Time- vs. frequency-domain identification of parametric radiation force models for marine structures at zero speed

The dynamics describing the motion response of a marine structure in waves can be represented within a linear framework by the Cummins Equation. This equation contains a convolution term that represents the component of the radiation forces associated with fluid memory effects. Several methods have been proposed in the literature for the identification of parametric models to approximate and replace this convolution term. This replacement can facilitate the model implementation in simulators and the analysis of motion control designs. Some of the reported identification methods consider the problem in the time domain while other methods consider the problem in the frequency domain. This paper compares the application of these identification methods. The comparison is based not only on the quality of the estimated models, but also on the ease of implementation, ease of use, and the flexibility of the identification method to incorporate prior information related to the model being identified. To illustrate the main points arising from the comparison, a particular example based on the coupled vertical motion of a modern containership vessel is presented.

Hybrid frequency–time domain models for dynamic response analysis of marine structures

Time-domain models of marine structures based on frequency domain data are usually built upon the Cummins equation. This type of model is a vector integro-differential equation which involves convolution terms. These convolution terms are not convenient for analysis and design of motion control systems. In addition, these models are not efficient with respect to simulation time, and ease of implementation in standard simulation packages. For these reasons, different methods have been proposed in the literature as approximate alternative representations of the convolutions. Because the convolution is a linear operation, different approaches can be followed to obtain an approximately equivalent linear system in the form of either transfer function or state-space models. This process involves the use of system identification, and several options are available depending on how the identification problem is posed. This raises the question whether one method is better than the others. This paper therefore has three objectives. The first objective is to revisit some of the methods for replacing the convolutions, which have been reported in different areas of analysis of marine systems: hydrodynamics, wave energy conversion, and motion control systems. The second objective is to compare the different methods in terms of complexity and performance. For this purpose, a model for the response in the vertical plane of a modern containership is considered. The third objective is to describe the implementation of the resulting model in the standard simulation environment Matlab/Simulink.

Assessment of gene expression of intracellular calcium channels, pumps and exchangers with epidermal growth factor-induced epithelial-mesenchymal transition in a breast cancer cell line

Background Epithelial-mesenchymal transition (EMT) is a process implicated in cancer metastasis that involves the conversion of epithelial cells to a more mesenchymal and invasive cell phenotype. In breast cancer cells EMT is associated with altered store-operated calcium influx and changes in calcium signalling mediated by activation of cell surface purinergic receptors. In this study, we investigated whether MDA-MB-468 breast cancer cells induced to undergo EMT exhibit changes in mRNA levels of calcium channels, pumps and exchangers located on intracellular calcium storing organelles, including the Golgi, mitochondria and endoplasmic reticulum (ER). Methods Epidermal growth factor (EGF) was used to induce EMT in MDA-MB-468 breast cancer cells. Serum-deprived cells were treated with EGF (50 ng/mL) for 12 h and gene expression was assessed using quantitative RT-PCR. Results and conclusions These data reveal no significant alterations in mRNA levels of the Golgi calcium pump secretory pathway calcium ATPases (SPCA1 and SPCA2), or the mitochondrial calcium uniporter (MCU) or Na+/Ca2+ exchanger (NCLX). However, EGF-induced EMT was associated with significant alterations in mRNA levels of specific ER calcium channels and pumps, including (sarco)-endoplasmic reticulum calcium ATPases (SERCAs), and inositol 1,4,5-trisphosphate receptor (IP3R) and ryanodine receptor (RYR) calcium channel isoforms. The most prominent change in gene expression between the epithelial and mesenchymal-like states was RYR2, which was enriched 45-fold in EGF-treated MDA-MB-468 cells. These findings indicate that EGF-induced EMT in breast cancer cells may be associated with major alterations in ER calcium homeostasis.

Type I collagen abrogates the clathrin-mediated internalization of membrane type 1 matrix metalloproteinase (MT1-MMP) via the MT1-MMP hemopexin domain

Type I collagen (Col I)-stimulated matrix metalloproteinase-2 (MMP-2) activation via membrane type 1 MMP (MT1-MMP) involves both a transcriptional increase in MT1-MMP expression and a nontranscriptional response mediated by preexisting MT1-MMP. In order to identify which MT1-MMP domains were required for the nontranscriptional response, MCF-7 cells that lack endogenous MT1-MMP were transfected with either wild type or domain mutant MT1-MMP constructs. We observed that mutant constructs lacking the MT1-MMP cytoplasmic tail were able to activate MMP-2 in response to Col I but not a construct lacking the MT1-MMP hemopexin domain. Col I did not alter total MT1-MMP protein levels; nor did it appear to directly induce MT1-MMP oligomerization. Col I did, however, redistribute preexisting MT1-MMP to the cell periphery compared with unstimulated cells that displayed amore diffuse staining pattern. In addition, Col I blocked the internalization of MT1-MMP in a dynamin-dependent manner via clathrin-coated pit-mediated endocytosis. This mechanism of impaired internalization is different from that reported for concanavalin A, since it is not mediated by the cytoplasmic tail of MT1-MMP but rather by the hemopexin domain. In summary, upon Col I binding to its cell surface receptor, MT1-MMP internalization via clathrin-coated pit-mediated endocytosis is impaired through interactions with the hemopexin domain, thereby regulating its function and ability to activate MMP-2.

Transmembrane/cytoplasmic domain-mediated membrane type 1-matrix metalloprotease docking to invadopodia is required for cellinvasion

The invasion of human malignant melanoma cells into the extracellular matrix (ECM) involves the accumulation of proteases at sites of ECM degradation where activation of matrix metalloproteases (MMP) occurs. Here, we show that when membrane type 1 MMP (MT-MMP) was overexpressed in RPMI7951 human melanoma cells, the cells made contact with the ECM, activated soluble and ECM-bound MMP-2, and degraded and invaded the ECM. Further experiments demonstrated the importance of localization of the MT-MMP to invadopodia. Overexpression of MT-MMP without invadopodial localization caused activation of soluble MMP-2, but did not facilitate ECM degradation or cell invasiveness. Up-regulation of endogenous MT-MMP with concanavalin A caused activation of MMP-2. However, concanavalin A treatment prevented invadopodial localization of MT-MMP and ECM degradation. Neither a truncated MT-MMP mutant lacking transmembrane (TM) and cytoplasmic domains (ΔTM(MT-MMP)), nor a chimeric MT-MMP containing the interleukin 2 receptor α chain (IL-2R) TM and cytoplasmic domains (ΔTM(MT-MMP)/TM(IL-2R)) were localized to invadopodia or exhibited ECM degradation. Furthermore, a chimera of the TM/cytoplasmic domain of MT-MMP (TM(MT-MMP)) with tissue inhibitor of MMP 1 (TIMP-1/TM(MT- MMP)) directed the TIMP-1 molecule to invadopodia. Thus, the MT-MMP TM/cytoplasmic domain mediates the spatial organization of MT-MMP into invadopodia and subsequent degradation of the ECM.

STI-GMaS : an open-source environment for simulation of sexually-transmitted infections

Background Sexually-transmitted pathogens often have severe reproductive health implications if treatment is delayed or absent, especially in females. The complex processes of disease progression, namely replication and ascension of the infection through the genital tract, span both extracellular and intracellular physiological scales, and in females can vary over the distinct phases of the menstrual cycle. The complexity of these processes, coupled with the common impossibility of obtaining comprehensive and sequential clinical data from individual human patients, makes mathematical and computational modelling valuable tools in developing our understanding of the infection, with a view to identifying new interventions. While many within-host models of sexually-transmitted infections (STIs) are available in existing literature, these models are difficult to deploy in clinical/experimental settings since simulations often require complex computational approaches. Results We present STI-GMaS (Sexually-Transmitted Infections – Graphical Modelling and Simulation), an environment for simulation of STI models, with a view to stimulating the uptake of these models within the laboratory or clinic. The software currently focuses upon the representative case-study of Chlamydia trachomatis, the most common sexually-transmitted bacterial pathogen of humans. Here, we demonstrate the use of a hybrid PDE–cellular automata model for simulation of a hypothetical Chlamydia vaccination, demonstrating the effect of a vaccine-induced antibody in preventing the infection from ascending to above the cervix. This example illustrates the ease with which existing models can be adapted to describe new studies, and its careful parameterisation within STI-GMaS facilitates future tuning to experimental data as they arise. Conclusions STI-GMaS represents the first software designed explicitly for in-silico simulation of STI models by non-theoreticians, thus presenting a novel route to bridging the gap between computational and clinical/experimental disciplines. With the propensity for model reuse and extension, there is much scope within STI-GMaS to allow clinical and experimental studies to inform model inputs and drive future model development. Many of the modelling paradigms and software design principles deployed to date transfer readily to other STIs, both bacterial and viral; forthcoming releases of STI-GMaS will extend the software to incorporate a more diverse range of infections.

Plasma-induced death of HepG2 cancer cells : intracellular effects of reactive species

Reports show that cold atmospheric-pressure plasmas can induce death of cancer cells in several minutes. However, very little is presently known about the mechanism of the plasma-induced death of cancer cells. In this paper, an atmospheric-pressure plasma plume is used to treat HepG2 cells. The experimental results show that the plasma can effectively control the intracellular concentrations of ROS, NO and lipid peroxide. It is shown that these concentrations are directly related to the mechanism of the HepG2 death, which involves several stages. First, the plasma generates NO species, which increases the NO concentration in the extracellular medium. Second, the intracellular NO concentration is increased due to the NO diffusion from the medium. Third, an increase in the intracellular NO concentration leads to the increase of the intracellular ROS concentration. Fourth, the increased oxidative stress results in more effective lipid peroxidation and consequently, cell injury. The combined action of NO, ROS and lipid peroxide species eventually results in the HepG2 cell death. The mechanism of death of human hepatocellular carcinoma cells (HepG2) induced by atmospheric-pressure room-temperature plasma, related to the plasma-controlled intracellular concentrations of reactive oxygen species (ROS), nitric oxide (NO) and lipid peroxide is revealed. Only 34.75 s are required to reduce the number of the viable HepG2 cells by 50%.

Modelling of arc welding : the importance of including the arc plasma in the computational domain

We present results of computational simulations of tungsten-inert-gas and metal-inert-gas welding. The arc plasma and the electrodes (including the molten weld pool when necessary) are included self-consistently in the computational domain. It is shown, using three examples, that it would be impossible to accurately estimate the boundary conditions on the weld-pool surface without including the arc plasma in the computational domain. First, we show that the shielding gas composition strongly affects the properties of the arc that influence the weld pool: heat flux density, current density, shear stress and arc pressure at the weld-pool surface. Demixing is found to be important in some cases. Second, the vaporization of the weld-pool metal and the diffusion of the metal vapour into the arc plasma are found to decrease the heat flux density and current density to the weld pool. Finally, we show that the shape of the wire electrode in metal-inert-gas welding has a strong influence on flow velocities in the arc and the pressure and shear stress at the weld-pool surface. In each case, we present evidence that the geometry and depth of the weld pool depend strongly on the properties of the arc.

Nanoscale phase domain structure and associated device performance of organic solar cells based on a diketopyrrolopyrrole polymer

We investigate the blend morphology and performance of bulk heterojunction organic photovoltaic devices comprising the donor polymer, pDPP-TNT (poly{3,6-dithiophene-2-yl-2,5-di(2-octyldodecyl)-pyrrolo[3,4-c]pyrrole-1, 4-dione-alt-naphthalene}) and the fullerene acceptor, [70]PCBM ([6,6]-phenyl C71-butyric acid methyl ester). The blend morphology is heavily dependent upon the solvent system used in the fabrication of thin films. Thin films spin-coated from chloroform possess a cobblestone-like morphology, consisting of thick, round-shaped [70]PCBM-rich mounds separated by thin polymer-rich valleys. The size of the [70]PCBM domains is found to depend on the overall film thickness. Thin films spin-coated from a chloroform:dichlorobenzene mixed solvent system are smooth and consist of a network of pDPP-TNT nanofibers embedded in a [70]PCBM-rich matrix. Rinsing the films in hexane selectively removes [70]PCBM and allows for analysis of domain size and purity. It also provides a means for investigating exciton dissociation efficiency through relative photoluminescence yield measurements. Devices fabricated from chloroform solutions show much poorer performance than the devices fabricated from the mixed solvent system; this disparity in performance is seen to be more pronounced with increasing film thickness. The primary cause for the improved performance of devices fabricated from mixed solvents is attributed to the greater donor-acceptor interfacial area and resulting greater capacity for charge carrier generation.

Domain-specific application analysis for customized instruction identification

With the increasing importance of Application Domain Specific Processor (ADSP) design, a significant challenge is to identify special-purpose operations for implementation as a customized instruction. While many methodologies have been proposed for this purpose, they all work for a single algorithm chosen from the target application domain. Such algorithm-specific approaches are not suitable for designing instruction sets applicable to a whole family of related algorithms. For an entire range of related algorithms, this paper develops a methodology for identifying compound operations, as a basis for designing “domain-specific” Instruction Set Architectures (ISAs) that can efficiently run most of the algorithms in a given domain. Our methodology combines three different static analysis techniques to identify instruction sequences common to several related algorithms: identification of (non-branching) instruction sequences that occur commonly across the algorithms; identification of instruction sequences nested within iterative constructs that are thus executed frequently; and identification of commonly-occurring instruction sequences that span basic blocks. Choosing different combinations of these results enables us to design domain-specific special operations with different desired characteristics, such as performance or suitability as a library function. To demonstrate our approach, case studies are carried out for a family of thirteen string matching algorithms. Finally, the validity of our static analysis results is confirmed through independent dynamic analysis experiments and performance improvement measurements.

Host-pathogen checkpoints and population bottlenecks in persistent and intracellular uropathogenic Escherichia coli bladder infection

Bladder infections affect millions of people yearly, and recurrent symptomatic infections (cystitis) are very common. The rapid increase in infections caused by multidrug-resistant uropathogens threatens to make recurrent cystitis an increasingly troubling public health concern. Uropathogenic Escherichia coli (UPEC) cause the vast majority of bladder infections. Upon entry into the lower urinary tract, UPEC face obstacles to colonization that constitute population bottlenecks, reducing diversity, and selecting for fit clones. A critical mucosal barrier to bladder infection is the epithelium (urothelium). UPEC bypass this barrier when they invade urothelial cells and form intracellular bacterial communities (IBCs), a process which requires type 1 pili. IBCs are transient in nature, occurring primarily during acute infection. Chronic bladder infection is common and can be either latent, in the form of the quiescent intracellular reservoir (QIR), or active, in the form of asymptomatic bacteriuria (ASB/ABU) or chronic cystitis. In mice, the fate of bladder infection, QIR, ASB, or chronic cystitis, is determined within the first 24 h of infection and constitutes a putative host–pathogen mucosal checkpoint that contributes to susceptibility to recurrent cystitis. Knowledge of these checkpoints and bottlenecks is critical for our understanding of bladder infection and efforts to devise novel therapeutic strategies.

Evolution to a chronic disease niche correlates with increased sensitivity to tryptophan availability for the obligate intracellular bacterium Chlamydia pneumoniae

The chlamydiae are obligate intracellular parasites that have evolved specific interactions with their various hosts and host cell types to ensure their successful survival and consequential pathogenesis. The species Chlamydia pneumoniae is ubiquitous, with serological studies showing that most humans are infected at some stage in their lifetime. While most human infections are asymptomatic, C. pneumoniae can cause more-severe respiratory disease and pneumonia and has been linked to chronic diseases such as asthma, atherosclerosis, and even Alzheimer's disease. The widely dispersed animal-adapted C. pneumoniae strains cause an equally wide range of diseases in their hosts. It is emerging that the ability of C. pneumoniae to survive inside its target cells, including evasion of the host's immune attack mechanisms, is linked to the acquisition of key metabolites. Tryptophan and arginine are key checkpoint compounds in this host-parasite battle. Interestingly, the animal strains of C. pneumoniae have a slightly larger genome, enabling them to cope better with metabolite restrictions. It therefore appears that as the evolutionarily more ancient animal strains have evolved to infect humans, they have selectively become more "susceptible" to the levels of key metabolites, such as tryptophan. While this might initially appear to be a weakness, it allows these human C. pneumoniae strains to exquisitely sense host immune attack and respond by rapidly reverting to a persistent phase. During persistence, they reduce their metabolic levels, halting progression of their developmental cycle, waiting until the hostile external conditions have passed before they reemerge.

Exploring the impact of shared domain knowledge on strategic alignment in the Australian public sector

In this age of ever-increasing information technology (IT) driven environments, governments/or public sector organisations (PSOs) are expected to demonstrate the business value of the investment in IT and take advantage of the opportunities offered by technological advancements. Strategic alignment (SA) emerged as a mechanism to bridge the gap between business and IT missions, objectives, and plans in order to ensure value optimisation from investment in IT and enhance organisational performance. However, achieving and sustaining SA remains a challenge requiring even more agility nowadays to keep up with turbulent organisational environments. The shared domain knowledge (SDK) between the IT department and other diverse organisational groups is considered as one of the factors influencing the successful implementation of SA. However, SDK in PSOs has received relatively little empirical attention. This paper presents findings from a study which investigated the influence of SDK on SA within organisations in the Australian public sector. The developed research model examined the relationship of SDK between business and IT domains with SA using a survey of 56 public sector professionals and executives. A key research contribution is the empirical demonstration that increasing levels of SDK between IT and business groups leads to increased SA.

GABAB receptors expressed in human aortic endothelial cells mediate intracellular calcium concentration regulation and endothelial nitric oxide synthase translocation

GABAB receptors regulate the intracellular Ca2+ concentration ([Ca2+]i) in a number of cells (e.g., retina, airway epithelium and smooth muscle), but whether they are expressed in vascular endothelial cells and similarly regulate the [Ca2+]i is not known. The purpose of this study was to investigate the expression of GABAB receptors, a subclass of receptors to the inhibitory neurotransmitter γ-aminobutyric acid (GABA), in cultured human aortic endothelial cells (HAECs), and to explore if altering receptor activation modified [Ca2+]i and endothelial nitric oxide synthase (eNOS) translocation. Real-time PCR, western blots and immunofluorescence were used to determine the expression of GABAB1 and GABAB2 in cultured HAECs. The effects of GABAB receptors on [Ca2+]i in cultured HAECs were demonstrated using fluo-3. The influence of GABAB receptors on eNOS translocation was assessed by immunocytochemistry. Both GABAB1 and GABAB2 mRNA and protein were expressed in cultured HAECs, and the GABAB1 and GABAB2 proteins were colocated in the cell membrane and cytoplasm. One hundred μM baclofen caused a transient increase of [Ca2+]i and eNOS translocation in cultured HAECs, and the effects were attenuated by pretreatment with the selective GABAB receptor antagonists CGP46381 and CGP55845. GABAB receptors are expressed in HAECs and regulate the [Ca2+]i and eNOS translocation. Cultures of HAECs may be a useful in vitro model for the study of GABAB receptors and vascular biology.

GABAB receptors are expressed in human aortic smooth muscle cells and regulate the intracellular Ca2+ concentration

The aim of this study was to investigate the expression of GABAB receptors, a subclass of receptors to the inhibitory neurotransmitter gamma-aminobutyric acid (GABAB), in human aortic smooth muscle cells (HASMCs), and to explore if altering receptor activation modified intracellular Ca(2+) concentration ([Ca(2+)]i) of HASMCs. Real-time PCR, western blots and immunofluorescence were used to determine the expression of GABABR1 and GABABR2 in cultured HASMCs. Immunohistochemistry was used to localize the two subunits in human left anterior descending artery (LAD). The effects of the GABAB receptor agonist baclofen on [Ca(2+)]i in cultured HASMCs were demonstrated using fluo-3. Both GABABR1 and GABABR2 mRNA and protein were identified in cultured HASMCs and antibody staining was also localized to smooth muscle cells of human LAD. 100 μM baclofen caused a transient increase of [Ca(2+)]i in cultured HASMCs regardless of whether Ca(2+) was added to the medium, and the effects were inhibited by pre-treatment with CGP46381 (selective GABAB receptor antagonist), pertussis toxin (a Gi/o protein inhibitor), and U73122 (a phospholipase C blocker). GABAB receptors are expressed in HASMCs and regulate the [Ca(2+)]i via a Gi/o-coupled receptor pathway and a phospholipase C activation pathway