Journal: BMC Genomics

Article Title: Metagenomic assemblies tend to break around antibiotic resistance genes

doi: 10.1186/s12864-024-10876-0

Figure Lengend Snippet: Visual representation of assembly results. The example used is one of the plasmids AP023079, containing two ARGs blaNDM and aph(3’’)-Ib . A visual representation of the plasmid was done using FARAO with light gray representing the backbone plasmid and the other colors representing correctly assembled contigs from samples with different total number of reads (“low” in pink, “medium” in teal, “high” in purple and “very high” in blue) and ARGs are in red. A visual representation of the corresponding assembly graphs was done using Bandage. The figures represent only part of the whole assembly graph corresponding to the AP023079 plasmid sequence, where blue lines correspond to BLAST hits of the assembled contigs to the plasmid and pink lines to the ARG regions

Article Snippet: First, the Illumina reads were mapped to each assembly using bowtie2 2.3.5.1 [ ] and the coverage was estimated for all full and truncated ARG hits (minimum 95% identity and 80% coverage) on the assembled contigs using the FARAO [ ] estimate_coverage function with -c 0 flag estimating coverage per all bases across the feature.

Techniques: Plasmid Preparation, Sequencing

Journal: BMC Genomics

Article Title: Metagenomic assemblies tend to break around antibiotic resistance genes

doi: 10.1186/s12864-024-10876-0

Figure Lengend Snippet: ARG quantification using either assembled contigs as a reference or by directly mapping short reads to the ResFinder database . Per base total coverage calculated using FARAO from aligning reads to the contigs, and using direct ARG quantification by mapping reads to the ResFinder database ( A ) and ResFinder clustered to 90% identity ( B )

Article Snippet: First, the Illumina reads were mapped to each assembly using bowtie2 2.3.5.1 [ ] and the coverage was estimated for all full and truncated ARG hits (minimum 95% identity and 80% coverage) on the assembled contigs using the FARAO [ ] estimate_coverage function with -c 0 flag estimating coverage per all bases across the feature.

Techniques:

Journal: Journal of Personalized Medicine

Article Title: Shear Wave Dispersion in Chronic Liver Disease: From Physical Principles to Clinical Usefulness

doi: 10.3390/jpm13060945

Figure Lengend Snippet: Clinical studies utilising shear wave dispersion (SWD) for CLD with mixed aetiologies.

Article Snippet: Currently, commercially available equipment with the SWD estimation function provides the result as SWDS, which is measured in (m/s)/kHz (i.e., by Aplio, Canon, Japan), or as a viscosity index, which is measured in Pa·s (i.e., by the Supersonic Shear Imagine (SSI, France) device using the Vi.Plus software).

Techniques: Shear, Dispersion, Activity Assay, Modification, Viscosity

Journal: Journal of Personalized Medicine

Article Title: Shear Wave Dispersion in Chronic Liver Disease: From Physical Principles to Clinical Usefulness

doi: 10.3390/jpm13060945

Figure Lengend Snippet: Clinical studies utilising shear wave dispersion (SWD) for non-alcoholic fatty liver disease (NAFLD).

Article Snippet: Currently, commercially available equipment with the SWD estimation function provides the result as SWDS, which is measured in (m/s)/kHz (i.e., by Aplio, Canon, Japan), or as a viscosity index, which is measured in Pa·s (i.e., by the Supersonic Shear Imagine (SSI, France) device using the Vi.Plus software).

Techniques: Shear, Dispersion, Viscosity, Biomarker Discovery