Datasets

Rationale: AXL expression has been identified as a prognostic factor in acute myeloid leukemia (AML) and is detectable in approximately 50% of AML patients. In this study, we developed AXL-specific single domain antibodies (sdAbs), cross-reactive for both mouse and human AXL protein, to non-invasively image and treat AXL-expressing cancer cells. Methods: AXL-specific sdAbs were induced by immunizing an alpaca with mouse and human AXL proteins. SdAbs were characterized using ELISA, flow cytometry, surface plasmon resonance and the AlphaFold2 software. A lead compound was selected and labeled ...

Additional file of A controlled study on the diagnostic accuracy of panoramic and peri-apical radiography for detecting furcation involvement

run_epcr.py is a Python script for batch in-silico PCR and probe finding. It scans an input directory for genome FASTA files and runs in-silico PCR on each file in parallel, reporting amplicons and probe matches. Features: Supports batch and single-genome in-silico PCR. Handles IUPAC ambiguity codes in primers and probes. Allows fuzzy matching (mismatches and indels). Parallel processing using multiple CPU threads. Outputs results as TSV tables, FASTA files, and amplicon count matrices. Logging to file and console. Latest version at https://gitlab.ilvo.be/stevebaeyen/run_epcr

This repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries. The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/bacterial-assembly-qc-snakemake

This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies. The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/nanopore-only-bacterial-assembly-snakemake.

This Illumina bacterial assembly snakemake repo is a snakemake workflow to assemble bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification, installation instructions provided in the README). The latest version of the scripts can be found at https://gitlab.ilvo.be/genomics/wgs/illumina-bacterial-assembly-snakemake.

The dataset contains the data supporting the development of dielectric spectroscopy using Nuclear Magnetic Resonance (NMR) probe heads. It shows how the detuning of the NMR probe head upon insertion of a sample can be be related to the dielectric permittivity of the sample. The dataset contains calibration curves for these measurements using standard commercial probe heads and the dielectric spectra of methanol, ethanol, 1-propanol, 1-pentanol, 1-octanol and water confined in a ZSM5-type (MFI) zeolite acquired using the new technique. Replication data of the paper published in DOI: ...

Mutations in the gene coding for leucine-rich repeat kinase 2 (LRRK2) are a leading cause of the inherited form of Parkinson's disease (PD), while LRRK2 overactivation is also associated with the more common idiopathic form of PD. LRRK2 is a large multidomain protein, including a GTPase as well as a Ser/Thr protein kinase domain. Common, disease-causing mutations increase LRRK2 kinase activity, presenting LRRK2 as an attractive target for drug discovery. Currently, drug development has mainly focused on ATP-competitive kinase inhibitors. Here, we report the identification and characterization ...

In the last decade, High-Throughput Sequencing (HTS) has revolutionized biology and medicine. This technology allows the sequencing of huge amount of DNA and RNA fragments at a very low price. In medicine, HTS tests for disease diagnostics are already brought into routine practice. However, the adoption in plant health diagnostics is still limited. One of the main bottlenecks is the lack of expertise and consensus on the standardization of the data analysis. The Plant Health Bioinformatic Network (PHBN) is an Euphresco project aiming to build a community network of ...

Theranostic systems that integrate therapeutic delivery with diagnostic imaging hold strong potential in biomedical applications. Nanocarriers with imaging and controlled release functions enable real-time tracking and localization of therapeutics, while hydrogels with diagnostic capabilities support applications such as sustained drug release, cell encapsulation, and cell tracking. Fluorine-19 magnetic resonance imaging (19F MRI) is a promising non-invasive complement to conventional proton MRI, though its clinical translation remains limited by the lack of optimal tracer systems. Herein, we ...