Time-delayed models of gene regulatory networks

We discuss different mathematical models of gene regulatory networks as relevant to the onset and development of cancer. After discussion of alternativemodelling approaches, we use a paradigmatic two-gene network to focus on the role played by time delays in the dynamics of gene regulatory networks. We contrast the dynamics of the reduced model arising in the limit of fast mRNA dynamics with that of the full model. The review concludes with the discussion of some open problems

Gravitational Waves from Mesoscopic Dynamics of the Extra Dimensions

Recent models which describe our world as a brane embedded in a higher dimensional space introduce new geometrical degrees of freedom: the shape and/or size of the extra dimensions, and the position of the brane. These modes can be coherently excited by symmetry breaking in the early universe even on ``mesoscopic'' scales as large as 1 mm, leading to detectable gravitational radiation. Two sources are described: relativistic turbulence caused by a first-order transition of a radion potential, and Kibble excitation of Nambu-Goldstone modes of brane displacement. Characteristic scales and spectral properties are estimated and the prospects for observation by LISA are discussed. Extra dimensions with scale between 10 \AA and 1 mm, which enter the 3+1-D era at cosmic temperatures between 1 and 1000 TeV, produce backgrounds with energy peaked at observed frequencies in the LISA band, between $10^{-1}$ and $10^{-4}$ Hz. The background is detectable above instrument and astrophysical foregrounds if initial metric perturbations are excited to a fractional amplitude of $10^{-3}$ or more, a likely outcome for the Nambu-Goldstone excitations.Comment: Latex, 5 pages, plus one figure, final version to appear in Phys. Rev. Let

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells.

Endothelial cells (ECs) are critical determinants of vascular homeostasis and inflammation, but transcriptional mechanisms specifying their identities and functional states remain poorly understood. Here, we report a genome-wide assessment of regulatory landscapes of primary human aortic endothelial cells (HAECs) under basal and activated conditions, enabling inference of transcription factor networks that direct homeostatic and pro-inflammatory programs. We demonstrate that 43% of detected enhancers are EC-specific and contain SNPs associated to cardiovascular disease and hypertension. We provide evidence that AP1, ETS, and GATA transcription factors play key roles in HAEC transcription by co-binding enhancers associated with EC-specific genes. We further demonstrate that exposure of HAECs to oxidized phospholipids or pro-inflammatory cytokines results in signal-specific alterations in enhancer landscapes and associate with coordinated binding of CEBPD, IRF1, and NFκB. Collectively, these findings identify cis-regulatory elements and corresponding trans-acting factors that contribute to EC identity and their specific responses to pro-inflammatory stimuli

Scales of the Extra Dimensions and their Gravitational Wave Backgrounds

Circumstances are described in which symmetry breaking during the formation of our three-dimensional brane within a higher-dimensional space in the early universe excites mesoscopic classical radion or brane-displacement degrees of freedom and produces a detectable stochastic background of gravitational radiation. The spectrum of the background is related to the unification energy scale and the the sizes and numbers of large extra dimensions. It is shown that properties of the background observable by gravitational-wave observatories at frequencies $f\approx 10^{-4}$ Hz to $10^3$ Hz contain information about unification on energy scales from 1 to $10^{10}$ TeV, gravity propagating through extra-dimension sizes from 1 mm to $10^{-18}$mm, and the dynamical history and stabilization of from one to seven extra dimensions.Comment: 6 pages, Latex, 1 figure, submitted to Phys. Re

Promising practices: What students, parents and teachers say about learning in a Big Picture context

This report identifies the key findings from a research project into the early implementation (the first 20 months) of the Big Picture Education (BPE) design for learning and school 1 in five different schools in Western Australia. The aim was to understand better how student engagement for learning and aspirations develop in a Big Picture context. These findings are reported more extensively in a series of Research Briefs, Combined Reports and papers. 2 Our goal in this document is to bring the findings together into the one summary report

A comparative framework: how broadly applicable is a 'rigorous' critical junctures framework?

The paper tests Hogan and Doyle's (2007, 2008) framework for examining critical junctures. This framework sought to incorporate the concept of ideational change in understanding critical junctures. Until its development, frameworks utilized in identifying critical junctures were subjective, seeking only to identify crisis, and subsequent policy changes, arguing that one invariably led to the other, as both occurred around the same time. Hogan and Doyle (2007, 2008) hypothesized ideational change as an intermediating variable in their framework, determining if, and when, a crisis leads to radical policy change. Here we test this framework on cases similar to, but different from, those employed in developing the exemplar. This will enable us determine whether the framework's relegation of ideational change to a condition of crisis holds, or, if ideational change has more importance than is ascribed to it by this framework. This will also enable us determined if the framework itself is robust, and fit for the purposes it was designed to perform — identifying the nature of policy change

Mass Outflow Rate From Accretion Discs around Compact Objects

We compute mass outflow rates from accretion disks around compact objects, such as neutron stars and black holes. These computations are done using combinations of exact transonic inflow and outflow solutions which may or may not form standing shock waves. Assuming that the bulk of the outflow is from the effective boundary layers of these objects, we find that the ratio of the outflow rate and inflow rate varies anywhere from a few percent to even close to a hundred percent (i.e., close to disk evacuation case) depending on the initial parameters of the disk, the degree of compression of matter near the centrifugal barrier, and the polytropic index of the flow. Our result, in general, matches with the outflow rates obtained through a fully time-dependent numerical simulation. In some region of the parameter space when the standing shock does not form, our results indicate that the disk may be evacuated and may produce quiescence states.Comment: 30 Latex pages and 13 figures. crckapb.sty; Published in Class. Quantum Grav. Vol. 16. No. 12. Pg. 387

A Characterisation of Strong Wave Tails in Curved Space-Times

A characterisation of when wave tails are strong is proposed. The existence of a curvature induced tail (i.e. a Green's function term whose support includes the interior of the light-cone) is commonly understood to cause backscattering of the field governed by the relevant wave equation. Strong tails are characterised as those for which the purely radiative part of the field is backscattered. With this definition, it is shown that electromagnetic waves in asymptotically flat space-times and fields governed by tail-free propagation have weak tails, but minimally coupled scalar fields in a cosmological scenario have strong tails.Comment: 17 pages, Revtex, to appear in Classical and Quantum Gravit

Purely gravito-magnetic vacuum space-times

It is shown that there are no vacuum space-times (with or without cosmological constant) for which the Weyl-tensor is purely gravito-magnetic with respect to a normal and timelike congruence of observers.Comment: 4 page

Measuring the Primordial Deuterium Abundance During the Cosmic Dark Ages

We discuss how measurements of fluctuations in the absorption of cosmic microwave background (CMB) photons by neutral gas during the cosmic dark ages, at redshifts z ~ 7--200, could reveal the primordial deuterium abundance of the Universe. The strength of the cross-correlation of brightness-temperature fluctuations due to resonant absorption of CMB photons in the 21-cm line of neutral hydrogen with those due to resonant absorption of CMB photons in the 92-cm line of neutral deuterium is proportional to the fossil deuterium to hydrogen ratio [D/H] fixed during big bang nucleosynthesis (BBN). Although technically challenging, this measurement could provide the cleanest possible determination of [D/H], free from contamination by structure formation processes at lower redshifts, and has the potential to improve BBN constraints to the baryon density of the Universe \Omega_{b} h^2. We also present our results for the thermal spin-change cross-section for deuterium-hydrogen scattering, which may be useful in a more general context than we describe here.Comment: 4 pages, 3 figures, submitted to Phys. Rev. Let