Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen Fasciola hepatica:Expansion of a repertoire of virulence-associated factors

Cathepsin L proteases secreted by the helminth pathogen Fasciola hepatica have functions in parasite virulence including tissue invasion and suppression of host immune responses. Using proteomics methods alongside phylogenetic studies we characterized the profile of cathepsin L proteases secreted by adult F. hepatica and hence identified those involved in host-pathogen interaction. Phylogenetic analyses showed that the Fasciola cathepsin L gene family expanded by a series of gene duplications followed by divergence that gave rise to three clades associated with mature adult worms (Clades 1, 2, and 5) and two clades specific to infective juvenile stages (Clades 3 and 4). Consistent with these observations our proteomics studies identified representatives from Clades 1, 2, and 5 but not from Clades 3 and 4 in adult F. hepatica secretory products. Clades 1 and 2 account for 67.39 and 27.63% of total secreted cathepsin Ls, respectively, suggesting that their expansion was positively driven and that these proteases are most critical for parasite survival and adaptation. Sequence comparison studies revealed that the expansion of cathepsin Ls by gene duplication was followed by residue changes in the S2 pocket of the active site. Our biochemical studies showed that these changes result in alterations in substrate binding and suggested that the divergence of the cathepsin L family produced a repertoire of enzymes with overlapping and complementary substrate specificities that could cleave host macromolecules more efficiently. Although the cathepsin Ls are produced as zymogens containing a prosegment and mature domain, all secreted enzymes identified by MS were processed to mature active enzymes. The prosegment region was highly conserved between the clades except at the boundary of prosegment and mature enzyme. Despite the lack of conservation at this section, sites for exogenous cleavage by asparaginyl endopeptidases and a Leu-Ser[downward arrow]His motif for autocatalytic cleavage by cathepsin Ls were preserved.

Efficient modelling and optimisation of hybrid multilayered plates subject to ballistic impact

Among the key challenges present in the modelling and optimisation of composite structures against impact is the computational expense involved in setting up accurate simulations of the impact event and then performing the iterations required to optimise the designs. It is of more interest to find good designs given the limitations of the resources and time available rather than the best possible design. In this paper, low cost but sufficiently accurate finite element (FE) models were generated in LS Dyna for several experimentally characterised materials by semi-automating the modelling process and using existing material models. These models were then used by an optimisation algorithm to generate new hybrid offspring, leading to minimum weight and/or cost designs from a selection of isotropic metals, polymers and orthotropic fibre-reinforced laminates that countered a specified impact threat. Experimental validation of the optimal designs thus identified was then successfully carried out using a single stage gas gun. With sufficient computational hardware, the techniques developed in this pilot study can further utilise fine meshes, equations of state and sophisticated material models, so that optimal hybrid systems can be identified from a wide range of materials, designs and threats.

On the application of genetic algorithms for optimising composites against impact loading

A genetic algorithm (GA) was adopted to optimise the response of a composite laminate subject to impact. Two different impact scenarios are presented: low-velocity impact of a slender laminated strip and high-velocity impact of a rectangular plate by a spherical impactor. In these cases, the GA's objective was to, respectively, minimise the peak deflection and minimise penetration by varying the ply angles.

The GA was coupled to a commercial finite-element (FE) package LS DYNA to perform the impact analyses. A comparison with a commercial optimisation package, LS OPT, was also made. The results showed that the GA was a robust, capable optimisation tool that produced near optimal designs, and performed well with respect to LS OPT for the more complex high-velocity impact scenario tested.

A progressive failure model for composite laminates subjected to low velocity impact damage

This paper presents a 3-D failure model for predicting the dynamic material response of composite laminates under impact loading. The formulation is based on the Continuum Damage Mechanics (CDM) approach and enables the control of the energy dissipation associated with each failure mode regardless of mesh refinement and fracture plane orientation. Internal thermodynamically irreversible damage variables were defined in order to quantify damage concentration associated with each possible failure mode and predict the gradual stiffness reduction during the impact damage process. The material model has been implemented into LS-DYNA explicit finite element code within solid elements and it has proven to be capable of reproducing experimental results with good accuracy in terms of static/dynamic responses, absorbed energy and extent of damage.

Delamination threshold load for dynamic impact on plates

A criterion is derived for delamination onset in transversely isotropic laminated plates under small mass, high velocity impact. The resulting delamination threshold load is about 21% higher than the corresponding quasi-static threshold load. A closed form approximation for the peak impact load is then used to predict the delamination threshold velocity. The theory is validated for a range of test cases by comparison with 3D finite element simulation using LS-DYNA and a newly developed interface element to model delamination onset and growth. The predicted delamination threshold loads and velocities are in very good agreement with the finite element simulations. Good agreement is also shown in a comparison with published experimental results. In contrast to quasi-static impacts, delamination growth occurs under a rapidly decreasing load. Inclusion of finite thickness effects and a proper description of the contact stiffness are found to be vital for accurate prediction of the delamination threshold velocity

Multicentre trial of weekly risedronate on bone density in adults with cystic fibrosis

Background: The aim of this study was to assess the efficacy, tolerability and safety of risedronate in adults with CF. Methods: Patients with a lumbar spine (LS), total hip (TH) or femoral neck (FN) bone mineral density (BMD) Z-score of -1 or less were randomised to receive risedronate 35mg weekly or placebo, and calcium (1g)+vitamin D (800IU). Results: At baseline, BMD Z-scores in the risedronate (n = 17) and placebo (n = 19) groups were similar. By 24. months, 7/17 risedronate patients vs 0/19 placebo patients stopped the study medication due to bone pain. After 24. months treatment, the mean difference (95% CI) in change in LS, TH and FN BMD between the risedronate vs placebo groups was 4.3% (0.4, 8.2) p = 0.03; 4.0% (-0.5, 8.6) p = 0.08; and 2.4% (-3.5, 8.2) p =0.41. Conclusions: After two years treatment there was a significant increase in LS BMD with weekly risedronate compared to placebo. © 2011 European Cystic Fibrosis Society.

Single-laboratory validation of a multiplex flow cytometric immunoassay for the simultaneous detection of coccidiostats in eggs and feed

Coccidiostats are authorized in the European Union (EU) to be used as poultry feed additives. Maximum (residue) levels (M(R)Ls) have been set within the EU for consumer and animal protection against unintended carry-over, and monitoring is compulsory. This paper describes the single-laboratory validation of a previously developed multiplex flow cytometric immunoassay (FCIA) as screening method for coccidiostats in eggs and feed and provides and compares different approaches for the calculation of the cut-off levels which are not described in detail within Commission Decision 2002/657/EC. Comparable results were obtained between the statistical (reference) approach and the rapid approaches. With the most rapid approach, the cut-off levels for narasin/salinomycin, lasalocid, diclazuril, nicarbazin (DNC) and monensin in egg, calculated as percentages of inhibition (%B/B0), were 60, 32, 76, 80 and 84, respectively. In feed, the cut-off levels for narasin/salinomycin, lasalocid, nicarbazin (DNC) and monensin were 70, 64, 72 and 78, respectively, and could not be determined for diclazuril. For all analytes, except for diclazuril in feed, the rate of false positives (false non-compliant) in blank samples was lower than 1 %, and the rate of false negatives (false compliant) at the M(R)Ls was below 5 %. Additionally, very good correlations (r ranging from 0.994 to 0.9994) were observed between two different analysers, a sophisticated flow cytometer (FlexMAP 3D(®)) and a more cost-efficient and transportable planar imaging detector (MAGPIX(®)), hence demonstrating adequate transferability.

Experimental investigation of hole boring and light sail regimes of RPA by varying laser and target parameters

Temporal evolution of plasma jets from micrometre-scale thick foils following the interaction of intense (3 × 10 W cm ) laser pulses is studied systematically by time resolved optical interferometry. The fluid velocity in the plasma jets is determined by comparing the data with 2D hydrodynamic simulation, which agrees with the expected hole-boring (HB) velocity due to the laser radiation pressure. The homogeneity of the plasma density across the jets has been found to be improved substantially when irradiating the laser at circular polarization compared to linear polarization. While overdense plasma jets were formed efficiently for micrometre thick targets, decreasing the target areal density and/or increasing the irradiance on the target have provided indication of transition from the 'HB' to the 'light sail (LS)' regime of RPA, characterized by the appearance of narrow-band spectral features at several MeV/nucleon in proton and carbon spectra.

Electron excitation of Ca XVII

Electron-excitation collision strengths have been calculated for transitions between the ten lowest levels of Ca XVII (2sS, 2s2p P, 2s2p P, 2pP 2p D, 2pS ). At high impact energies, where all the channels are open, the calculation was carried out in the LS-coupling approximation by means of the R-matrix method. Transitions between the fine structure levels were then determined by application of a unitary transformation to the LS-coupled K-matrices. At low impact energies, where some of the channels may be closed, an extension of the R-matrix method was employed to take account of relativistic effects directly in the scattering equations. In general, results are in good agreement with recent distorted-wave calculations. Electron-excitation rates are given for a range of electron temperatures.

Electron-impact excitation of FeII - Collision strengths and effective collision strengths for low-lying fine-structure forbidden transitions

Context. Absorption or emission lines of Fe II are observed in many astrophysical spectra and accurate atomic data are required to interpret these lines. The calculation of electron-impact excitation rates for transitions among even the lowest lying levels of Fe II is a formidable task for theoreticians.

Aims. In this paper, we present collision strengths and effective collision strengths for electron-impact excitation of Fe II for low-lying forbidden transitions among the lowest 16 fine-structure levels arising from the four LS states 3d(6)4s D-6(e), 3d(7) F-4(e), 3d(6)4s D-4(e), and 3d(7) P-4(e). The effective collision strengths are calculated for a wide range of electron temperatures of astrophysical importance from 30-100 000 K.

Methods. The parallel suite of Breit-Pauli codes are utilised to compute the collision cross sections for electron-impact excitation of Fe II and relativistic terms are included explicitly in both the target and the scattering approximation. 100 LS or 262-jj levels formed from the basis configurations 3d(6)4s, 3d(7), and 3d(6)4p were included in the wavefunction representation of the target, including all doublet, quartet, and sextet terms. Collision strengths for a total of 34191 individual transitions were computed.

Results. A detailed comparison is made with previous theoretical works and significant differences were found to occur in the effective collision strengths, particularly at low temperatures.

Oscillator strengths and transition probabilities for the W xlv ion

In this paper we present oscillator strengths and transition probabilities for W xlv transitions between levels arising from configurations 3d¹⁰4s²,4p²,4d², 3d¹⁰4k4l (k = s,p,d,f and l = p,d,f), 3d⁹4s²4l (l = p,d,f) and 3d⁹4s4p². The model used to calculate these contained all configurations which can be constructed from the available orbitals (up to n = 4), with either a 3d¹⁰ or 3d⁹ core. The calculations were performed with the configuration interaction CIV3 program with the inclusion of relativistic effects achieved through the use of the Breit-Pauli approximation. We compare our ab initio energy levels, oscillator strengths and transition rates with other experimental and theoretical values available in the literature. There is generally good agreement when only levels with 3d¹⁰ cores are considered. The literature is sparse for levels in which the 3d-subshell is opened: for the majority of the fine-structure lines considered, there is either no comparison data available or substantial differences are found. This paper also investigates how the inclusion of relativistic effects can result in a significant redistribution of the oscillator strength from the LS calculations.

Modelling Static and Dynamic FRP-Concrete Bond Behaviour Using a Local Concrete Damage Model

This paper presents a study on the bond behaviour of FRP-concrete bonded joints under static and dynamic loadings, by developing a meso-scale finite element model using the K&C concrete damage model in LS-DYNA. A significant number of single shear experiments under static pull-off loading were modelled with an extensive parametric study covering key factors in the K&C model, including the crack band width, the compressive fracture energy and the shear dilatation factor. It is demonstrated that the developed model can satisfactorily simulate the static debonding behaviour, in terms of mesh objectivity, the load-carrying capacity and the local bond-slip behaviour, provided that proper consideration is given to the selection of crack band width and shear dilatation factor. A preliminary study of the effect of the dynamic loading rate on the debonding behaviour was also conducted by considering a dynamic increase factor (DIF) for the concrete strength as a function of strain rate. It is shown that a higher loading rate leads to a higher load-carrying capacity, a longer effective bond length, and a larger damaged area of concrete in the single shear loading scenario.

Pattern Recognition Approach for Road Collision Hotspots Analysis: Case Study of Northern Ireland

In order to address road safety effectively, it is essential to understand all the factors, which
attribute to the occurrence of a road collision. This is achieved through road safety
assessment measures, which are primarily based on historical crash data. Recent advances
in uncertain reasoning technology have led to the development of robust machine learning
techniques, which are suitable for investigating road traffic collision data. These techniques
include supervised learning (e.g. SVM) and unsupervised learning (e.g. Cluster Analysis).
This study extends upon previous research work, carried out in Coll et al. [3], which
proposed a non-linear aggregation framework for identifying temporal and spatial hotspots.
The results from Coll et al. [3] identified Lisburn area as the hotspot, in terms of road safety,
in Northern Ireland. This study aims to use Cluster Analysis, to investigate and highlight any
hidden patterns associated with collisions that occurred in Lisburn area, which in turn, will
provide more clarity in the causation factors so that appropriate countermeasures can be put
in place.

In vitro studies on the infection and replication of porcine circovirus type 2 in cells of the porcine immune system

Porcine circovirus type 2 (PCV2) nucleic acid and/or antigens are consistently observed in cells of monocytic morphology in lesions of pigs affected by post-weaning multisystemic wasting syndrome (PMWS). In this study, PCV2 antigen was detected in the cytoplasm of monocytes, pulmonary macrophages (PMs) and monocyte-derived macrophages exposed to the virus in vitro, by immunofluorescence analysis (IFA) and the phenotype of these cells confirmed by detection of monocytic cell surface markers using flow cytometry. Viral antigen was not observed in lymphocytic cells. Replication of the virus in PMs was investigated further by comparison to that observed in the continuous pig kidney cell line (PK15A) using quantitative virus titration, quantitative PCR and by the detection of double stranded DNA intermediates of viral replication by Southern blotting analyses. Although increases in viral DNA and levels of infectious virus progeny and the presence of replicative intermediates, indicative of viral replication, were observed in PK15A cells, no such changes were observed in PMs in spite of the fact that infectious virus, viral antigen and viral DNA persisted in the cells for at least the duration of the experiment. These results suggest that in vivo, monocytic cells may not represent the primary target for PCV2 replication. (C) 2003 Elsevier B.V. All rights reserved.

Malware detection: program run length against detection rate

N-gram analysis is an approach that investigates the structure of a program using bytes, characters or text strings. This research uses dynamic analysis to investigate malware detection using a classification approach based on N-gram analysis. A key issue with dynamic analysis is the length of time a program has to be run to ensure a correct classification. The motivation for this research is to find the optimum subset of operational codes (opcodes) that make the best indicators of malware and to determine how long a program has to be monitored to ensure an accurate support vector machine (SVM) classification of benign and malicious software. The experiments within this study represent programs as opcode density histograms gained through dynamic analysis for different program run periods. A SVM is used as the program classifier to determine the ability of different program run lengths to correctly determine the presence of malicious software. The findings show that malware can be detected with different program run lengths using a small number of opcodes