Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ~200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Delivery of AAV2/9-microdystrophin genes incorporating helix 1 of the coiled-coil motif in the C-terminal domain of dystrophin improves muscle pathology and restores the level of α1-syntrophin and α-dystrobrevin in skeletal muscles of mdx mice. Level of α1-Syntrophin and α-Dystrobrevin in Skeletal Muscles of mdx Mice

Duchenne muscular dystrophy is a severe X-linked inherited muscle wasting disorder caused by mutations in the dystrophin gene. Adeno-associated virus (AAV) vectors have been extensively used to deliver genes efficiently for dystrophin expression in skeletal muscles. To overcome limited packaging capacity of AAV vectors (<5 kb), truncated recombinant microdystrophin genes with deletions of most of rod and carboxyl-terminal (CT) domains of dystrophin have been developed. We have previously shown the efficiency of mRNA sequence–optimized microdystrophin (ΔR4-23/ΔCT, called MD1) with deletion of spectrin-like repeat domain 4 to 23 and CT domain in ameliorating the pathology of dystrophic mdx mice. However, the CT domain of dystrophin is thought to recruit part of the dystrophin-associated protein complex, which acts as a mediator of signalling between extracellular matrix and cytoskeleton in muscle fibers. In this study, we extended the ΔR4-23/ΔCT microdystrophin by incorporating helix 1 of the coiled-coil motif in the CT domain of dystrophin (MD2), which contains the α1-syntrophin and α-dystrobrevin binding sites. Intramuscular injection of AAV2/9 expressing CT domain–extended microdystrophin showed efficient dystrophin expression in tibialis anterior muscles of mdx mice. The presence of the CT domain of dystrophin in MD2 increased the recruitment of α1-syntrophin and α-dystrobrevin at the sarcolemma and significantly improved the muscle resistance to lengthening contraction–induced muscle damage in the mdx mice compared with MD1. These results suggest that the incorporation of helix 1 of the coiled-coil motif in the CT domain of dystrophin to the microdystrophins will substantially improve their efficiency in restoring muscle function in patients with Duchenne muscular dystrophy.

The domain derivative in rough-surface scattering and rigorous estimates for first-order perturbation theory

We investigate Fréchet differentiability of the scattered field with respect to variation in the boundary in the case of time–harmonic acoustic scattering by an unbounded, sound–soft, one–dimensional rough surface. We rigorously prove the differentiability of the scattered field and derive a characterization of the Fréchet derivative as the solution to a Dirichlet boundary value problem. As an application of these results we give rigorous error estimates for first–order perturbation theory, justifying small perturbation methods that have a long history in the engineering literature. As an application of our rigorous estimates we show that a plane acoustic wave incident on a sound–soft rough surface can produce an unbounded scattered field.

Evaluation of a boundary integral representation for the conformal mapping of the unit disk onto a simply-connected domain

A representation of the conformal mapping g of the interior or exterior of the unit circle onto a simply-connected domain Ω as a boundary integral in terms ofƒ|∂Ω is obtained, whereƒ :=g -l. A product integration scheme for the approximation of the boundary integral is described and analysed. An ill-conditioning problem related to the domain geometry is discussed. Numerical examples confirm the conclusions of this discussion and support the analysis of the quadrature scheme.

Nonlinear stability of Euler flows in two-dimensional periodic domains

The non-quadratic conservation laws of the two-dimensional Euler equations are used to show that the gravest modes in a doubly-periodic domain with aspect ratio L = 1 are stable up to translations (or structurally stable) for finite-amplitude disturbances. This extends a previous result based on conservation of energy and enstrophy alone. When L 1, a saturation bound is established for the mode with wavenumber |k| = L −1 (the next-gravest mode), which is linearly unstable. The method is applied to prove nonlinear structural stability of planetary wave two on a rotating sphere.

The contributions of domain-general and numerical factors to third-grade arithmetic skills and mathematical learning disability

Explanations of the marked individual differences in elementary school mathematical achievement and mathematical learning disability (MLD or dyscalculia) have involved domain-general factors (working memory, reasoning, processing speed and oral language) and numerical factors that include single-digit processing efficiency and multi-digit skills such as number system knowledge and estimation. This study of third graders (N = 258) finds both domain-general and numerical factors contribute independently to explaining variation in three significant arithmetic skills: basic calculation fluency, written multi-digit computation, and arithmetic word problems. Estimation accuracy and number system knowledge show the strongest associations with every skill and their contributions are both independent of each other and other factors. Different domain-general factors independently account for variation in each skill. Numeral comparison, a single digit processing skill, uniquely accounts for variation in basic calculation. Subsamples of children with MLD (at or below 10th percentile, n = 29) are compared with low achievement (LA, 11th to 25th percentiles, n = 42) and typical achievement (above 25th percentile, n = 187). Examination of these and subsets with persistent difficulties supports a multiple deficits view of number difficulties: most children with number difficulties exhibit deficits in both domain-general and numerical factors. The only factor deficit common to all persistent MLD children is in multi-digit skills. These findings indicate that many factors matter but multi-digit skills matter most in third grade mathematical achievement.

Maximum principles for vectorial approximate minimisers on non-convex functionals

We establish Maximum Principles which apply to vectorial approximate minimizers of the general integral functional of Calculus of Variations. Our main result is a version of the Convex Hull Property. The primary advance compared to results already existing in the literature is that we have dropped the quasiconvexity assumption of the integrand in the gradient term. The lack of weak Lower semicontinuity is compensated by introducing a nonlinear convergence technique, based on the approximation of the projection onto a convex set by reflections and on the invariance of the integrand in the gradient term under the Orthogonal Group. Maximum Principles are implied for the relaxed solution in the case of non-existence of minimizers and for minimizing solutions of the Euler–Lagrange system of PDE.

A high frequency $hp$ boundary element method for scattering by convex polygons

In this paper we propose and analyze a hybrid $hp$ boundary element method for the solution of problems of high frequency acoustic scattering by sound-soft convex polygons, in which the approximation space is enriched with oscillatory basis functions which efficiently capture the high frequency asymptotics of the solution. We demonstrate, both theoretically and via numerical examples, exponential convergence with respect to the order of the polynomials, moreover providing rigorous error estimates for our approximations to the solution and to the far field pattern, in which the dependence on the frequency of all constants is explicit. Importantly, these estimates prove that, to achieve any desired accuracy in the computation of these quantities, it is sufficient to increase the number of degrees of freedom in proportion to the logarithm of the frequency as the frequency increases, in contrast to the at least linear growth required by conventional methods.

Thermodynamics/dynamics coupling in weakly compressible turbulent stratified fluids

In traditional and geophysical fluid dynamics, it is common to describe stratified turbulent fluid flows with low Mach number and small relative density variations by means of the incompressible Boussinesq approximation. Although such an approximation is often interpreted as decoupling the thermodynamics from the dynamics, this paper reviews recent results and derive new ones that show that the reality is actually more subtle and complex when diabatic effects and a nonlinear equation of state are retained. Such an analysis reveals indeed: (1) that the compressible work of expansion/contraction remains of comparable importance as the mechanical energy conversions in contrast to what is usually assumed; (2) in a Boussinesq fluid, compressible effects occur in the guise of changes in gravitational potential energy due to density changes. This makes it possible to construct a fully consistent description of the thermodynamics of incompressible fluids for an arbitrary nonlinear equation of state; (3) rigorous methods based on using the available potential energy and potential enthalpy budgets can be used to quantify the work of expansion/contraction B in steady and transient flows, which reveals that B is predominantly controlled by molecular diffusive effects, and act as a significant sink of kinetic energy.

The linearly modulated IRSL red emission from feldspars

This paper uses the linear modulation technique to study red IRSL emission of potassium feldspars. Sub-samples were subjected to various pre-treatment and measurement conditions in an attempt to understand the relevant mechanisms of charge transfer. The linear modulation curves fitted most successfully to a sum of three first order components and we present supporting empirical evidence for the presence of three separate signal components. Additionally, the form of the red emission was observed to closely resemble the UV emission, implying the same donor charge concentrations may supply different recombination centres (assuming emission wavelength depends on centre type).

Analytical solutions of a minimal model of species migration in a bounded domain

A minimal model of species migration is presented which takes the form of a parabolic equation with boundary conditions and initial data. Solutions to the differential problem are obtained that can be used to describe the small- and large-time evolution of a species distribution within a bounded domain. These expressions are compared with the results of numerical simulations and are found to be satisfactory within appropriate temporal regimes. The solutions presented can be used to describe existing observations of nematode distributions, can be used as the basis for further work on nematode migration, and may also be interpreted more generally.

A MATLAB GUI for learning controller design in the frequency domain

A MATLAB GUI is presented which is used to help students learn to design controllers in the frequency domain. It complements the author’s two previous GUIs for plotting and identification of systems in the frequency domain. It also incorporates the concept used in the “electronic calculator that makes students think” to assist learning. Positive student feedback affirms that the GUI has helped their understanding.

Single-carrier frequency domain equalisation for hammerstein communication systems using complex-valued neural networks

Single-carrier (SC) block transmission with frequency-domain equalisation (FDE) offers a viable transmission technology for combating the adverse effects of long dispersive channels encountered in high-rate broadband wireless communication systems. However, for high bandwidthefficiency and high power-efficiency systems, the channel can generally be modelled by the Hammerstein system that includes the nonlinear distortion effects of the high power amplifier (HPA) at transmitter. For such nonlinear Hammerstein channels, the standard SC-FDE scheme no longer works. This paper advocates a complex-valued (CV) B-spline neural network based nonlinear SC-FDE scheme for Hammerstein channels. Specifically, We model the nonlinear HPA, which represents the CV static nonlinearity of the Hammerstein channel, by a CV B-spline neural network, and we develop two efficient alternating least squares schemes for estimating the parameters of the Hammerstein channel, including both the channel impulse response coefficients and the parameters of the CV B-spline model. We also use another CV B-spline neural network to model the inversion of the nonlinear HPA, and the parameters of this inverting B-spline model can easily be estimated using the standard least squares algorithm based on the pseudo training data obtained as a natural byproduct of the Hammerstein channel identification. Equalisation of the SC Hammerstein channel can then be accomplished by the usual one-tap linear equalisation in frequency domain as well as the inverse B-spline neural network model obtained in time domain. Extensive simulation results are included to demonstrate the effectiveness of our nonlinear SC-FDE scheme for Hammerstein channels.

The acquisition of person and number morphology within the verbal domain in Early Greek

The aim of this paper is to examine the acquisition pattern of person and number verb morphology within the generative framework and to compare the results of the analyses with previous research in Greek and other European languages. The study considers previous data on the acquisition of subject-verb agreement, and thereafter, examines the acquisition of person and number morphology in a new dataset of two monolingual Greek-speaking children. The analyses present quantitative data of accuracy of person and number marking, error data, and qualitative analyses addressing the productivity of person and number marking. The results suggest that person and number morphology is used correctly and productively from a very early age in Greek speaking children. The findings provide new insight into early Greek language acquisition and are also relevant for research in early development of languages with rich inflectional morphology.

Sensitivity of simulated regional Arctic climate to the choice of coupled model domain

The climate over the Arctic has undergone changes in recent decades. In order to evaluate the coupled response of the Arctic system to external and internal forcing, our study focuses on the estimation of regional climate variability and its dependence on large-scale atmospheric and regional ocean circulations. A global ocean–sea ice model with regionally high horizontal resolution is coupled to an atmospheric regional model and global terrestrial hydrology model. This way of coupling divides the global ocean model setup into two different domains: one coupled, where the ocean and the atmosphere are interacting, and one uncoupled, where the ocean model is driven by prescribed atmospheric forcing and runs in a so-called stand-alone mode. Therefore, selecting a specific area for the regional atmosphere implies that the ocean–atmosphere system can develop ‘freely’ in that area, whereas for the rest of the global ocean, the circulation is driven by prescribed atmospheric forcing without any feedbacks. Five different coupled setups are chosen for ensemble simulations. The choice of the coupled domains was done to estimate the influences of the Subtropical Atlantic, Eurasian and North Pacific regions on northern North Atlantic and Arctic climate. Our simulations show that the regional coupled ocean–atmosphere model is sensitive to the choice of the modelled area. The different model configurations reproduce differently both the mean climate and its variability. Only two out of five model setups were able to reproduce the Arctic climate as observed under recent climate conditions (ERA-40 Reanalysis). Evidence is found that the main source of uncertainty for Arctic climate variability and its predictability is the North Pacific. The prescription of North Pacific conditions in the regional model leads to significant correlation with observations, even if the whole North Atlantic is within the coupled model domain. However, the inclusion of the North Pacific area into the coupled system drastically changes the Arctic climate variability to a point where the Arctic Oscillation becomes an ‘internal mode’ of variability and correlations of year-to-year variability with observational data vanish. In line with previous studies, our simulations provide evidence that Arctic sea ice export is mainly due to ‘internal variability’ within the Arctic region. We conclude that the choice of model domains should be based on physical knowledge of the atmospheric and oceanic processes and not on ‘geographic’ reasons. This is particularly the case for areas like the Arctic, which has very complex feedbacks between components of the regional climate system.