FEniCS in Linux Containers

FEniCS'15 Workshop at Imperial College London, 29th June - 1st July 2015

Containers for Portable, Productive, and Performant Scientific Computing

Containers are an emerging technology that holds promise for improving productivity and code portability in scientific computing. The authors examine Linux container technology for the distribution of a nontrivial scientific computing software stack and its execution on a spectrum of platforms from laptop computers through high-performance computing systems. For Python code run on large parallel computers, the runtime is reduced inside a container due to faster library imports. The software distribution approach and data that the authors present will help developers and users decide on whether container technology is appropriate for them. The article also provides guidance for vendors of HPC systems that rely on proprietary libraries for performance on what they can do to make containers work seamlessly and without performance penalty

Durability of Benefits From Supervised Treadmill Exercise in People With Peripheral Artery Disease.

Background It is currently unknown whether 6 months of supervised treadmill exercise has a durable benefit on 6-minute walk performance, even after exercise is completed, in people with peripheral artery disease. Methods and Results A total of 156 participants with peripheral artery disease were randomized to 1 of 3 groups: supervised treadmill exercise, supervised resistance training, or attention control. Participants received supervised sessions during months 1 to 6 and telephone contact during months 6 to 12. Primary outcomes were change in 6-minute walk distance and short physical performance battery at 6-month follow-up and have been reported previously. Secondary outcomes were change in 6-minute walk and short physical performance battery at 12-month follow-up and are reported here. A group of 134 participants (86%) completed the 12-month follow-up. At 6-month follow-up, compared with control, 6-minute walk distance improved in the treadmill exercise group (+36.1 m, 95% CI =13.9-58.3, P=0.001). Between 6- and 12-month follow-up, 6-minute walk distance significantly declined (-28.6 m, 95% CI=-52.6 to -4.5, P=0.020) and physical activity declined -272 activity units (95% CI =-546 to +2, P=0.052) in the treadmill exercise group compared with controls. At 12-month follow-up, 6 months after completing supervised treadmill exercise, change in 6-minute walk distance was not different between the treadmill exercise and control groups (+7.5, 95% CI =-17.5 to +32.6, P=0.56). There were no differences in short physical performance battery change between either exercise group and control at 6-month or 12-month follow-up. Conclusions A 6-month supervised treadmill exercise intervention that improved 6-minute walk distance at 6-month follow-up did not have persistent benefit at 12-month follow-up. These results do not support a durable benefit of supervised treadmill exercise in peripheral artery disease. Clinical Trial Registration URL : https://www.clinicaltrials.gov . Identifier: NCT 00106327

Racial Differences in the Effect of Granulocyte Macrophage Colony-Stimulating Factor on Improved Walking Distance in Peripheral Artery Disease: The PROPEL Randomized Clinical Trial.

Background The effects of race on response to medical therapy in people with peripheral artery disease ( PAD ) are unknown. Methods and Results In the PROPEL (Progenitor Cell Release Plus Exercise to Improve Functional Performance in PAD) Trial, PAD participants were randomized to 1 of 4 groups for 6 months: supervised treadmill exercise+granulocyte-macrophage colony-stimulating factor ( GM - CSF ) (Group 1), exercise+placebo (Group 2), attention control+ GM - CSF (Group 3), or attention control+placebo (Group 4). Change in 6-minute walk distance was measured at 12- and 26-week follow-up. In these exploratory analyses, groups receiving GM - CSF (Groups 1 and 3), placebo (Groups 2 and 4), exercise (Groups 1 and 2), and attention control (Groups 2 and 4) were combined, maximizing statistical power for studying the effects of race on response to interventions. Of 210 PAD participants, 141 (67%) were black and 64 (30%) were white. Among whites, GM - CSF improved 6-minute walk distance by +22.0 m (95% CI : -4.5, +48.5, P=0.103) at 12 weeks and +44.4 m (95% CI : +6.9, +82.0, P=0.020) at 26 weeks, compared with placebo. Among black participants, there was no effect of GM - CSF on 6-minute walk distance at 12-week ( P=0.26) or 26-week (-5.0 m [-27.5, +17.5, P=0.66]) follow-up, compared with placebo. There was an interaction of race on the effect of GM - CSF on 6-minute walk change at 26-week follow-up ( P=0.018). Exercise improved 6-minute walk distance in black ( P=0.006) and white ( P=0.034) participants without interaction. Conclusions GM - CSF improved 6-minute walk distance in whites with PAD but had no effect in black participants. Further study is needed to confirm racial differences in GM - CSF efficacy in PAD . Clinical Trial Registration URL : http://www.clinicaltrials.gov . Unique identifier: NCT 01408901

Sequences of Tibetan Macaque (Macaca thibetana) and Tourist Behaviors at Mt. Huangshan, China

Previous research on Tibetan macaques (Macaca thibetana) at Mt. Huangshan, China, suggested that ecotourism can have detrimental consequences. This study identified sequences of behaviors that typically occur in macaque-tourist interactions to examine whether particular tourist behaviors precipitate monkey responses. Focal sampling was used to record relevant behaviors from tourists and 10 macaques over 28 data collection sessions in August 2006. Data collectors recorded whether each behavior occurred as part of a sequence. Sequences were defined as two or more behaviors in which each behavior occurred within five seconds of the previous behavior. Of 3,129 total behaviors, 2,539 (81.1%) were from tourists and 590 (18.9%) were from monkeys. Tourists initiated significantly more sequences than did macaques (412 [84.6%] versus 75 [15.4%]). Tourist pointing, rail slapping, fleeing, and rock showing occurred significantly more than expected in tourist-macaque sequences. Points were also among the most common tourist behaviors preceding macaque threats. By discouraging tourists from engaging in these behaviors, macaque threats could be reduced, thereby improving macaque-tourist interactions. These results may aid in the management of other macaque tourist sites to minimize stress-inducing interactions

Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans

Arabinogalactan-proteins (AGPs) are complex glycoconjugates that are commonly found at the cell surface and in secretions of plants. Their location and diversity of structures have made them attractive targets as modulators of plant development but definitive proof of their direct role(s) in biological processes remains elusive. Here we overview the current state of knowledge on AGPs, identify key challenges impeding progress in the field and propose approaches using modern bioinformatic, (bio)chemical, cell biological, molecular and genetic techniques that could be applied to redress these gaps in our knowledge

Dependence of Microstructure and Mechanical Properties on Heat Treat Cycles of Electron Beam Melted Ti-6Al-4V

The EBM Ti-6Al-4V alloy has generally superior mechanical properties, owing to finely spaced α−β laths which give a good combination of strength and ductility. The grain structures in the as-printed structures are long columnar which can give rise to anisotropic mechanical properties. Moreover the non-uniformity in microstructure can also arise from part geometry where the thin features have propensity to form martensite phase. Heat treatment provides a viable solution to modify the microstructure and to tailor to the properties as desired. A wide range of heat treatment experiments were performed, followed by microstructure and tensile property analyses. It was observed that the microstructure and the tensile properties significantly changed depending on the heat treat cycle performed. Tensile properties of solution treated air-cool plus aged samples yielded globular equiaxed grains with fine α−β lath structure, which were found to be the best among the different heat treated samples and better than ASTM F1472 specifications.Mechanical Engineerin

Superconducting Coherence and the Helicity Modulus in Vortex Line Models

We show how commonly used models for vortex lines in three dimensional superconductors can be modified to include k=0 excitations. We construct a formula for the k=0 helicity modulus in terms of fluctuations in the projected area of vortex loops. This gives a convenient criterion for the presence of superconducting coherence. We also present Monte Carlo simulations of a continuum vortex line model for the melting of the Abrikosov vortex lattice in pure YBCO.Comment: 4 pages RevTeX, 2 eps figures included using eps

Nano-assemblies of cationic mPEG brush block copolymers with gadolinium polyoxotungstate [Gd(W5O18)2]9− form stable, high relaxivity MRI contrast agents

Polyoxometalates (POMs) incorporating paramagnetic ions, such as gadolinium, show promise as contrast agents for application in magnetic resonance imaging (MRI). Specifically, [Gd(W5O18)2]9− (denoted as GdWO) has been reported to have a higher relaxivity than commercially available contrast agents, but it's clinical utility has been limited by the intrinsic instability of POMs at physiological pH (7.4). In the current report we present a stability study on neat GdWO and nano-assemblies of block copolymers with GdWO in the pH range 5.0–7.4 to assess their suitability as MRI contrast agents. Neat GdWO only maintained structural stability between pH 5.4 and 6.4, and demonstrated poor MRI contrast at pH 7.4. To address this pH instability, GdWO was self-assembled with cationic mPEG brush block copolymers containing 20 or 40 units derived from the cationic monomer, 2-dimethylaminoethyl methacrylate (DMAEMA). Nano-assemblies with different charge ratios were synthesised and characterised according to their size, stability, contrasting properties and toxicity. The longitudinal relaxivity (r1) of the nano-assemblies was found to be dependent on the charge ratio, but not on the length of the cationic polymer block. Further investigation of PDMAEMA20 nano-assemblies demonstrated that they were stable over the pH range 5.0–7.4, exhibiting a higher r1 than either neat GdWO (2.77 s−1 mM−1) or clinical MRI contrast agent Gd-DTPA (4.1 s−1 mM−1) at pH 7.4. Importantly, the nano-assembly with the lowest charge ratio (0.2), showed the highest r1 (12.1 s−1 mM−1) whilst, stabilising GdWO over the pH range studied, eliciting low toxicity with MDA-MB231 cells