The methodology for endoluminal irreversible electroporation in porcine models

The aim of this study was to describe the methodology of the surgical technique for endoluminal irreversible electroporation in the biliary tract performed within the perihilar region in porcine models. Endoluminal irreversible electroporation of the common bile duct was performed on eight porcine models using an endoluminal device inserted during laparotomy. The endoluminal device consisted of three electrodes 1 cm in length, attached at 120 degrees around the balloon catheter. The procedure was conducted with the following parameters: number of pulses 90, voltage of 1500 V between each couple of electrodes. Cross sectional imaging and histopathological assessment were employed for evaluations of the ablation zone. Models were sacrificed 24 h and 96 h after ablation. The treatment was successful in all porcine models. All animals survived the defined study period. Peri-ablation oedema within the hepatoduodenal ligament and adjacent liver tissue could be measured on post-procedural MRI or CT. Perforation in the site of ablation developed in one model. Histopathological examination showed heavy regressive changes of the ablated tissue. The elastic membranes of the adjacent portal vein were preserved in all models. In our experience, this novel endoluminal modality used within the perihilar region in porcine models is a feasible and well predictable procedure. Further studies should explore the optimal protocol of catheter-based ablation to limit complications

Niget: Nanoindentation general evaluation tool

We introduce Niget, a new tool for evaluating nanoindentation measurement data. Unlike software provided by the manufacturers of most indentation devices, Niget offers a range of analysis methods with adjustable parameters and evaluates measurement uncertainties. Keywords: Nanoindentation, Uncertainties, Orthogonal distance regressio

16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling

Abstract 16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio of human to bacterial DNA. However, due to the off-target amplification of human DNA, current protocols are inadequate for bioptic samples. Here we present an efficient, reliable, and affordable method for the bacteriome analysis of clinical samples human DNA content predominates. We determined the microbiota profile in a total of 40 human biopsies of the esophagus, stomach, and duodenum using 16S rRNA amplicon sequencing with the widely used 515F-806R (V4) primers targeting the V4 region, 68F-338R primers and a modified set of 68F-338R (V1-V2M) primers targeting the V1–V2 region. With the V4 primers, on average 70% of amplicon sequence variants (ASV) mapped to the human genome. On the other hand, this off-target amplification was absent when using the V1–V2M primers. Moreover, the V1–V2M primers provided significantly higher taxonomic richness and reproducibility of analysis compared to the V4 primers. We conclude that the V1–V2M 16S rRNA sequencing method is reliable, cost-effective, and applicable for low-bacterial abundant human samples in medical research