RORS: Enhanced Rule-based OWL Reasoning on Spark

The rule-based OWL reasoning is to compute the deductive closure of an ontology by applying RDF/RDFS and OWL entailment rules. The performance of the rule-based OWL reasoning is often sensitive to the rule execution order. In this paper, we present an approach to enhancing the performance of the rule-based OWL reasoning on Spark based on a locally optimal executable strategy. Firstly, we divide all rules (27 in total) into four main classes, namely, SPO rules (5 rules), type rules (7 rules), sameAs rules (7 rules), and schema rules (8 rules) since, as we investigated, those triples corresponding to the first three classes of rules are overwhelming (e.g., over 99% in the LUBM dataset) in our practical world. Secondly, based on the interdependence among those entailment rules in each class, we pick out an optimal rule executable order of each class and then combine them into a new rule execution order of all rules. Finally, we implement the new rule execution order on Spark in a prototype called RORS. The experimental results show that the running time of RORS is improved by about 30% as compared to Kim & Park's algorithm (2015) using the LUBM200 (27.6 million triples).Comment: 12 page

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Experimental and modeling investigation on the viscoelastic-viscoplastic deformation of polyamide 12 printed by multi jet fusion

The viscoelastic-viscoplastic deformation of Multi Jet Fusion-printed polyamide 12 (MJF PA12) was investigated with experimental and numerical approaches. Multi-loading–unloading–recovery tests were conducted to distinguish between the viscoelastic and viscoplastic deformations. The influence of the void defects on deformation of PA12 was investigated through the microcomputed tomography (μCT) and field emission scanning electron microscope. A finite-strain viscoelastic-viscoplastic constitutive model based on the logarithmic stress rate for the matrix of MJF PA12 was developed within the thermodynamic framework as well as an introduction of the accumulated plastic deformation–induced damage into the proposed model. A representative volume element was modeled based on the μCT results of MJF PA12. The simulated results, such as stress–strain and strain–time curves, agreed with the experimental results. Moreover, the model revealed the mechanism that the low tensile ductility of MJF PA12 is caused by the increase in strain localization and narrowing of the shear band.Part of this research was conducted in collaboration with HP Inc. and supported by Nanyang Technological University and the Singapore Government through the Industry Alignment Fund-Industry Collaboration Projects Grant (I1801E0028)

Achieving work hardening by forming boundaries on the nanoscale in a Ti-based metallic glass matrix composite

Achieving work hardening in metallic glass matrix composites (MGMCs) is the key to the extensive use of these attractive materials in structural and functional applications. In this study, we investigated the formation of nanoscale boundaries resulted from the interaction between matrix and dendrites, which favors the work-hardening deformation in an in-situ Ti41Zr32Ni6Ta7Be14 MGMC with β-Ti dendrites in a glassy matrix at room temperature. The microstructures of samples after tension were observed by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD). The work-hardening mechanism of the present composites involves: (1) appearance of dense dislocation walls (DDWs), (2) proliferation of shear bands, (3) formation of boundaries on the nanoscale, and (4) interactions between hard and soft phases. A theoretical model combined with experimental data reveals the deformation mechanisms in the present work, proving that the in-situ dendrites with outstanding hardening ability in the glass matrix can provide the homogeneous deformation under tensile loading at room temperature

Heterodimeric interaction and interfaces of S100A1 and S100P

With the widespread use of yeast two-hybrid systems, many heterodimeric forms of S100 proteins have been found, although their biological significance is unknown. In the present study, S100A1 was found to interact with another S100 protein, S100P, by using the yeast two-hybrid system. The binding parameters of the interaction were obtained using an optical biosensor and show that S100P has a slightly higher affinity for S100A1 (K(d)=10–20 nM) when compared with that for self-association (K(d)=40–120 nM). The physical interaction of S100A1 and S100P was also demonstrated in living mammalian cells using a fluorescence resonance energy transfer technique. Preincubation of recombinant S100P with S100A1, before the biosensor assay, reduced by up to 50% the binding of S100P to a recombinant C-terminal fragment of non-muscle myosin A, one of its target molecules. Site-specific mutations of S100P and S100A1, combined with homology modelling of an S100P/S100A1 heterodimer using known S100P and S100A1 structures, allowed the hydrophobic interactions at the dimeric interface of the heterodimer to be defined and provide an explanation for the heterodimerization of S100P and S100A1 at the molecular level. These results have revealed the similarities and the differences between the S100P homodimer and the S100A1/S100P heterodimer