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A Hitchhiker's Guide Toward CSF Biomarkers for Neuro-Oncology.
Neuro Oncol
December 2024
Department of Neurological Surgery, Mayo Clinic, Rochester, MN, USA.
Cerebrospinal fluid (CSF) has emerged as a valuable liquid biopsy source for glioma biomarker discovery and validation. CSF produced within the ventricles circulates through the subarachnoid space, where the composition of glioma-derived analytes is influenced by the proximity and anatomical location of sampling relative to tumor, in addition to underlying tumor biology. The substantial gradients observed between lumbar and intracranial CSF compartments for tumor-derived analytes underscore the importance of sampling site selection.
View Article and Find Full Text PDFA hitchhiker's guide to active motion.
Eur Phys J E Soft Matter
January 2025
Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
Intelligent decisions in response to external informative input can allow organisms to achieve their biological goals while spending very little of their own resources. In this paper, we develop and study a minimal model for a navigational task, performed by an otherwise completely motorless particle that possesses the ability of hitchhiking in a bath of active Brownian particles (ABPs). Hitchhiking refers to identifying and attaching to suitable surrounding bath particles.
View Article and Find Full Text PDFA hitchhiker's guide to deep chemical language processing for bioactivity prediction.
Digit Discov
December 2024
Eindhoven University of Technology, Institute for Complex Molecular Systems, Eindhoven AI Systems Institute, Dept. Biomedical Engineering Eindhoven Netherlands
Deep learning has significantly accelerated drug discovery, with 'chemical language' processing (CLP) emerging as a prominent approach. CLP approaches learn from molecular string representations (, Simplified Molecular Input Line Entry Systems [SMILES] and Self-Referencing Embedded Strings [SELFIES]) with methods akin to natural language processing. Despite their growing importance, training predictive CLP models is far from trivial, as it involves many 'bells and whistles'.
View Article and Find Full Text PDFA hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.
Int J Cancer
December 2024
Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) & University Medical Center Utrecht, Utrecht, The Netherlands.
Genetic mutations are well known to influence tumorigenesis, tumor progression, treatment response and relapse, but the role of epigenetic variation in cancer progression is still largely unexplored. The lack of epigenetic understanding in cancer evolution is in part due to the limited availability of methods to examine such a heterogeneous disease. However, in the last decade the development of several single-cell methods to profile diverse chromatin features (chromatin accessibility, histone modifications, DNA methylation, etc.
View Article and Find Full Text PDFComputer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.
J Comput Chem
January 2025
Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc, Czech Republic.
Guanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies, as GQs are potential targets for anticancer drugs and other therapeutics. Although experimental and theoretical techniques have provided valuable insights into different stages of the GQ folding, the structural complexity of GQs poses significant challenges, and our understanding remains incomplete.
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