Published in Genome Biology
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large ge...
Published in npj Breast Cancer
Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management frame...
Published in Veterinary Research
The porcine Helicobacter suis and canine-feline H. heilmannii are gastric Helicobacter species with zoonotic potential. However, little is known about the pathogenesis of human infections with these Helicobacter species. To gain more insight into the interactions of both zoonotic Helicobacter species with human gastric epithelial cells, we investig...
Published in Veterinary Research
The presence of non-aureus staphylococci (NAS) in bovine rectal feces has recently been described. Similar to other mastitis causing pathogens, shedding of NAS in the environment could result in intramammary infection. The objective of this study was to investigate whether NAS strains present in feces can cause intramammary infection, likely via te...
Published in Scientific Data
Measurement(s) Diversity • Fish • spatial patternTechnology Type(s)digital curationFactor Type(s)geographic locationSample Characteristic - OrganismfishSample Characteristic - Environmentdrainage basinSample Characteristic - LocationAmazon Basin Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11920800
Published in Veterinary Research
Butyrate has been used extensively as a feed additive to improve gut health and to decrease Salmonella colonization in poultry. Salmonella mainly colonizes the ceca so butyrate concentrations should be increased in this gut segment. Discrepancies on the effects of butyrate on Salmonella colonization, described in the scientific literature, could th...
Published in npj Breast Cancer
Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variabili...
Published in Scientific Data
Measurement(s) species abundance • species trait • environmental feature • latitude • longitudeTechnology Type(s)digital curationFactor Type(s)year of data collection • type of ecosystem • level of human disturbanceSample Characteristic - Environmentterrestrial natural environment • fresh water • marine biome • anthropogenic terrestrial biome • nat...
Published in npj Breast Cancer
Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research comm...
Published in Microbiome
BackgroundThe archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.MethodsFollowing the rec...
