A Similarity Measure for GPU Kernel Subgraph Matching

Accelerator architectures specialize in executing SIMD (single instruction, multiple data) in lockstep. Because the majority of CUDA applications are parallelized loops, control flow information can provide an in-depth characterization of a kernel. CUDAflow is a tool that statically separates CUDA binaries into basic block regions and dynamically measures instruction and basic block frequencies. CUDAflow captures this information in a control flow graph (CFG) and performs subgraph matching across various kernel's CFGs to gain insights to an application's resource requirements, based on the shape and traversal of the graph, instruction operations executed and registers allocated, among other information. The utility of CUDAflow is demonstrated with SHOC and Rodinia application case studies on a variety of GPU architectures, revealing novel thread divergence characteristics that facilitates end users, autotuners and compilers in generating high performing code

Experiments on Multidimensional Solitons

This article presents an overview of experimental efforts in recent years related to multidimensional solitons in Bose-Einstein condensates. We discuss the techniques used to generate and observe multidimensional nonlinear waves in Bose-Einstein condensates with repulsive interactions. We further summarize observations of planar soliton fronts undergoing the snake instability, the formation of vortex rings, and the emergence of hybrid structures.Comment: review paper, to appear as Chapter 5b in "Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment," edited by P. G. Kevrekidis, D. J. Frantzeskakis, and R. Carretero-Gonzalez (Springer-Verlag

Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi

© The Author(s) 2016. Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community

Structure of a seeded palladium nanoparticle and its dynamics during the hydride phase transformation

Palladium absorbs large volumetric quantities of hydrogen at room temperature and ambient pressure, making the palladium hydride system a promising candidate for hydrogen storage. Here, we use Bragg coherent diffraction imaging to map the strain associated with defects in three dimensions before and during the hydride phase transformation of an individual octahedral palladium nanoparticle, synthesized using a seed-mediated approach. The displacement distribution imaging unveils the location of the seed nanoparticle in the final nanocrystal. By comparing our experimental results with a finite-element model, we verify that the seed nanoparticle causes a characteristic displacement distribution of the larger nanocrystal. During the hydrogen exposure, the hydride phase is predominantly formed on one tip of the octahedra, where there is a high number of lower coordinated Pd atoms. Our experimental and theoretical results provide an unambiguous method for future structure optimization of seed-mediated nanoparticle growth and in the design of palladium-based hydrogen storage systems

Yoga and pilates in the management of low back pain

Many interventions for the management of low back pain exist, however most have modest efficacy at best, and there are few with clearly demonstrated benefits once pain becomes chronic. Therapeutic exercise, on the other hand, does appear to have significant benefits for managing patients with chronic low back pain (CLBP) in terms of decreasing pain and improving function. In addition, because chronic pain is complex and does not fit a simple model, there have also been numerous trials investigating and demonstrating the efficacy of multidisciplinary pain programs for CLBP. It follows that interventions that treat more than one aspect of LBP would have significant benefits for this patient population. Yoga and Pilates which have, both been gaining in popularity over the last decade are two mind–body exercise interventions that address both the physical and mental aspects of pain with core strengthening, flexibility, and relaxation. There has been a slow evolution of these nontraditional exercise regimens into treatment paradigms for LBP, although few studies examining their effects have been published. The following article will focus on the scientific and theoretical basis of using yoga and Pilates in the management of CLBP

Human COL5A1 rs12722 gene polymorphism and tendon properties in vivo in an asymptomatic population

Purpose Gene variants encoding for proteins involved in homeostatic processes within tendons may influence its material and mechanical properties in humans. The purpose of this study was to examine the association between one such gene variant, gene encoding collagen type V alpha 1 chain (COL5A1) rs12722, and patellar tendon dimensions and mechanical properties in vivo. Methods Eighty-four recreationally active, Caucasian, men and women, aged 18–39, with no history of injuries to the knee and a body mass index between 18.5 and 30 were recruited. Women were not recruited if they were pregnant or using any form of hormone-based contraception. The COL5A1 rs12722 genotype was determined using real-time polymerase chain reaction. Patellar tendon dimensions (volume) and functional (elastic modulus) properties were assessed in vivo using geometric modelling, isokinetic dynamometry, electromyography and ultrasonography. Results After adjustments for non-genetic factors, no significant associations were evident between the COL5A1 rs12722 gene variant and either patellar tendon volume (P = 0.933) or elastic modulus (P = 0.206), nor with a calculated Z score that combined these dimensional and functional properties into a composite value (P = 0.647). Similarly, no association was evident when comparing individuals with/without the rare C allele (volume, P = 0.883; elastic modulus, P = 0.129; Z score, P = 0.631). Conclusions Tendon properties do not seem to be influenced by the COL5A1 rs12722 gene variant. Although the COL5A1 rs12722 polymorphism has previously been associated with the risk of tendon pathology, that association is unlikely to be mediated via underlying tendon dimensional and functional properties

Erratum to: Variants within the MMP3 gene and patellar tendon properties in vivo in an asymptomatic population (vol 114, pg 2625, 2014)

Erratum to: Eur J Appl Physiol (2014) 114:2625–2634 DOI 10.1007/s00421-014-2986-7 Unfortunately, one of the affiliations of the co-author, Alun G. Williams, has been missed in the original publication of the article. The correct information is as follows: Alun G. Williams Institute for Performance Research, Manchester Metropolitan University, Crewe CW1 5DU, U

Multi-scale three-dimensional characterization of iron particles in dusty olivine: Implications for paleomagnetism of chondritic meteorites

Dusty olivine (olivine containing multiple sub-micrometer inclusions of metallic iron) in chondritic meteorites is considered an ideal carrier of paleomagnetic remanence, capable of maintaining a faithful record of pre-accretionary magnetization acquired during chondrule formation. Here we show how the magnetic architecture of a single dusty olivine grain from the Semarkona LL3.0 ordinary chondrite meteorite can be fully characterised in three dimensions, using a combination of Focussed-Ion-Beam nanotomography (FIB-nT), electron tomography and finite-element micromagnetic modelling. We present a three-dimensional (3D) volume reconstruction of a dusty olivine grain, obtained by selective milling through a region of interest in a series of sequential 20 nm slices, which are then imaged using scanning electron microscopy. The data provide a quantitative description of the iron particle ensemble, including the distribution of particle sizes, shapes, interparticle spacings and orientations. Iron particles are predominantly oblate ellipsoids with average radii 242 ± 94 nm by 199 ± 80 nm by 123 ± 58 nm. Using analytical TEM we observe that the particles nucleate on sub-grain boundaries and are loosely arranged in a series of sheets parallel to (001) of the olivine host. This is in agreement with the orientation data collected using the FIB-nT, and highlights how the underlying texture of the dusty olivine is crystallographically constrained by the olivine host. The shortest dimension of the particles is oriented normal to the sheets and their longest dimension is preferentially aligned within the sheets. Individual particle geometries are converted to a finite-element mesh and used to perform micromagnetic simulations. The majority of particles adopt a single vortex state, with ‘bulk’ spins that rotate around a central vortex core. We observed no particles, which are in a true single domain state. The results of the micromagnetic simulations challenge some pre-conceived ideas about the remanence carrying properties of vortex states. There is often not a simple predictive relationship between the major, intermediate and minor axes of the particles and the remanence vector imparted in different fields. Although the orientation of the vortex core is determined largely by the ellipsoidal geometry (i.e., parallel to the major axis for prolate ellipsoids and parallel to the minor axis for oblate ellipsoids), the core and remanence vectors can sometimes lie at very large (tens of degree) angles to the principal axes. The subtle details of the morphology can control the overall remanence state, leading in some cases to a dominant contribution from the bulk spins to the net remanence, with profound implications for predicting the anisotropy of the sample. The particles have very high switching fields (several hundred mT), demonstrating their high stability and suitability for paleointensity studies.The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC grant agreements 291522-3DIMAGE (P.A.M.) and 320750 - Nanopaleomagnetism (J.F.E., R.J.H., and P.A.M.). BPW and RRF were supported by NASA Emerging Worlds program grant #NNX15AH72G, the NASA Solar System Exploration and Research Virtual Institute grant #NNA14AB01A, and a generous gift from Thomas F. Peterson, Jr. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No. 320832-Imagine. (W.W . and P.O.C.) W.W. was also supported for this research under NERC grant NE/J020966/1 - Predicting the reliability with which the geomagnetic field can be recorded in igneous rocks.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by the Mineralogical Society of America

SmartEx: a case study on user profiling and adaptation in exhibition booths

An investigation into user profiling and adaptation with exhibition booth as a case study is reported. First a review of the field of exhibitions and trade fairs and a summary introduction to adaptation and profiling are given. We then introduce three criteria for the evaluation of exhibition booth: effectiveness, efficiency and affect. Effectiveness is related the amount of information collected, efficiency is a measurement of the time taken to collect the information, and affect is the perception of the experience and the mood booth visitors have during and after their visit. We have selected these criteria to assess adaptive and profiled exhibition booths, we call smart exhibition (SmartEx). The assessment is performed with an experiment with three test conditions (non-profiled/non adaptive, profiled/non-adaptive and profiled adaptive presentations). Results of the experiment are presented along discussion. While there is significant improvements of effectiveness and efficiency between the two-first test conditions, the improvement is not significant for the last test condition, for reasons explained. As for the affect, the results show that it has an under-estimated importance in people minds and that it should be addressed more carefully