DIRK Schemes with High Weak Stage Order

Runge-Kutta time-stepping methods in general suffer from order reduction: the observed order of convergence may be less than the formal order when applied to certain stiff problems. Order reduction can be avoided by using methods with high stage order. However, diagonally-implicit Runge-Kutta (DIRK) schemes are limited to low stage order. In this paper we explore a weak stage order criterion, which for initial boundary value problems also serves to avoid order reduction, and which is compatible with a DIRK structure. We provide specific DIRK schemes of weak stage order up to 3, and demonstrate their performance in various examples.Comment: 10 pages, 5 figure

Batch solution of small PDEs with the OPS DSL

In this paper we discuss the challenges and optimisations opportunities when solving a large number of small, equally sized discretised PDEs on regular grids. We present an extension of the OPS (Oxford Parallel library for Structured meshes) embedded Domain Specific Language, and show how support can be added for solving multiple systems, and how OPS makes it easy to deploy a variety of transformations and optimisations. The new capabilities in OPS allow to automatically apply data structure transformations, as well as execution schedule transformations to deliver high performance on a variety of hardware platforms. We evaluate our work on an industrially representative finance simulation on Intel CPUs, as well as NVIDIA GPUs

Promoting health and welfare in organic laying hens. Recommendations to ensure hen health and welfare in organic husbandry

In the HealthyHens project we investigated laying hen health and welfare in organic poultry systems in eight European countries. This leaflet presents our findings and recommendations. Most of our recommendations are also relevant for conventional poultry systems

Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer

<p>Abstract</p> <p>Background</p> <p>LIM kinase 1 (LIMK1), a LIM domain containing serine/threonine kinase, modulates actin dynamics through inactivation of the actin depolymerizing protein cofilin. Recent studies have indicated an important role of LIMK1 in growth and invasion of prostate and breast cancer cells; however, the molecular mechanism whereby LIMK1 induces tumor progression is unknown. In this study, we investigated the effects of ectopic expression of LIMK1 on cellular morphology, cell cycle progression and expression profile of LIMK1 in prostate tumors.</p> <p>Results</p> <p>Ectopic expression of LIMK1 in benign prostatic hyperplasia cells (BPH), which naturally express low levels of LIMK1, resulted in appearance of abnormal mitotic spindles, multiple centrosomes and smaller chromosomal masses. Furthermore, a transient G1/S phase arrest and delayed G2/M progression was observed in BPH cells expressing LIMK1. When treated with chemotherapeutic agent Taxol, no metaphase arrest was noted in these cells. We have also noted increased nuclear staining of LIMK1 in tumors with higher Gleason Scores and incidence of metastasis.</p> <p>Conclusion</p> <p>Our results show that increased expression of LIMK1 results in chromosomal abnormalities, aberrant cell cycle progression and alteration of normal cellular response to microtubule stabilizing agent Taxol; and that LIMK1 expression may be associated with cancerous phenotype of the prostate.</p

Geochronology of volcanically associated hydrocarbon charge in the pre-salt carbonates of the Namibe Basin, Angola

In volcanic rifted margins, the timing of hydrocarbon charge is difficult to predict, but is important in understanding fluid genesis. We investigated whether igneous activity was linked to hydrocarbon charge in the prolific South Atlantic pre-salt petroleum system. To do this, we applied in situ carbonate U-Pb geochronology, a relatively novel tool for dating hydrocarbon migration, to bituminous veins in pre-salt travertines from the rifted onshore Namibe Basin (Angola). To test if fluid flow was synchronous with known volcanic pulses, we also obtained new 40Ar/39/Ar geochronology from a nearby volcanic complex. Bitumen is associated with calcite in a first generation of veins and vugs, and with dolomite in younger veins. The dated calcite veins yielded a pooled U-Pb age of 86.2 ± 2.4 Ma, which overlaps the volcanism 40Ar/39/Ar age of 89.9 ± 1.8 Ma. The overlapping dates and the localized bitumen occurrence around the dated volcanic center show a clear genetic relationship between Late Cretaceous igneous activity and hydrocarbon charge. The dolomite was dated at 56.8 ± 4.8 Ma, revealing a previously unknown Paleocene/Eocene fluid-flow phase in the basin

Sporulation, bacterial cell envelopes, and the origin of life

Electron cryotomography (ECT) enables the 3D reconstruction of intact cells in a near-native state. Images produced by ECT have led to the proposal that an ancient sporulation-like event gave rise to the second membrane in diderm bacteria. Tomograms of sporulating monoderm and diderm bacterial cells show how sporulation can lead to the generation of diderm cells. Tomograms of Gram-negative and Gram-positive cell walls and purified sacculi suggest that they are more closely related than previously thought and support the hypothesis that they share a common origin. Mapping the distribution of cell envelope architectures onto a recent phylogenetic tree of life indicates that the diderm cell plan, and therefore the sporulation-like event that gave rise to it, must be very ancient. One explanation for this model is that during the cataclysmic transitions of the early Earth, cellular evolution may have gone through a bottleneck in which only spores survived, which implies that the last bacterial common ancestor was a spore