Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.

Aims, Patients & Methods: Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.

A Novel Model Using Serum Thymidine Kinase 1 and Low-dose Computed Tomography Parameters to Predict Three-year Lung Cancer Risk in People with Pulmonary Nodules: A Retrospective Study.

This study was designed to develop a model of serum thymidine kinase 1 protein (STK1p) concentration in combination with low-dose computed tomography (LDCT) to predict the risk of benign pulmonary nodules progressing into lung cancer within three years in a large screening population. The study included a retrospective cohort of 6,841 individuals aged > 30 years who had LDCT-detected pulmonary nodules, but no cancer history or baseline cancer. The outcome was a lung cancer diagnosis recorded within three years after the first detection of pulmonary nodules.

Development of a Novel Recombinant Full-Length IgY Monoclonal Antibody against Human Thymidine Kinase 1 for Automatic Chemiluminescence Analysis on a Sandwich Biotin-Streptavidin Platform for Early Tumour Discovery.

Serum thymidine kinase 1 protein (STK1p) concentration has been used successfully as a reliable proliferating serum biomarker in early tumour discovery and clinical settings. It is detected by an enhanced chemiluminescence (ECL) dot blot assay with the biotin-streptavidin (BSA) platform (a gold standard) based on chicken anti-human thymidine kinase 1 IgY polyclonal antibody (hTK1-IgY-pAb). However, ECL dot blotting is a semiautomatic method that has been limited to large-scale applications due to the differences among batches of antibodies from individual hens, and the skill level of operation technicians sometimes results in unstable STK1p values.

Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.

Motivation: Feature-based counting is commonly used in RNA-sequencing (RNA-seq) analyses. Here, sequences must align to target features (like genes or non-coding RNAs) and related sequences with different compositions are counted into the same feature. Consequently, sequence integrity is lost, making results less traceable against raw data.