Computational and Mathematical Modelling of the EGF Receptor System

This chapter gives an overview of computational and mathematical modelling of the EGF receptor system. It begins with a survey of motivations for producing such models, then describes the main approaches that are taken to carrying out such modelling, viz. differential equations and individual-based modelling. Finally, a number of projects that applying modelling and simulation techniques to various aspects of the EGF receptor system are described

Computational study of unsteady couple stress magnetic nanofluid flow from a stretching sheet with ohmic dissipation

To provide a deeper insight of the transport phenomena inherent to the manufacturing of magnetic nano-polymer materials, in the present work a mathematical model is developed for time-dependent hydromagnetic rheological nanopolymer boundary layer flow and heat transfer over a stretching sheet in the presence of a transverse static magnetic field. Joule heating (Ohmic dissipation) and viscous heating effects are included since these phenomena arise frequently in magnetic materials processing. Stokes’ couple stress model is deployed to simulate non-Newtonian micro-structural characteristics. The Tiwari-Das nanoscale model is adopted which permits different nano-particles to be simulated (in this article both copper-water and aluminium oxide-water nanofluids are considered). Similarity transformations are utilized to convert the governing partial differential conservation equations into a system of coupled, nonlinear ordinary differential equations with appropriate wall and free stream boundary conditions. The shooting technique is used to solve the reduced nonlinear coupled ordinary differential boundary value problem via MATLAB symbolic software. Validation with published results from the literature is included for the special cases of non-dissipative and Newtonian nanofluid flows. Fluid velocity and temperature profiles for both Copper and Aluminium Oxide (Al2O3) nanofluids are observed to be enhanced with greater non-Newtonian couple stress parameter and magnetic parameter whereas the opposite trend is computed with greater values of unsteadiness parameter. The boundary layer flow is accelerated with increasing buoyancy parameter, elastic sheet stretching parameter and convection parameter. Temperatures are generally increased with greater couple stress rheological parameter and are consistently higher for the Aluminium oxide nanoparticle case. Temperatures are also boosted with magnetic parameter and exhibit an overshoot near the wall when magnetic parameter exceeds unity (magnetic force exceeds viscous force). A decrease in temperatures is induced with increasing sheet stretching parameter. Increasing Eckert number elevates temperatures considerably. With greater nanoparticle volume fraction both skin friction and Nusselt number are elevated and copper nano-particles achieve higher magnitudes than aluminium oxide

PainDroid: An android-based virtual reality application for pain assessment

Earlier studies in the field of pain research suggest that little efficient intervention currently exists in response to the exponential increase in the prevalence of pain. In this paper, we present an Android application (PainDroid) with multimodal functionality that could be enhanced with Virtual Reality (VR) technology, which has been designed for the purpose of improving the assessment of this notoriously difficult medical concern. Pain- Droid has been evaluated for its usability and acceptability with a pilot group of potential users and clinicians, with initial results suggesting that it can be an effective and usable tool for improving the assessment of pain. Participant experiences indicated that the application was easy to use and the potential of the application was similarly appreciated by the clinicians involved in the evaluation. Our findings may be of considerable interest to healthcare providers, policy makers, and other parties that might be actively involved in the area of pain and VR research

Registration Issues in the Fusion of Eddy Current and Ultrasound NDE Data Using Q-Transforms

Data fusion methods are finding increasing application in nondestructive evaluation (NDE) [2, 3, 4] for enhancing the reliability of inspection. These techniques typically combine information from two or more NDE modalities to improve the probability of detecting flaws and enhance specimen characterization results [1]. Eddy current methods rely on diffusion for propagating energy. Ultrasonic methods, in contrast, rely on wave propagation. Consequently, the two tests rely on different material/energy interaction processes and can potentially provide complementary perspectives of the flaw in a specimen. This paper proposes a novel phenomenological approach using Q-transforms for addressing the registration issue in the fusion of eddy current and ultrasonic data. Specifically, ultrasonic signals are Q-transformed to the diffusion domain. The transformation allows the superposition of the transformed field on the eddy current field as shown in Figure 1. It is anticipated that the resulting field will have a lower signal-to-noise ratio

Pseudogap temperature as a Widom line in doped Mott insulators

The pseudogap refers to an enigmatic state of matter with unusual physical properties found below a characteristic temperature $T^*$ in hole-doped high-temperature superconductors. Determining $T^*$ is critical for understanding this state. Here we study the simplest model of correlated electron systems, the Hubbard model, with cluster dynamical mean-field theory to find out whether the pseudogap can occur solely because of strong coupling physics and short nonlocal correlations. We find that the pseudogap characteristic temperature $T^*$ is a sharp crossover between different dynamical regimes along a line of thermodynamic anomalies that appears above a first-order phase transition, the Widom line. The Widom line emanating from the critical endpoint of a first-order transition is thus the organizing principle for the pseudogap phase diagram of the cuprates. No additional broken symmetry is necessary to explain the phenomenon. Broken symmetry states appear in the pseudogap and not the other way around.Comment: 6 pages, 4 figures and supplementary information; published versio

Epidemiology of Subpatent Plasmodium Falciparum Infection: Implications for Detection of Hotspots with Imperfect Diagnostics.

At the local level, malaria transmission clusters in hotspots, which may be a group of households that experience higher than average exposure to infectious mosquitoes. Active case detection often relying on rapid diagnostic tests for mass screen and treat campaigns has been proposed as a method to detect and treat individuals in hotspots. Data from a cross-sectional survey conducted in north-western Tanzania were used to examine the spatial distribution of Plasmodium falciparum and the relationship between household exposure and parasite density. Dried blood spots were collected from consenting individuals from four villages during a survey conducted in 2010. These were analysed by PCR for the presence of P. falciparum, with the parasite density of positive samples being estimated by quantitative PCR. Household exposure was estimated using the distance-weighted PCR prevalence of infection. Parasite density simulations were used to estimate the proportion of infections that would be treated using a screen and treat approach with rapid diagnostic tests (RDT) compared to targeted mass drug administration (tMDA) and Mass Drug Administration (MDA). Polymerase chain reaction PCR analysis revealed that of the 3,057 blood samples analysed, 1,078 were positive. Mean distance-weighted PCR prevalence per household was 34.5%. Parasite density was negatively associated with transmission intensity with the odds of an infection being subpatent increasing with household exposure (OR 1.09 per 1% increase in exposure). Parasite density was also related to age, being highest in children five to ten years old and lowest in those > 40 years. Simulations of different tMDA strategies showed that treating all individuals in households where RDT prevalence was above 20% increased the number of infections that would have been treated from 43 to 55%. However, even with this strategy, 45% of infections remained untreated. The negative relationship between household exposure and parasite density suggests that DNA-based detection of parasites is needed to provide adequate sensitivity in hotspots. Targeting MDA only to households with RDT-positive individuals may allow a larger fraction of infections to be treated. These results suggest that community-wide MDA, instead of screen and treat strategies, may be needed to successfully treat the asymptomatic, subpatent parasite reservoir and reduce transmission in similar settings

D-brane Charges in Gravitational Duals of 2+1 Dimensional Gauge Theories and Duality Cascades

We perform a systematic analysis of the D-brane charges associated with string theory realizations of d=3 gauge theories, focusing on the examples of the N=4 supersymmetric U(N)xU(N+M) Yang-Mills theory and the N=3 supersymmetric U(N)xU(N+M) Yang-Mills-Chern-Simons theory. We use both the brane construction of these theories and their dual string theory backgrounds in the supergravity approximation. In the N=4 case we generalize the previously known gravitational duals to arbitrary values of the gauge couplings, and present a precise mapping between the gravity and field theory parameters. In the N=3 case, which (for some values of N and M) flows to an N=6 supersymmetric Chern-Simons-matter theory in the IR, we argue that the careful analysis of the charges leads to a shift in the value of the B-field in the IR solution by 1/2, in units where its periodicity is one, compared to previous claims. We also suggest that the N=3 theories may exhibit, for some values of N and M, duality cascades similar to those of the Klebanov-Strassler theory.Comment: 47 pages, 9 figures; minor changes, references adde

Genome Wide Transcriptome Analysis of Dendritic Cells Identifies Genes with Altered Expression in Psoriasis

Activation of dendritic cells by different pathogens induces the secretion of proinflammatory mediators resulting in local inflammation. Importantly, innate immunity must be properly controlled, as its continuous activation leads to the development of chronic inflammatory diseases such as psoriasis. Lipopolysaccharide (LPS) or peptidoglycan (PGN) induced tolerance, a phenomenon of transient unresponsiveness of cells to repeated or prolonged stimulation, proved valuable model for the study of chronic inflammation. Thus, the aim of this study was the identification of the transcriptional diversity of primary human immature dendritic cells (iDCs) upon PGN induced tolerance. Using SAGESeq approach, a tag-based transcriptome sequencing method, we investigated gene expression changes of primary human iDCs upon stimulation or restimulation with Staphylococcus aureus derived PGN, a widely used TLR2 ligand. Based on the expression pattern of the altered genes, we identified non-tolerizeable and tolerizeable genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (Kegg) analysis showed marked enrichment of immune-, cell cycle- and apoptosis related genes. In parallel to the marked induction of proinflammatory mediators, negative feedback regulators of innate immunity, such as TNFAIP3, TNFAIP8, Tyro3 and Mer are markedly downregulated in tolerant cells. We also demonstrate, that the expression pattern of TNFAIP3 and TNFAIP8 is altered in both lesional, and non-lesional skin of psoriatic patients. Finally, we show that pretreatment of immature dendritic cells with anti-TNF-α inhibits the expression of IL-6 and CCL1 in tolerant iDCs and partially releases the suppression of TNFAIP8. Our findings suggest that after PGN stimulation/restimulation the host cell utilizes different mechanisms in order to maintain critical balance between inflammation and tolerance. Importantly, the transcriptome sequencing of stimulated/restimulated iDCs identified numerous genes with altered expression to date not associated with role in chronic inflammation, underlying the relevance of our in vitro model for further characterization of IFNprimed iDCs

Biochemical properties of Paracoccus denitrificans FnrP:Reactions with molecular oxygen and nitric oxide

In Paracoccus denitrificans, three CRP/FNR family regulatory proteins, NarR, NnrR and FnrP, control the switch between aerobic and anaerobic (denitrification) respiration. FnrP is a [4Fe-4S] cluster containing homologue of the archetypal O2 sensor FNR from E. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to O2, and also NO, availability. Here we show that FnrP undergoes O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion that involves up to 2 O2 per cluster, with significant oxidation of released cluster sulfide to sulfane observed at higher O2 concentrations. The rate of the cluster reaction was found to be ~6-fold lower than that of E. coli FNR, suggesting that FnrP can remain transcriptionally active under microaerobic conditions. This is consistent with a role for FnrP in activating expression of the high O2 affinity cytochrome c oxidase under microaerobic conditions. Cluster conversion resulted in dissociation of the transcriptionally active FnrP dimer into monomers. Therefore, along with E. coli FNR, FnrP belongs to the subset of FNR proteins in which cluster type is correlated with association state. Interestingly, two key charged residues, Arg140 and Asp154, that have been shown to play key roles in the monomer-dimer equilibrium in E. coli FNR are not conserved in FnrP, indicating that different protomer interactions are important for this equilibrium. Finally, the FnrP [4Fe-4S] cluster is shown to undergo reaction with multiple NO molecules, resulting in iron nitrosyl species and dissociation into monomers