Using argument notation to engineer biological simulations with increased confidence

The application of computational and mathematical modelling to explore the mechanics of biological systems is becoming prevalent. To significantly impact biological research, notably in developing novel therapeutics, it is critical that the model adequately represents the captured system. Confidence in adopting in silico approaches can be improved by applying a structured argumentation approach, alongside model development and results analysis. We propose an approach based on argumentation from safety-critical systems engineering, where a system is subjected to a stringent analysis of compliance against identified criteria. We show its use in examining the biological information upon which a model is based, identifying model strengths, highlighting areas requiring additional biological experimentation and providing documentation to support model publication. We demonstrate our use of structured argumentation in the development of a model of lymphoid tissue formation, specifically Peyer's Patches. The argumentation structure is captured using Artoo (www.york.ac.uk/ycil/software/artoo), our Web-based tool for constructing fitness-for-purpose arguments, using a notation based on the safety-critical goal structuring notation. We show how argumentation helps in making the design and structured analysis of a model transparent, capturing the reasoning behind the inclusion or exclusion of each biological feature and recording assumptions, as well as pointing to evidence supporting model-derived conclusions

Osteoinduction in human fat derived stem cells by recombinant human bone morphogenetic protein-2 produced in Escherichia coli

Bioactive recombinant human bone morphogenetic protein-2 (rhBMP-2) was obtained using Escherichia coli pET-25b expression system: 55 mg purified rhBMP-2 were achieved per g cell dry wt, with up to 95% purity. In murine C2C12 cell line, rhBMP-2 induced an increase in the transcription of Smads and of osteogenic markers Runx2/Cbfa1 and Osterix, measured by semi-quantitative RT-PCR. Bioassays performed in human fat-derived stem cells showed an increased activity of the early osteogenic marker, alkaline phosphatase, and the absence of cytotoxicity

2013 WSES guidelines for management of intra-abdominal infections

Peer reviewe

Bond strength of resin modified glass ionomer cement to primary dentin after cutting with different bur types and dentin conditioning

The aim of this in vitro study was to evaluate the effect of different bur types and acid etching protocols on the shear bond strength (SBS) of a resin modified glass ionomer cement (RM-GIC) to primary dentin. Forty-eight clinically sound human primary molars were selected and randomly assigned to four groups (n=12). In G1, the lingual surface of the teeth was cut with a carbide bur until a 2.0-mm-diameter dentin area was exposed, followed by the application of RM-GIC (Vitremer - 3M/ESPE) prepared according to the manufacturer's instructions. The specimens of G2, received the same treatment of G1, however the dentin was conditioned with phosphoric acid. In groups G3 and G4 the same procedures of G1 and G2 were conducted respectively, nevertheless dentin cutting was made with a diamond bur. The specimens were stored in distilled water at 37ºC for 24h, and then tested in a universal testing machine. SBS. data were submitted to 2-way ANOVA (= 5%) and indicated that SBS values of RM-GIC bonded to primary dentin cut with different burs were not statistically different, but the specimens that were conditioned with phosphoric acid presented SBS values significantly higher that those without conditioning. To observe micromorphologic characteristics of the effects of dentin surface cut by diamond or carbide rotary instruments and conditioners treatment, some specimens were examined by scanning electron microscopy. Smear layer was present in all specimens regardless of the type of rotary instrument used for dentin cutting, and specimens etched with phosphoric acid presented more effective removal of smear layer. It was concluded that SBS of a RM-GIC to primary dentin was affected by the acid conditioning but the bur type had no influence