Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Maser Oscillation in a Whispering-Gallery-Mode Microwave Resonator

We report the first observation of above-threshold maser oscillation in a whispering-gallery(WG)-mode resonator, whose quasi-transverse-magnetic, 17th azimuthal-order WG mode, at a frequency of approx. 12.038 GHz, with a loaded Q of several hundred million, is supported on a cylinder of mono-crystalline sapphire. An electron spin resonance (ESR) associated with Fe3+ ions, that are substitutively included within the sapphire at a concentration of a few parts per billion, coincides in frequency with that of the (considerably narrower) WG mode. By applying a c.w. `pump' to the resonator at a frequency of approx. 31.34 GHz, with no applied d.c. magnetic field, the WG (`signal') mode is energized through a three-level maser scheme. Preliminary measurements demonstrate a frequency stability (Allan deviation) of a few times 1e-14 for sampling intervals up to 100 s.Comment: REVTeX v.4, 3 pages, with a separate .bbl file and 3 .eps figure

Time invariance violating nuclear electric octupole moments

The existence of a nuclear electric octupole moment (EOM) requires both parity and time invariance violation. The EOMs of odd $Z$ nuclei that are induced by a particular T- and P-odd interaction are calculated. We compare such octupole moments with the collective EOMs that can occur in nuclei having a static octupole deformation. A nuclear EOM can induce a parity and time invariance violating atomic electric dipole moment, and the magnitude of this effect is calculated. The contribution of a nuclear EOM to such a dipole moment is found, in most cases, to be smaller than that of other mechanisms of atomic electric dipole moment production.Comment: Uses RevTex, 25 page

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2009 Orton et al.BACKGROUND: The Epidermal Growth Factor Receptor (EGFR) activated Extracellular-signal Regulated Kinase (ERK) pathway is a critical cell signalling pathway that relays the signal for a cell to proliferate from the plasma membrane to the nucleus. Deregulation of the EGFR/ERK pathway due to alterations affecting the expression or function of a number of pathway components has long been associated with numerous forms of cancer. Under normal conditions, Epidermal Growth Factor (EGF) stimulates a rapid but transient activation of ERK as the signal is rapidly shutdown. Whereas, under cancerous mutation conditions the ERK signal cannot be shutdown and is sustained resulting in the constitutive activation of ERK and continual cell proliferation. In this study, we have used computational modelling techniques to investigate what effects various cancerous alterations have on the signalling flow through the ERK pathway. RESULTS: We have generated a new model of the EGFR activated ERK pathway, which was verified by our own experimental data. We then altered our model to represent various cancerous situations such as Ras, B-Raf and EGFR mutations, as well as EGFR overexpression. Analysis of the models showed that different cancerous situations resulted in different signalling patterns through the ERK pathway, especially when compared to the normal EGF signal pattern. Our model predicts that cancerous EGFR mutation and overexpression signals almost exclusively via the Rap1 pathway, predicting that this pathway is the best target for drugs. Furthermore, our model also highlights the importance of receptor degradation in normal and cancerous EGFR signalling, and suggests that receptor degradation is a key difference between the signalling from the EGF and Nerve Growth Factor (NGF) receptors. CONCLUSION: Our results suggest that different routes to ERK activation are being utilised in different cancerous situations which therefore has interesting implications for drug selection strategies. We also conducted a comparison of the critical differences between signalling from different growth factor receptors (namely EGFR, mutated EGFR, NGF, and Insulin) with our results suggesting the difference between the systems are large scale and can be attributed to the presence/absence of entire pathways rather than subtle difference in individual rate constants between the systems.This work was funded by the Department of Trade and Industry (DTI), under their Bioscience Beacon project programme. AG was funded by an industrial PhD studentship from Scottish Enterprise and Cyclacel

Salicylamide derivatives for iron and aluminium sequestration. From synthesis to complexation studies

This paper presents an easy, fast and economic synthesis of chelating agents for medical, environmental and analytical applications, and the evaluation of the stability of their complexes with Fe3+ and Al3+. Complex formation equilibria with Cu2+ and Zn2+ metal ions were also studied to evaluate if the chelating agents can perturb the homeostatic equilibria of these essential metal ions. Effective chelating agents for metal ions, in addition to their well-known medical uses, find an increasing number of applications in environmental remediation, agricultural applications (supplying essential elements in an easily available form), and in analytical chemistry as colorimetric reagents. Besides the stability of the complexes, the lack of toxicity and the low cost are the basic requisites of metal chelating agents. With these aims in mind, we utilized ethyl salicylate, a cheap molecule without toxic effects, and adopted a simple synthetic strategy to join two salicylate units through linear diamines of variable length. Actually, the mutual position of the metal binding oxygen groups, as well as the linker length, affected protonation and complex formation equilibria. A thorough study of the ligands is presented. In particular, the complex formation equilibria of the three ligands toward Fe3+, Al3+, Zn2+ and Cu2+ ions were investigated by combined potentiometric and spectrophotometric techniques. The results are encouraging: all the three ligands form stable complexes with all the investigated metal ions, involving the oxygen donor atoms from the 2-hydroxybenzamido unit, and nitrogen atoms in copper and zinc coordination

Optical constants of liquid and solid methane

The optical constants n(sub r) + in(sub i) of liquid methane and phase 1 solid methane were determined over the entire spectral range by the use of various data sources published in the literature. Kramers-Kronig analyses were performed on the absorption spectra of liquid methane at the boiling point (111 K) and the melting point (90 K) and on the absorption spectra of phase 1 solid methane at the melting point and at 30 K. Measurements of the static dielectric constant at these temperatures and refractive indices determined over limited spectral ranges were used as constraints in the analyses. Applications of methane optical properties to studies of outer solar system bodies are described

Effectiveness of early intervention programs for parents of preterm infants: a meta-review of systematic reviews

Background: Various intervention programs exist for parents of preterm babies and some systematic reviews (SRs) have synthesised the evidence of their effectiveness. These reviews are, however, limited to specific interventions, components, or outcomes, and a comprehensive evidence base is lacking. The aim of this meta-review was to appraise and meta-synthesise the evidence from existing SRs to provide a comprehensive evidence base on the effectiveness of interventions for parents of preterm infants on parental and infant outcomes. Methods: We conducted a comprehensive search of the following databases to identify relevant SRs: Cochrane library, Web of science, EMBASE, CINAHL, British Nursing Index, PsycINFO, Medline, ScienceDirect, Scopus, IBSS, DOAJ, ERIC, EPPI-Centre, PROSPERO, WHO Library. Additional searches were conducted using authors’ institutional libraries, Google Scholar, and the reference lists of identified reviews. Identified articles were screened in two stages against an inclusion criteria with titles and abstracts screened first followed by full-text screening. Selected SRs were appraised using the AMSTAR tool. Extracted data using a predesigned tool were synthesised narratively examining the direction of impact on outcomes. Results: We found 11 SRs eligible for inclusion that synthesised a total of 343 quantitative primary studies. The average quality of the SRs was ‘medium’. Thirty four interventions were reported across the SRs with considerable heterogeneity in the structural framework and the targeted outcomes that included maternal-infant dyadic, maternal/parental, and infant outcomes. Among all interventions, Kangaroo Care (KC) showed the most frequent positive impact across outcomes (n = 19) followed by Mother Infant Transaction Program (MITP) (n = 14). Other interventions with most consistent positive impact on infant outcomes were Modified-Mother Infant Transaction Program (M-MITP) (n = 6), Infant Health and Development Program (IHDP) (n = 5) and Creating Opportunities for Parent Empowerment (COPE) (n = 5). Overall, interventions with both home and facility based components showed the most frequent positive impact across outcomes. Conclusions: Neonatal care policy and planning for preterm babies should consider the implementation of interventions with most positive impact on outcomes. The heterogeneity in interventions and outcomes calls for the development and implementation of an integrated program for parents of preterm infants with a clearly defined global set of parental and infant outcomes

The Influence of Fat Suppression Technique on Diffusion-weighted (DW) MRI in Lung Cancer

Purpose: To qualitatively and quantitatively investigate the effect of common vendor-related sequence variations in fat suppression techniques on the diagnostic performance of free-breathing DW protocols for lung imaging.Methods: 8 patients with malignant lung lesions were scanned in free breathing using two diffusion-weighted (DW) protocols with different fat suppression techniques: DWA used short-tau inversion recovery (STIR), and DWB used Spectral Adiabatic Inversion Recovery (SPAIR). Both techniques were obtained at two time points, between 1 hour and 1 week apart. Image quality was assessed using a 5-point scoring system. The number of lesions visible within lung, mediastinum and at thoracic inlet on the DW (b=800 s/mm2) images was compared. Signal-to-noise ratios (SNR) were calculated for lesions and para-spinal muscle. Repeatability of ADC values of the lesions was estimated for both protocols together and separately.Results: There was a signal void at the thoracic inlet in all patients with DWB but not with DWA. DWA images were rated significantly better than DWB images overall quality domains. (Cohens κ = 1). Although 8 more upper mediastinal/thoracic inlet lymph nodes were detected with DWA than DWB, this did not reach statistical significance (p = 0.23). Tumour ADC values were not significantly different between protocols (p=0.93), their ADC reproducibility was satisfactory (CoV=7.7%) and repeatability of each protocol separately was comparable (CoVDWA=3.7% (95% CI 2.5 7.1%) and CoVDWB=4.6% (95% CI 3.18.8%)).Conclusion: In a free-breathing DW-MRI protocol for lung, STIR fat suppression produced images of better diagnostic quality than SPAIR, while maintaining comparable SNR and providing repeatable quantitative ADC acceptable for use in a multicentre trial setting

Coordination Chemistry and Sensing Properties Towards Anions and Metal Ions of a Simple Fluorescent Urea

The coordination and sensing properties towards anions and transition metal ions of the simple novel fluorescent urea 1-(2-aminophenyl)-3-(naphthalen-1)-yl)urea (L) were investigated in solution, and in the solid state. An electron donating amine group in the molecular skeleton of L decreased the acidity of the urea NHs that are usually deprotonated by basic anions and allowed for a good degree of affinity towards fluoride in DMSO-d6-0.5 %H2O. Moreover, the amine moiety acted as a further binding group for metal ions. Indeed, L was able to bind Zn2+ both in solution and in the solid state, and to respond to the presence of this metal ion in MeCN with an enhancement of the fluorescence emission. Although solution studies evidenced the formation of a 1 : 1 complex of L with Zn2+, complexes with a 2 : 1 ligand-to-metal stoichiometry were isolated in the solid state. DFT calculations helped to clarify the stability reasons behind these results