Non-thermal Plasma Exposure Rapidly Attenuates Bacterial AHL-Dependent Quorum Sensing and Virulence.

The antimicrobial activity of atmospheric pressure non-thermal plasma has been exhaustively characterised, however elucidation of the interactions between biomolecules produced and utilised by bacteria and short plasma exposures are required for optimisation and clinical translation of cold plasma technology. This study characterizes the effects of non-thermal plasma exposure on acyl homoserine lactone (AHL)-dependent quorum sensing (QS). Plasma exposure of AHLs reduced the ability of such molecules to elicit a QS response in bacterial reporter strains in a dose-dependent manner. Short exposures (30-60 s) produce of a series of secondary compounds capable of eliciting a QS response, followed by the complete loss of AHL-dependent signalling following longer exposures. UPLC-MS analysis confirmed the time-dependent degradation of AHL molecules and their conversion into a series of by-products. FT-IR analysis of plasma-exposed AHLs highlighted the appearance of an OH group. In vivo assessment of the exposure of AHLs to plasma was examined using a standard in vivo model. Lettuce leaves injected with the rhlI/lasI mutant PAO-MW1 alongside plasma treated N-butyryl-homoserine lactone and n-(3-oxo-dodecanoyl)-homoserine lactone, exhibited marked attenuation of virulence. This study highlights the capacity of atmospheric pressure non-thermal plasma to modify and degrade AHL autoinducers thereby attenuating QS-dependent virulence in P. aeruginosa.

Spin and spatial dynamics in electron-impact scattering off S-wave He using R-matrix with Time-Dependence theory

R-matrix with time-dependence theory is applied to electron-impact ionisation processes for He in the S-wave model. Cross sections for electron-impact excitation, ionisation and ionisation with excitation for impact energies between 25 and 225 eV are in excellent agreement with benchmark cross sections. Ultra-fast dynamics induced by a scattering event is observed through time-dependent signatures associated with autoionisation from doubly excited states. Further insight into dynamics can be obtained through examination of the spin components of the time-dependent wavefunction.

Heating the Early Universe : Numerical Methods and Their Analysis

During the epoch when the first collapsed structures formed (6<z<50) our Universe went through an extended period of changes. Some of the radiation from the first stars and accreting black holes in those structures escaped and changed the state of the Intergalactic Medium (IGM). The era of this global phase change in which the state of the IGM was transformed from cold and neutral to warm and ionized, is called the Epoch of Reionization.In this thesis we focus on numerical methods to calculate the effects of this escaping radiation. We start by considering the performance of the cosmological radiative transfer code C2-Ray. We find that although this code efficiently and accurately solves for the changes in the ionized fractions, it can yield inaccurate results for the temperature changes. We introduce two new elements to improve the code. The first element, an adaptive time step algorithm, quickly determines an optimal time step by only considering the computational cells relevant for this determination. The second element, asynchronous evolution, allows different cells to evolve with different time steps. An important constituent of methods to calculate the effects of ionizing radiation is the transport of photons through the computational domain or ``ray-tracing''. We devise a novel ray tracing method called PYRAMID which uses a new geometry - the pyramidal geometry. This geometry shares properties with both the standard Cartesian and spherical geometries. This makes it on the one hand easy to use in conjunction with a Cartesian grid and on the other hand ideally suited to trace radiation from a radially emitting source. A time-dependent photoionization calculation not only requires tracing the path of photons but also solving the coupled set of photoionization and thermal equations. Several different solvers for these equations are in use in cosmological radiative transfer codes. We conduct a detailed and quantitative comparison of four different standard solvers in which we evaluate how their accuracy depends on the choice of the time step. This comparison shows that their performance can be characterized by two simple parameters and that the C2-Ray generally performs best.

Variationelle Zeitdiskretisierungen höherer Ordnung der Konvektions-Diffusions-Reaktions-Gleichungen in zeitabhängigen Gebieten

Wir betrachten zeitabhängige Konvektions-Diffusions-Reaktions-Gleichungen in zeitabhängi- gen Gebieten, wobei die Bewegung des Gebietsrandes bekannt ist. Die zeitliche Entwicklung des Gebietes wird durch die ALE-Formulierung behandelt, die die Nachteile der klassischen Euler- und Lagrange-Betrachtungsweisen behebt. Die Position des Randes und seine Geschwindigkeit werden dabei so in das Gebietsinnere fortgesetzt, dass starke Gitterdeformationen verhindert werden. Als Zeitdiskretisierungen höherer Ordnung werden stetige Galerkin-Petrov-Verfahren (cGP) und unstetige Galerkin-Verfahren (dG) auf Probleme in zeitabhängigen Gebieten angewendet. Weiterhin werden das C 1 -stetige Galerkin-Petrov-Verfahren und das C 0 -stetige Galerkin- Verfahren vorgestellt. Deren Lösungen lassen sich auch in zeitabhängigen Gebieten durch ein einfaches einheitliches Postprocessing aus der Lösung des cGP-Problems bzw. dG-Problems erhalten. Für Problemstellungen in festen Gebieten und mit zeitlich konstanten Konvektions- und Reaktionstermen werden Stabilitätsresultate sowie optimale Fehlerabschätzungen für die nachbereiteten Lösungen der cGP-Verfahren und der dG-Verfahren angegeben. Für zeitabhängige Konvektions-Diffusions-Reaktions-Gleichungen in zeitabhängigen Gebieten präsentieren wir konservative und nicht-konservative Formulierungen, wobei eine besondere Aufmerksamkeit der Behandlung der Zeitableitung und der Gittergeschwindigkeit gilt. Stabilität und optimale Fehlerschätzungen für die in der Zeit semi-diskretisierten konservativen und nicht-konservativen Formulierungen werden vorgestellt. Abschließend wird das volldiskretisierte Problem betrachtet, wobei eine Finite-Elemente-Methode zur Ortsdiskretisierung der Konvektions-Diffusions-Reaktions-Gleichungen in zeitabhängigen Gebieten im ALE-Rahmen einbezogen wurde. Darüber hinaus wird eine lokale Projektionsstabilisierung (LPS) eingesetzt, um der Konvektionsdominanz Rechnung zu tragen. Weiterhin wird numerisch untersucht, wie sich die Approximation der Gebietsgeschwindigkeit auf die Genauigkeit der Zeitdiskretisierungsverfahren auswirkt.

Pattern formation with a conservation law

Pattern formation in systems with a conserved quantity is considered by studying the appropriate amplitude equations. The conservation law leads to a large-scale neutral mode that must be included in the asymptotic analysis for pattern formation near onset. Near a stationary bifurcation, the usual Ginzburg--Landau equation for the amplitude of the pattern is then coupled to an equation for the large-scale mode. These amplitude equations show that for certain parameters all roll-type solutions are unstable. This new instability differs from the Eckhaus instability in that it is amplitude-driven and is supercritical. Beyond the stability boundary, there exist stable stationary solutions in the form of strongly modulated patterns. The envelope of these modulations is calculated in terms of Jacobi elliptic functions and, away from the onset of modulation, is closely approximated by a sech profile. Numerical simulations indicate that as the modulation becomes more pronounced, the envelope broadens. A number of applications are considered, including convection with fixed-flux boundaries and convection in a magnetic field, resulting in new instabilities for these systems.

Triptolide induces cell apoptosis in human stomach cancer cell via caspase 3-dependent cascade pathway

Purpose: To evaluate the effect of triptolide on the induction of cell apoptosis in human gastric cancer BGC-823 cells. Methods: The cytotoxicity of triptolide was evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2, 5- diphenyltetrazolium bromide (MTT) assay. The effect of triptolide on cell proliferation was measured using lactate dehydrogenase (LDH) assay. Cell apoptosis was determined by Annexin V/propidium iodide (PI) double-staining assay. Results: MTT results indicate that triptolide significantly decreased cancer cell numbers in dose- and time-dependent manners in MTT assay. Data from LDH assay showed that triptolide markedly induced cytotoxicity in gastric cancer cells. Triptolide also remarkably induced both early and late apoptotic process in BGC-823 cells. In addition, the compound down-regulated the expression of anti-apoptotic Bcell lymphoma-2 (bcl-2) and up-regulated the expression of pro-apoptotic BCL-2-associated X (bax) in a dose-dependent manner. Furthermore, the pro-apoptotic activity of triptolide was involved in the activation of caspase-3 pathway in BGC-823 cells. Conclusion: Taken together, the findings strongly indicates that the pro-apoptotic activity of triptolide is regulated by caspase 3-dependent cascade pathway, and thus needs to be further developed for cancer therapy.

Comparison of ultrafine particle release from hardcopy devices in emission test chambers and office rooms

The release of ultrafine particles (UFP) from laser printers and office equipment was analyzed using a particle counter (FMPS; Fast Mobility Particle Sizer) with a high time resolution, as well as the appropriate mathematical models. Measurements were carried out in a 1 m³ chamber, a 24 m³ chamber and an office. The time-dependent emission rates were calculated for these environments using a deconvolution model, after which the total amount of emitted particles was calculated. The total amounts of released particles were found to be independent of the environmental parameters and therefore, in principle, they were appropriate for the comparison of different printers. On the basis of the time-dependent emission rates, “initial burst” emitters and constant emitters could also be distinguished. In the case of an “initial burst” emitter, the comparison to other devices is generally affected by strong variations between individual measurements. When conducting exposure assessments for UFP in an office, the spatial distribution of the particles also had to be considered. In this work, the spatial distribution was predicted on a case by case basis, using CFD simulation.

A numerical method to quantify the axial shortening of vertical elements in concrete buildings

Differential axial shortening, distortion and deformation in high rise buildings is a serious concern. They are caused by three time dependent modes of volume change; “shrinkage”, “creep” and “elastic shortening” that takes place in every concrete element during and after construction. Vertical concrete components in a high rise building are sized and designed based on their strength demand to carry gravity and lateral loads. Therefore, columns and walls are sized, shaped and reinforced differently with varying concrete grades and volume to surface area ratios. These structural components may be subjected to the detrimental effects of differential axial shortening that escalates with increasing the height of buildings. This can have an adverse impact on other structural and non-structural elements. Limited procedures are available to quantify axial shortening, and the results obtained from them differ because each procedure is based on various assumptions and limited to few parameters. All these prompt to a need to develop an accurate numerical procedure to quantify the axial shortening of concrete buildings taking into account the important time varying functions of (i) construction sequence (ii) Young’s Modulus and (iii) creep and shrinkage models associated with reinforced concrete. General assumptions are refined to minimize variability of creep and shrinkage parameters to improve accuracy of the results. Finite element techniques are used in the procedure that employs time history analysis along with compression only elements to simulate staged construction behaviour. This paper presents such a procedure and illustrates it through an example. Keywords: Differential Axial Shortening, Concrete Buildings, Creep and Shrinkage, Construction Sequence, Finite Element Method.

Using a longitudinal model to estimate the effect of methicillin-resistant staphylococcus aureus infection on length of stay in an intensive care unit

Healthcare-associated methicillin-resistant Staphylococcus aureus(MRSA) infection may cause increased hospital stay or, sometimes, death. Quantifying this effect is complicated because it is a time-dependent exposure: infection may prolong hospital stay, while longer stays increase the risk of infection. We overcome these problems by using a multinomial longitudinal model for estimating the daily probability of death and discharge. We then extend the basic model to estimate how the effect of MRSA infection varies over time, and to quantify the number of excess ICU days due to infection. We find that infection decreases the relative risk of discharge (relative risk ratio = 0.68, 95% credible interval: 0.54, 0.82), but is only indirectly associated with increased mortality. An infection on the first day of admission resulted in a mean extra stay of 0.3 days (95% CI: 0.1, 0.5) for a patient with an APACHE II score of 10, and 1.2 days (95% CI: 0.5, 2.0) for a patient with an APACHE II score of 30. The decrease in the relative risk of discharge remained fairly constant with day of MRSA infection, but was slightly stronger closer to the start of infection. These results confirm the importance of MRSA infection in increasing ICU stay, but suggest that previous work may have systematically overestimated the effect size.

Kallikrein-related peptidase 4 activation of protease-activated receptor family members and association with prostate cancer

Two areas of particular importance in prostate cancer progression are primary tumour development and metastasis. These processes involve a number of physiological events, the mediators of which are still being discovered and characterised. Serine proteases have been shown to play a major role in cancer invasion and metastasis. The recently discovered phenomenon of their activation of a receptor family known as the protease activated receptors (PARs) has extended their physiological role to that of signaling molecule. Several serine proteases are expressed by malignant prostate cancer cells, including members of the kallikreinrelated peptidase (KLK) serine protease family, and increasingly these are being shown to be associated with prostate cancer progression. KLK4 is highly expressed in the prostate and expression levels increase during prostate cancer progression. Critically, recent studies have implicated KLK4 in processes associated with cancer. For example, the ectopic over-expression of KLK4 in prostate cancer cell lines results in an increased ability of these cells to form colonies, proliferate and migrate. In addition, it has been demonstrated that KLK4 is a potential mediator of cellular interactions between prostate cancer cells and osteoblasts (bone forming cells). The ability of KLK4 to influence cellular behaviour is believed to be through the selective cleavage of specific substrates. Identification of relevant in vivo substrates of KLK4 is critical to understanding the pathophysiological roles of this enzyme. Significantly, recent reports have demonstrated that several members of the KLK family are able to activate PARs. The PARs are relatively new members of the seven transmembrane domain containing G protein coupled receptor (GPCR) family. PARs are activated through proteolytic cleavage of their N-terminus by serine proteases, the resulting nascent N-terminal binds intramolecularly to initiate receptor activation. PARs are involved in a number of patho-physiological processes, including vascular repair and inflammation, and a growing body of evidence suggests roles in cancer. While expression of PAR family members has been documented in several types of cancers, including prostate, the role of these GPCRs in prostate cancer development and progression is yet to be examined. Interestingly, several studies have suggested potential roles in cellular invasion through the induction of cytoskeletal reorganisation and expression of basement membrane-degrading enzymes. Accordingly, this program of research focussed on the activation of the PARs by the prostate cancer associated enzyme KLK4, cellular processing of activated PARs and the expression pattern of receptor and agonist in prostate cancer. For these studies KLK4 was purified from the conditioned media of stably transfected Sf9 insect cells expressing a construct containing the complete human KLK4 coding sequence in frame with a V5 epitope and poly-histidine encoding sequences. The first aspect of this study was the further characterisation of this recombinant zymogen form of KLK4. The recombinant KLK4 zymogen was demonstrated to be activatable by the metalloendopeptidase thermolysin and amino terminal sequencing indicated that thermolysin activated KLK4 had the predicted N-terminus of mature active KLK4 (31IINED). Critically, removal of the pro-region successfully generated a catalytically active enzyme, with comparable activity to a previously published recombinant KLK4 produced from S2 insect cells. The second aspect of this study was the activation of the PARs by KLK4 and the initiation of signal transduction. This study demonstrated that KLK4 can activate PAR-1 and PAR-2 to mobilise intracellular Ca2+, but failed to activate PAR-4. Further, KLK4 activated PAR-1 and PAR-2 over distinct concentration ranges, with KLK4 activation and mobilisation of Ca2+ demonstrating higher efficacy through PAR-2. Thus, the remainder of this study focussed on PAR-2. KLK4 was demonstrated to directly cleave a synthetic peptide that mimicked the PAR-2 Nterminal activation sequence. Further, KLK4 mediated Ca2+ mobilisation through PAR-2 was accompanied by the initiation of the extra-cellular regulated kinase (ERK) cascade. The specificity of intracellular signaling mediated through PAR-2 by KLK4 activation was demonstrated by siRNA mediated protein depletion, with a reduction in PAR-2 protein levels correlating to a reduction in KLK4 mediated Ca2+mobilisation and ERK phosphorylation. The third aspect of this study examined cellular processing of KLK4 activated PAR- 2 in a prostate cancer cell line. PAR-2 was demonstrated to be expressed by five prostate derived cell lines including the prostate cancer cell line PC-3. It was also demonstrated by flow cytometry and confocal microscopy analyses that activation of PC-3 cell surface PAR-2 by KLK4 leads to internalisation of this receptor in a time dependent manner. Critically, in vivo relevance of the interaction between KLK4 and PAR-2 was established by the observation of the co-expression of receptor and agonist in primary prostate cancer and prostate cancer bone lesion samples by immunohistochemical analysis. Based on the results of this study a number of exciting future studies have been proposed, including, delineating differences in KLK4 cellular signaling via PAR-1 and PAR-2 and the role of PAR-1 and PAR-2 activation by KLK4 in prostate cancer cells and bone cells in prostate cancer progression.

Simulation of delaminations in composite laminates

Lamb waves propagation in composite materials has been studied extensively since it was first observed in 1982. In this paper, we show a procedure to simulate the propagation of Lamb waves in composite laminates using a two-dimensional model in ANSYS. This is done by simulating the Lamb waves propagating along the plane of the structure in the form of a time dependent force excitation. In this paper, an 8-layered carbon reinforced fibre plastic (CRFP) is modelled as transversely isotropic and dissipative medium and the effect of flaws is analyzed with respect to the defects induced between various layers of the composite laminate. This effort is the basis for the future development of a 3D model for similar applications.

Infrastructure sustainability : differential axial shortening of concrete structures

High density development has been seen as a contribution to sustainable development. However, a number of engineering issues play a crucial role in the sustainable construction of high rise buildings. Non linear deformation of concrete has an adverse impact on high-rise buildings with complex geometries, due to differential axial shortening. These adverse effects are caused by time dependent behaviour resulting in volume change known as ‘shrinkage’, ‘creep’ and ‘elastic’ deformation. These three phenomena govern the behaviour and performance of all concrete elements, during and after construction. Reinforcement content, variable concrete modulus, volume to surface area ratio of the elements, environmental conditions, and construction quality and sequence influence on the performance of concrete elements and differential axial shortening will occur in all structural systems. Its detrimental effects escalate with increasing height and non vertical load paths resulting from geometric complexity. The magnitude of these effects has a significant impact on building envelopes, building services, secondary systems, and lifetime serviceability and performance. Analytical and test procedures available to quantify the magnitude of these effects are limited to a very few parameters and are not adequately rigorous to capture the complexity of true time dependent material response. With this in mind, a research project has been undertaken to develop an accurate numerical procedure to quantify the differential axial shortening of structural elements. The procedure has been successfully applied to quantify the differential axial shortening of a high rise building, and the important capabilities available in the procedure have been discussed. A new practical concept, based on the variation of vibration characteristic of structure during and after construction and used to quantify the axial shortening and assess the performance of structure, is presented.

Axial shortening in reinforced concrete members using vibration characteristics - Part 1 - Theory

Differential axial shortening in vertical members of reinforced concrete high-rise buildings occurs due to shrinkage, creep and elastic shortening, which are time dependent effects of concrete. This has to be quantified in order to make adequate provisions and mitigate its adverse effects. This paper presents a novel procedure for quantifying the axial shortening of vertical members using the variations in vibration characteristics of the structure, in lieu of using gauges which can pose problems in use during and after the construction. This procedure is based on the changes in the modal flexiblity matrix which is expressed as a function of the mode shapes and the reciprocal of the natural frequencies. This paper will present the development of this novel procedure.

Axial shortening in reinforced concrete members using vibration characteristics - part 2 - Application

Controlling differential axial shortening in vertical load bearing concrete elements is a major concern for new generation tall buildings with complex geometries and mechanisms. Quantification of axial shortening using gauges to verify the pre-estimated numerical values used at the design stage is a well established method. This method makes adequate provision to mitigate the adverse effects during the construction. However, this method is becoming increasingly unusable due to its drawbacks. This highlights the need a novel method to quantify the axial shortening using ambient measurements. This paper will first brief introduce the method and then illustrate its application to a high-rise building with two outrigger and belt systems. Moreover, this procedure can be used as a health or performance monitoring tool of the building structure, both during and after construction.

A vibration based method to update axial shortening of load bearing elements

Axial shortening in vertical load bearing elements of reinforced concrete high-rise buildings is caused by the time dependent effects of shrinkage, creep and elastic shortening of concrete under loads. Such phenomenon has to be predicted at design stage and then updated during and after construction of the buildings in order to provide mitigation against the adverse effects of differential axial shortening among the elements. Existing measuring methods for updating previous predictions of axial shortening pose problems. With this in mind, a innovative procedure with a vibration based parameter called axial shortening index is proposed to update axial shortening of vertical elements based on variations in vibration characteristics of the buildings. This paper presents the development of the procedure and illustrates it through a numerical example of an unsymmetrical high-rise building with two outrigger and belt systems. Results indicate that the method has the capability to capture influence of different tributary areas, shear walls of outrigger and belt systems as well as the geometric complexity of the building.