LBFextract: Unveiling transcription factor dynamics from liquid biopsy data.

Motivation: The analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns.

Results: We introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies.

GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level.

Analyses of cell-free DNA (cfDNA) are increasingly being employed for various diagnostic and research applications. Many technologies aim to increase resolution, e.g.

Blocking STAT3/5 through direct or upstream kinase targeting in leukemic cutaneous T-cell lymphoma.

Leukemic cutaneous T-cell lymphomas (L-CTCL) are lymphoproliferative disorders of skin-homing mature T-cells causing severe symptoms and high mortality through chronic inflammation, tissue destruction, and serious infections. Despite numerous genomic sequencing efforts, recurrent driver mutations have not been identified, but chromosomal losses and gains are frequent and dominant. We integrated genomic landscape analyses with innovative pharmacologic interference studies to identify key vulnerable nodes in L-CTCL.

Dynamic Changes of Circulating Tumor DNA Predict Clinical Outcome in Patients With Advanced Non-Small-Cell Lung Cancer Treated With Immune Checkpoint Inhibitors.

Purpose: Immune checkpoint inhibitors (ICIs) are increasingly being used in non-small-cell lung cancer (NSCLC), yet biomarkers predicting their benefit are lacking. We evaluated if on-treatment changes of circulating tumor DNA (ctDNA) from ICI start (t) to after two cycles (t) assessed with a commercial panel could identify patients with NSCLC who would benefit from ICI.

Patients And Methods: The molecular ctDNA response was evaluated as a predictor of radiographic tumor response and long-term survival benefit of ICI.

Technical Evaluation of Commercial Mutation Analysis Platforms and Reference Materials for Liquid Biopsy Profiling.

Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven.

Influence of Bitter Taste on Affective Facial Processing: An ERP Study.

Previous research showed that a bitter taste in the mouth is able to enhance hostile response tendencies to social rejection. The present event-related potential (ERP) study sought to investigate neuronal components of this effect. We presented 52 participants (39 women and 13 men; mean age = 23.

Disgust evoked by strong wormwood bitterness influences the processing of visual food cues in women: An ERP study.

The perception of intense bitterness is associated with disgust and food rejection. The present cross-modal event-related potential (ERP) study investigated whether a bitter aftertaste is able to influence affective ratings and the neuronal processing of visual food cues. We presented 39 healthy normal-weight women (mean age: 22.