Using Flow Specifications of Parameterized Cache Coherence Protocols for Verifying Deadlock Freedom

We consider the problem of verifying deadlock freedom for symmetric cache coherence protocols. In particular, we focus on a specific form of deadlock which is useful for the cache coherence protocol domain and consistent with the internal definition of deadlock in the Murphi model checker: we refer to this deadlock as a system- wide deadlock (s-deadlock). In s-deadlock, the entire system gets blocked and is unable to make any transition. Cache coherence protocols consist of N symmetric cache agents, where N is an unbounded parameter; thus the verification of s-deadlock freedom is naturally a parameterized verification problem. Parametrized verification techniques work by using sound abstractions to reduce the unbounded model to a bounded model. Efficient abstractions which work well for industrial scale protocols typically bound the model by replacing the state of most of the agents by an abstract environment, while keeping just one or two agents as is. However, leveraging such efficient abstractions becomes a challenge for s-deadlock: a violation of s-deadlock is a state in which the transitions of all of the unbounded number of agents cannot occur and so a simple abstraction like the one above will not preserve this violation. In this work we address this challenge by presenting a technique which leverages high-level information about the protocols, in the form of message sequence dia- grams referred to as flows, for constructing invariants that are collectively stronger than s-deadlock. Efficient abstractions can be constructed to verify these invariants. We successfully verify the German and Flash protocols using our technique

Engineering a static verification tool for GPU kernels

We report on practical experiences over the last 2.5 years related to the engineering of GPUVerify, a static verification tool for OpenCL and CUDA GPU kernels, plotting the progress of GPUVerify from a prototype to a fully functional and relatively efficient analysis tool. Our hope is that this experience report will serve the verification community by helping to inform future tooling efforts. © 2014 Springer International Publishing

Effects of built environment on walking among Hong Kong older adults

 Key Messages1. Reliable and valid intervieweradministered questionnaires were developed to investigate associations of perceived neighbourhood attributes of Hong Kong older adults with their walking for transportation and recreation.2. Access to and availability of different types of services and destinations, provision offacilities for resting/sitting in the neighbourhood, and easy access to/from residentialbuildings may help maintain an active lifestyle by facilitating walking for transport in the neighbourhood.3. Access to services, indoor places for walking, environmental aesthetics, low traffic, and absence of physical barriers may promote recreational walking

The Horizontal Component of Photospheric Plasma Flows During the Emergence of Active Regions on the Sun

The dynamics of horizontal plasma flows during the first hours of the emergence of active region magnetic flux in the solar photosphere have been analyzed using SOHO/MDI data. Four active regions emerging near the solar limb have been considered. It has been found that extended regions of Doppler velocities with different signs are formed in the first hours of the magnetic flux emergence in the horizontal velocity field. The flows observed are directly connected with the emerging magnetic flux; they form at the beginning of the emergence of active regions and are present for a few hours. The Doppler velocities of flows observed increase gradually and reach their peak values 4-12 hours after the start of the magnetic flux emergence. The peak values of the mean (inside the +/-500 m/s isolines) and maximum Doppler velocities are 800-970 m/s and 1410-1700 m/s, respectively. The Doppler velocities observed substantially exceed the separation velocities of the photospheric magnetic flux outer boundaries. The asymmetry was detected between velocity structures of leading and following polarities. Doppler velocity structures located in a region of leading magnetic polarity are more powerful and exist longer than those in regions of following polarity. The Doppler velocity asymmetry between the velocity structures of opposite sign reaches its peak values soon after the emergence begins and then gradually drops within 7-12 hours. The peak values of asymmetry for the mean and maximal Doppler velocities reach 240-460 m/s and 710-940 m/s, respectively. An interpretation of the observable flow of photospheric plasma is given.Comment: 20 pages, 10 figures, 3 tables. The results of article were presented at the ESPM-13 (12-16 September 2011, Rhodes, Greece, Abstract Book p. 102, P.4.12, http://astro.academyofathens.gr/espm13/documents/ESPM13_abstract_programme_book.pdf

The Relationship Between Plasma Flow Doppler Velocities and Magnetic Field Parameters During the Emergence of Active Regions at the Solar Photospheric Level

A statistical study has been carried out of the relationship between plasma flow Doppler velocities and magnetic field parameters during the emergence of active regions at the solar photospheric level with data acquired by the Michelson Doppler Imager (MDI) onboard the Solar and Heliospheric Observatory (SOHO). We have investigated 224 emerging active regions with different spatial scales and positions on the solar disc. The following relationships for the first hours of the emergence of active regions have been analysed: i) of peak negative Doppler velocities with the position of the emerging active regions on the solar disc; ii) of peak plasma upflow and downflow Doppler velocities with the magnetic flux growth rate and magnetic field strength for the active regions emerging near the solar disc centre (the vertical component of plasma flows); iii) of peak positive and negative Doppler velocities with the magnetic flux growth rate and magnetic field strength for the active regions emerging near the limb (the horizontal component of plasma flows); iv) of the magnetic flux growth rate with the density of emerging magnetic flux; v) of the Doppler velocities and magnetic field parameters for the first hours of the appearance of active regions with the total unsigned magnetic flux at the maximum of their development.Comment: 14 pages, 8 figures. The results of article were presented at the ESPM-13 (12-16 September 2011, Rhodes, Greece, Abstract Book p. 102-103, P.4.13, http://astro.academyofathens.gr/espm13/documents/ESPM13_abstract_programme_book.pdf

Lifetimes of High-Degree p Modes in the Quiet and Active Sun

We study variations of the lifetimes of high-degree solar p-modes in the quiet and active Sun with the solar activity cycle. The lifetimes in the degree range 300 - 600 and frequency 2.5 - 4.5 mHz were computed from SOHO/MDI data in an area including active regions and quiet Sun using the time-distance technique. We applied our analysis to the data in four different phases of solar activity: in 1996 (at minimum), 1998 (rising phase), 2000 (at maximum) and 2003 (declining phase). The results from the area with active regions show that the lifetime decreases as activity increases. The maximal lifetime variations are between solar minimum in 1996 and maximum in 2000; the relative variation averaged over all mode degree values and frequencies is a decrease of about 13%. The lifetime reductions relative to 1996 are about 7% in 1998 and about 10% in 2003. The lifetime computed in the quiet region still decreases with solar activity although the decrease is smaller. On average, relative to 1996, the lifetime decrease is about 4% in 1998, 10% in 2000 and 8% in 2003. Thus, measured lifetime increases when regions of high magnetic activity are avoided. Moreover, the lifetime computed in quiet regions also shows variations with activity cycle.Comment: 13 pages, 5 figures; Accepted for publication in Solar Physic

Nitric oxide and cyclic nucleotides: Their roles in junction dynamics and spermatogenesis

Spermatogenesis is a highly complicated process in which functional spermatozoa (haploid, 1n) are generated from primitive mitotic spermatogonia (diploid, 2n). This process involves the differentiation and transformation of several types of germ cells as spermatocytes and spermatids undergo meiosis and differentiation. Due to its sophistication and complexity, testis possesses intrinsic mechanisms to modulate and regulate different stages of germ cell development under the intimate and indirect cooperation with Sertoli and Leydig cells, respectively. Furthermore, developing germ cells must translocate from the basal to the apical (adluminal) compartment of the seminiferous epithelium. Thus, extensive junction restructuring must occur to assist germ cell movement. Within the seminiferous tubules, three principal types of junctions are found namely anchoring junctions, tight junctions, and gap junctions. Other less studied junctions are desmosome-like junctions and hemidesmosome junctions. With these varieties of junction types, testes are using different regulators to monitor junction turnover. Among the uncountable junction modulators, nitric oxide (NO) is a prominent candidate due to its versatility and extensive downstream network. NO is synthesized by nitric oxide synthase (NOS). Three traditional NOS, specified as endothelial NOS (eNOS), inducible NOS (iNOS), and neuronal NOS (nNOS), and one testis-specific nNOS (TnNOS) are found in the testis. For these, eNOS and iNOS were recently shown to have putative junction regulation properties. More important, these two NOSs likely rely on the downstream soluble guanylyl cyclase/cGMP/protein kinase G signaling pathway to regulate the structural components at the tight junctions and adherens junctions in the testes. Apart from the involvement in junction regulation, NOS/NO also participates in controlling the levels of cytokines and hormones in the testes. On the other hand, NO is playing a unique role in modulating germ cell viability and development, and indirectly acting on some aspects of male infertility and testicular pathological conditions. Thus, NOS/NO bears an irreplaceable role in maintaining the homeostasis of the microenvironment in the seminiferous epithelium via its different downstream signaling pathways

GWAS analysis of handgrip and lower body strength in older adults in the CHARGE consortium

Decline in muscle strength with aging is an important predictor of health trajectory in the elderly. Several factors, including genetics, are proposed contributors to variability in muscle strength. To identify genetic contributors to muscle strength, a meta-analysis of genomewide association studies of handgrip was conducted. Grip strength was measured using a handheld dynamometer in 27 581 individuals of European descent over 65 years of age from 14 cohort studies. Genomewide association analysis was conducted on ~2.7 million imputed and genotyped variants (SNPs). Replication of the most significant findings was conducted using data from 6393 individuals from three cohorts. GWAS of lower body strength was also characterized in a subset of cohorts. Two genomewide significant (P-value< 5 × 10−8) and 39 suggestive (P-value< 5 × 10−5) associations were observed from meta-analysis of the discovery cohorts. After meta-analysis with replication cohorts, genomewide significant association was observed for rs752045 on chromosome 8 (β = 0.47, SE = 0.08, P-value = 5.20 × 10−10). This SNP is mapped to an intergenic region and is located within an accessible chromatin region (DNase hypersensitivity site) in skeletal muscle myotubes differentiated from the human skeletal muscle myoblasts cell line. This locus alters a binding motif of the CCAAT/enhancer-binding protein-β (CEBPB) that is implicated in muscle repair mechanisms. GWAS of lower body strength did not yield significant results. A common genetic variant in a chromosomal region that regulates myotube differentiation and muscle repair may contribute to variability in grip strength in the elderly. Further studies are needed to uncover the mechanisms that link this genetic variant with muscle strength