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

Crystal structure prediction of organic pigments: quinacridone as an example

The structures of the α, β and γ polymorphs of quinacridone were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality powder pattern is available

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

Prediction of poor clinical outcome in vascular cognitive impairment: TRACE-VCI study

INTRODUCTION: Prognostication in memory clinic patients with vascular brain injury (eg possible vascular cognitive impairment [VCI]) is often uncertain. We created a risk score to predict poor clinical outcome. METHODS: Using data from two longitudinal cohorts of memory clinic patients with vascular brain injury without advanced dementia, we created (n = 707) and validated (n = 235) the risk score. Poor clinical outcome was defined as substantial cognitive decline (change of Clinical Dementia Rating ≥1 or institutionalization) or major vascular events or death. Twenty‐four candidate predictors were evaluated using Cox proportional hazard models. RESULTS: Age, clinical syndrome diagnosis, Disability Assessment for Dementia, Neuropsychiatric Inventory, and medial temporal lobe atrophy most strongly predicted poor outcome and constituted the risk score (C‐statistic 0.71; validation cohort 0.78). Of note, none of the vascular predictors were retained in this model. The 2‐year risk of poor outcome was 6.5% for the lowest (0‐5) and 55.4% for the highest sum scores (10‐13). DISCUSSION: This is the first, validated, prediction score for 2‐year clinical outcome of patients with possible VCI

Role of age in presentation, response to therapy and outcome of autoimmune hepatitis

Background: Few studies with diverging results and a small sample size have compared autoimmune hepatitis (AIH) in the elderly to younger patients.Aim: To unbiasedly investigate the role of age in behaviour and treatment outcome of AIH.Methods: All patients with probable or definite AIH type 1 in four tertiary academic centres were included in this retrospective- and since 2006 prospective-cohort study. Influence of age on presentation, remission and outcome of AIH were investigated.Results: 359 patients were included. Presence of cirrhosis at AIH diagnosis around 30% was independent of age. ALAT was higher at age 30-60 years on AIH diagnosis, and above age 60 there were less acute onset, less jaundice and more concurrent autoimmune disease. Remission was reached in 80.2%, incomplete remission in 18.7%, only 1.1% (all aged 50-65) was treatment-refractory. Age was not an independent predictor of remission, while cirrhosis was. Above age 45 there was more diabetes, above age 60 more loss of remission. Rate of progression to cirrhosis was 10% in the 10 years after diagnosis and unrelated to age at AIH diagnosis. With onset below age 30, there was more development of decompensated cirrhosis over time. With higher age at AIH diagnosis there was a lower survival free of liver-related death or liver transplantation.Conclusions: AIH presents at all ages. Age influences features at diagnosis, but not response to treatment, while survival without liver-related death or liver transplantation decreases with higher age at diagnosis.</p

Imaging the nanoscale organization of peptidoglycan in living Lactococcus lactis cells

Peptidoglycans provide bacterial cell walls with mechanical strength. The spatial organization of peptidoglycan has previously been difficult to study. Here, atomic force microscopy, together with cells carrying mutations in cell-wall polysaccharides, has allowed an in-depth study of these molecules

Neural Dynamics during Anoxia and the “Wave of Death”

Recent experiments in rats have shown the occurrence of a high amplitude slow brain wave in the EEG approximately 1 minute after decapitation, with a duration of 5–15 s (van Rijn et al, PLoS One 6, e16514, 2011) that was presumed to signify the death of brain neurons. We present a computational model of a single neuron and its intra- and extracellular ion concentrations, which shows the physiological mechanism for this observation. The wave is caused by membrane potential oscillations, that occur after the cessation of activity of the sodium-potassium pumps has lead to an excess of extracellular potassium. These oscillations can be described by the Hodgkin-Huxley equations for the sodium and potassium channels, and result in a sudden change in mean membrane voltage. In combination with a high-pass filter, this sudden depolarization leads to a wave in the EEG. We discuss that this process is not necessarily irreversible

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

Plasma Extracellular Vesicle Serpin G1 and CD14 Levels are Associated with Major Adverse Cardiovascular Events and Major Adverse Limb Events in Patients Undergoing Femoral Endarterectomy

Objective: Plasma extracellular vesicles (EV) are an emerging source of biomarkers for diagnosis and prognosis of cardiovascular disease (CVD). Risk stratification for common adverse events such as major adverse limb events (MALE) and major adverse cardiovascular events (MACE) by an EV blood sample could improve healthcare management by individualising drug therapy or improving informed decision making regarding revascularisations in patients with peripheral artery disease (PAD). As such, this study investigated the associations between plasma EV proteins and prospectively registered MALE and MACE in consecutive patients undergoing femoral endarterectomy. Methods: Using the Athero-Express biobank study, four EV proteins (Cystatin C, CD14, Serpin C1, and Serpin G1) were measured in the high density lipoprotein subfraction isolated from plasma of 317 PAD patients undergoing arterial revascularisation. Multivariable Cox proportional hazard regression was used to investigate the association between plasma EV protein levels and MACE and MALE in the three year post-operative period. Results: Most patients were treated for claudication (Fontaine II, 52.8%), although rest pain (Fontaine III, 30.1%) and ischaemic wounds (Fontaine IV, 17.1%) were common in this cohort. Within three years 51 patients died, amongst whom 25 deaths were due to CVD, 39 patients experienced a MACE, and 125 patients experienced a MALE. Multivariable regression models, based on statistically proven covariables and literature, showed a significant association of Serpin G1 (HR 1.49; 95% CI 1.08 – 2.06; p = .016) and CD14 (HR 1.40; 1.03 – 1.90; p = .029) with MACE, and of Serpin G1 (HR 1.29; 1.07 – 1.57; p = .009) with MALE. Conclusion: Serpin G1 and CD14 plasma EV protein levels are associated with future MACE and MALE in patients with severe PAD

Role of age in presentation, response to therapy and outcome of autoimmune hepatitis

Background: Few studies with diverging results and a small sample size have compared autoimmune hepatitis (AIH) in the elderly to younger patients. Aim: To unbiasedly investigate the role of age in behaviour and treatment outcome of AIH. Methods: All patients with probable or definite AIH type 1 in four tertiary academic centres were included in this retrospective - and since 2006 prospective - cohort study. Influence of age on presentation, remission and outcome of AIH were investigated. Results: 359 patients were included. Presence of cirrhosis at AIH diagnosis around 30% was independent of age. ALAT was higher at age 30-60 years on AIH diagnosis, and above age 60 there were less acute onset, less jaundice and more concurrent autoimmune disease. Remission was reached in 80.2%, incomplete remission in 18.7%, only 1.1% (all aged 50-65) was treatment-refractory. Age was not an independent predictor of remission, while cirrhosis was. Above age 45 there was more diabetes, above age 60 more loss of remission. Rate of progression to cirrhosis was 10% in the 10 years after diagnosis and unrelated to age at AIH diagnosis. With onset below age 30, there was more development of decompensated cirrhosis over time. With higher age at AIH diagnosis there was a lower survival free of liver-related death or liver transplantation. Conclusions: AIH presents at all ages. Age influences features at diagnosis, but not response to treatment, while survival without liver-related death or liver transplantation decreases with higher age at diagnosis