell RNA Sequencing Data: A Nonlinear One-Class Support Vector Machine Method.

Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemne...

Label-free identification of protein aggregates using deep learning.

Protein misfolding and aggregation play central roles in the pathogenesis of various neurodegenerative diseases (NDDs), including Huntington's disease...

Deep-qGFP: A Generalist Deep Learning Assisted Pipeline for Accurate Quantification of Green Fluorescent Protein Labeled Biological Samples in Microreactors.

Absolute quantification of biological samples provides precise numerical expression levels, enhancing accuracy, and performance for rare templates. Cu...

XGraphCDS: An explainable deep learning model for predicting drug sensitivity from gene pathways and chemical structures.

Cancer is a highly complex disease characterized by genetic and phenotypic heterogeneity among individuals. In the era of precision medicine, understa...

What are the most relevant publications in Clinical Microbiology in the last two years?

This minireview describes some of the articles published in the last two years related to innovative technologies including CRISPR-Cas, surface-enhanc...

CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms.

Linking cis-regulatory sequences to target genes has been a long-standing challenge. In this study, we introduce CREaTor, an attention-based deep neur...

Waterborne pathogens detection technologies: advances, challenges, and future perspectives.

The World Health Organization (WHO) estimated that pathogens like Escherichia coli, primarily linked to food and water contamination, are associated w...

Identifying the Interaction Between Tuberculosis and SARS-CoV-2 Infections via Bioinformatics Analysis and Machine Learning.

The number of patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 is still increasing. In the case of COVID-19 and tuberc...

The Performance of Machine Learning for Prediction of H3K27 M Mutation in Midline Gliomas: A Systematic Review and Meta-Analysis.

BACKGROUND: Diffuse midline gliomas (DMGs) encompass a set of tumors, and those tumors with H3K27 M mutation carry a poor prognosis. In recent years, ...

Machine learning and single-cell transcriptome profiling reveal regulation of fibroblast activation through THBS2/TGFβ1/P-Smad2/3 signalling pathway in hypertrophic scar.

Hypertrophic scar (HS) is a chronic inflammatory skin disorder characterized by excessive deposition of extracellular matrix, and the mechanisms under...

Transformer with convolution and graph-node co-embedding: An accurate and interpretable vision backbone for predicting gene expressions from local histopathological image.

Inferring gene expressions from histopathological images has long been a fascinating yet challenging task, primarily due to the substantial disparitie...

Phase retrieval for X-ray differential phase contrast radiography with knowledge transfer learning from virtual differential absorption model.

Grating-based X-ray phase contrast radiography and computed tomography (CT) are promising modalities for future medical applications. However, the ill...

Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction.

Machine learning has been increasingly utilized in the field of protein engineering, and research directed at predicting the effects of protein mutati...

DCDA: CircRNA-Disease Association Prediction with Feed-Forward Neural Network and Deep Autoencoder.

Circular RNA is a single-stranded RNA with a closed-loop structure. In recent years, academic research has revealed that circular RNAs play critical r...

Differences in the choice of beef artificial insemination sires used by dairy producers versus beef producers.

The growing demand among dairy producers for suitable beef sires to mate to their females creates the possibility of separate breeding programs to gen...

DNABERT-based explainable lncRNA identification in plant genome assemblies.

Long non-coding ribonucleic acids (lncRNAs) have been shown to play an important role in plant gene regulation, involving both epigenetic and transcri...