The Burkholderia cenocepacia sensor kinase hybrid AtsR is a global regulator modulating quorum-sensing signalling

Burkholderia cenocepacia is commonly found in the environment and also as an important opportunistic pathogen infecting patients with cystic fibrosis. Successful infection by this bacterium requires coordinated expression of virulence factors, which is achieved through different quorum sensing (QS) regulatory systems. Biofilm formation and Type 6 secretion system (T6SS) expression in B. cenocepacia K56-2 are positively regulated by QS and negatively regulated by the sensor kinase hybrid AtsR. This study reveals that in addition to affecting biofilm and T6SS activity, the deletion of atsR in B. cenocepacia leads to overproduction of other QS-regulated virulence determinants including proteases and swarming motility. Expression of the QS genes, cepIR and cciIR, was upregulated in the ?atsR mutant and resulted in early and increased N-acylhomoserine lactone (AHL) production, suggesting that AtsR plays a role in controlling the timing and fine-tuning of virulence gene expression by modulating QS signalling. Furthermore, a ?atsR?cepI?cciI mutant could partially upregulate the same virulence determinants indicating that AtsR also modulates the expression of virulence genes by a second mechanism, independently of any AHL production. Together, our results strongly suggest that AtsR is a global virulence regulator in B. cenocepacia.

A novel sensor kinase-response regulator hybrid controls biofilm formation and type VI secretion system activity in Burkholderia cenocepacia

Burkholderia cenocepacia is an important opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis (CF). Adaptation of B. cenocepacia to the CF airways may play an important role in the persistence of the infection. We have identified a sensor kinase-response regulator (BCAM0379) named AtsR in B. cenocepacia K56-2 that shares 19% amino acid identity with RetS from Pseudomonas aeruginosa. atsR inactivation led to increased biofilm production and a hyperadherent phenotype in both abiotic surfaces and lung epithelial cells. Also, the atsR mutant overexpressed and hypersecreted an Hcp-like protein known to be specifically secreted by the type VI secretion system (T6SS) in other gram-negative bacteria. Amoeba plaque assays demonstrated that the atsR mutant was more resistant to Dictyostelium predation than the wild-type strain and that this phenomenon was T6SS dependent. Macrophage infection assays also demonstrated that the atsR mutant induces the formation of actin-mediated protrusions from macrophages that require a functional Hcp-like protein, suggesting that the T6SS is involved in actin rearrangements. Three B. cenocepacia transposon mutants that were found in a previous study to be impaired for survival in chronic lung infection model were mapped to the T6SS gene cluster, indicating that the T6SS is required for infection in vivo. Together, our data show that AtsR is involved in the regulation of genes required for virulence in B. cenocepacia K56-2, including genes encoding a T6SS.

Trophic dynamics within a hybrid zone - interactions between an abundant cyprinid hybrid and sympatric parental species

1. Recent proliferation of hybridisation in response to anthropogenic ecosystem change, coupled with increasing evidence of the importance of ancient hybridisation events in the formation of many species, has moved hybridisation to the forefront of evolutionary theory.

2. In spite of this, the mechanisms (e. g. differences in trophic ecology) by which hybrids co-exist with parental taxa are poorly understood. A unique hybrid zone exists in Irish freshwater systems, whereby hybrid offspring off two non-native cyprinid fishes often outnumber both parental species.

3. Using stable isotope and gut content analyses, we determined the trophic interactions between sympatric populations of roach (Rutilus rutilus), bream (Abramis brama) and their hybrid in lacustrine habitats.

4. The diet of all three groups displayed little variation across the study systems, and dietary overlap was observed between both parental species and hybrids. Hybrids displayed diet, niche breadth and trophic position that were intermediate between the two parental species while also exhibiting greater flexibility in diet across systems.

Touching at a Distance: Resistance, Tactility, Proxemics and the Development of a Hybrid Virtual/Physical Performance System

This is a paper about resistance and affordance as they relate to music-making in the most extended sense, and perhaps about empathy if this is understood as a capacity to ‘read’ the resistances and affordances of objects, bodies, people and environments. It proceeds from a set of broad working assumptions which inform one individual’s musical practice, via a description a musical-instrument making project which is a hybrid of physical and virtual elements and is designed to test those assumptions, to a speculative finale in which it is suggested that musicking might, in some circumstances, be regarded in itself as a form of resistance. It moves from the intimate and personal, through what might be regarded as local concerns to more global observation, prefiguring the structure of the performance system it describes: the Virtual-Physical Feedback flute

Hybrid FIB milling strategy for the fabrication of plasmonic nanostructures on semiconductor substrates

The optical properties of plasmonic semiconductor devices fabricated by focused ion beam (FIB) milling deteriorate because of the amorphisation of the semiconductor substrate. This study explores the effects of combining traditional 30 kV FIB milling with 5 kV FIB patterning to minimise the semiconductor damage and at the same time maintain high spatial resolution. The use of reduced acceleration voltages is shown to reduce the damage from higher energy ions on the example of fabrication of plasmonic crystals on semiconductor substrates leading to 7-fold increase in transmission. This effect is important for focused-ion beam fabrication of plasmonic structures integrated with photodetectors, light-emitting diodes and semiconductor lasers.

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.

Intralaminar toughness characterisation of unbalanced hybrid plain weave laminates

A numerical and experimental investigation on the mode-I intralaminar toughness of a hybrid plain weave composite laminate manufactured using resin infusion under flexible tooling (RIFT) process is presented in this paper. The pre-cracked geometries consisted of overheight compact tension (OCT), double edge notch (DEN) and centrally cracked four-point-bending (4PBT) test specimens. The position as well as the strain field ahead of the crack tip during the loading stage was determined using a digital speckle photogrammetry system. The limitation on the applicability of the standard data reduction schemes for the determination of intralaminar toughness of composite materials is presented and discussed. A methodology based on the numerical evaluation of the strain energy release rate using the J-integral method is proposed to derive new geometric correction functions for the determination of the stress intensity factor for composites. The method accounts for material anisotropy and finite specimen dimension effects regardless of the geometry. The approach has been validated for alternative non-standard specimen geometries. A comparison between different methods currently available for computing the intralaminar fracture toughness in composite laminates is presented and a good agreement between numerical and experimental results using the proposed methodology was obtained. 

An automated hybrid procedure for capturing mode-jumping in postbuckling composite stiffened structures

This paper presents a robust finite element procedure for modelling the behaviour of postbuckling structures undergoing mode-jumping. Current non-linear implicit finite element solution schemes, found in most finite element codes, are discussed and their shortcomings highlighted. A more effective strategy is presented which combines a quasi-static and a pseudo-transient routine for modelling this behaviour. The switching between these two schemes is fully automated and therefore eliminates the need for user intervention during the solution process. The quasi-static response is modelled using the are-length constraint while the pseudo-transient routine uses a modified explicit dynamic routine, which is more computationally efficient than standard implicit and explicit dynamic schemes. The strategies for switching between the quasi-static and pseudo-transient routines are presented

Strategies for Energy-Efficient Resource Management of Hybrid Programming Models

Many scientific applications are programmed using hybrid programming models that use both message passing and shared memory, due to the increasing prevalence of large-scale systems with multicore, multisocket nodes. Previous work has shown that energy efficiency can be improved using software-controlled execution schemes that consider both the programming model and the power-aware execution capabilities of the system. However, such approaches have focused on identifying optimal resource utilization for one programming model, either shared memory or message passing, in isolation. The potential solution space, thus the challenge, increases substantially when optimizing hybrid models since the possible resource configurations increase exponentially. Nonetheless, with the accelerating adoption of hybrid programming models, we increasingly need improved energy efficiency in hybrid parallel applications on large-scale systems. In this work, we present new software-controlled execution schemes that consider the effects of dynamic concurrency throttling (DCT) and dynamic voltage and frequency scaling (DVFS) in the context of hybrid programming models. Specifically, we present predictive models and novel algorithms based on statistical analysis that anticipate application power and time requirements under different concurrency and frequency configurations. We apply our models and methods to the NPB MZ benchmarks and selected applications from the ASC Sequoia codes. Overall, we achieve substantial energy savings (8.74 percent on average and up to 13.8 percent) with some performance gain (up to 7.5 percent) or negligible performance loss.