Evaluation of the performance of five diagnostic tests for Fasciola hepatica infection in naturally infected cattle using a Bayesian no gold standard approach

The clinical and economic importance of fasciolosis has been recognised for centuries, yet diagnostic tests available for cattle are far from perfect. Test evaluation has mainly been carried out using gold standard approaches or under experimental settings, the limitations of which are well known. In this study, a Bayesian no gold standard approach was used to estimate the diagnostic sensitivity and specificity of five tests for fasciolosis in cattle. These included detailed liver necropsy including gall bladder egg count, faecal egg counting, a commercially available copro-antigen ELISA, an in-house serum excretory/secretory antibody ELISA and routine abattoir liver inspection. In total 619 cattle slaughtered at one of Scotland’s biggest abattoirs were sampled, during three sampling periods spanning summer 2013, winter 2014 and autumn 2014. Test sensitivities and specificities were estimated using an extension of the Hui Walter no gold standard model, where estimates were allowed to vary between seasons if tests were a priori believed to perform differently for any reason. The results of this analysis provide novel information on the performance of these tests in a naturally infected cattle population and at different times of the year where different levels of acute or chronic infection are expected. Accurate estimates of sensitivity and specificity will allow for routine abattoir liver inspection to be used as a tool for monitoring the epidemiology of F. hepatica as well as evaluating herd health planning. Furthermore, the results provide evidence to suggest that the copro-antigen ELISA does not cross-react with Calicophoron daubneyi rumen fluke parasites, while the serum antibody ELISA does

The impact of transposable element activity on therapeutically relevant human stem cells

Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapiesS.R.H. and P.T.R. are funded by the Government of Spain (MINECO, RYC-2016- 21395 and SAF2015–71589-P [S.R.H.]; PEJ-2014-A-31985 and SAF2015–71589- P [P.T.R.]). GGS is supported by a grant from the Ministry of Health of the Federal Republic of Germany (FKZ2518FSB403)

Chemical stability and leaching behavior of one-part geopolymer from soil and coal fly ash mixtures

Aluminosilicate minerals have become an important resource for an emerging sustainable material for construction known as geopolymer. Geopolymer, an alkali-activated material, is becoming an attractive alternative to Portland cement because of its lower carbon footprint and embodied energy. However, the synthesis process requires typically a two-part system for alkali activation wherein the solid geopolymer precursor is mixed with aqueous alkali solutions. These alkali activators are corrosive and may be difficult to handle in the field-scale application. In this study, a one-part geopolymer in which coal fly ash was mixed with solid alkali activators such as sodium hydroxide and sodium silicate to form a powdery cementitious binder was developed. This binder mixed with soil only requires water to form the soil-fly ash (SO-CFA) geopolymer cement, which can be used as stabilized soil for backfill/foundation. This geopolymer product was then evaluated for chemical stability by immersing the material with 5% by weight of sulfuric acid solution for 28 days. Indication suggests that the geopolymer exhibited high resistance against acid attack with an observed increase of unconfined compressive strength even when the immersion time in acidic solution was increased to 56 days. The mineralogical phase, microstructure, and morphology of the material were characterized by X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX), respectively. Results not only confirmed the formation of gypsum due to acid attack but also indicated the dissolution of anorthite and albite that may have caused the microstructure to be composed of sodium aluminosilicate hydrate (N–A–S–H) and calcium (alumino) silicate hydrate (C(–A)–S–H) with poly(ferro-sialate-siloxo) and poly(ferro-sialate-disiloxo) networks. A column leaching test with deionized water was also performed on the soil-fly ash geopolymer to study the leachability of metals in the material. Results showed that arsenic exhibits higher mobility in the geopolymer as compared to that of cadmium, chromium, and lead

Identification of misclassified ClinVar variants using disease population prevalence

ABSTRACTThere is a significant interest in the standardized classification of human genetic variants. The availability of new large datasets generated through genome sequencing initiatives provides a ground for the computational evaluation of the supporting evidence. We used whole genome sequence data from 8,102 unrelated individuals to analyze the adequacy of estimated rates of disease on the basis of genetic risk and the expected population prevalence of the disease. Analyses included the ACMG recommended 56 gene-condition sets for incidental findings and 631 genes associated with 348 OrphaNet conditions. A total of 21,004 variants were used to identify patterns of inflation (i.e. excess genetic risk). Inflation, i.e., misclassification, increases as the level of evidence in ClinVar supporting the pathogenic nature of the variant decreases. The burden of rare variants was a main contributing factor of the observed inflation indicating misclassified benign private mutations. We also analyzed the dynamics of re-classification of variant pathogenicity in ClinVar over time. The study strongly suggests that ClinVar includes a significant proportion of wrongly ascertained variants, and underscores the critical role of ClinVar to contrast claims, and foster validation across submitters.</jats:p