Formalization of Phase Ordering

Phasers pose an interesting synchronization mechanism that generalizes many collective synchronization patterns seen in parallel programming languages, including barriers, clocks, and point-to-point synchronization using latches or semaphores. This work characterizes scheduling constraints on phaser operations, by relating the execution state of two tasks that operate on the same phaser. We propose a formalization of Habanero phasers, May-Happen-In-Parallel, and Happens-Before relations for phaser operations, and show that these relations conform with the semantics. Our formalization and proofs are fully mechanized using the Coq proof assistant, and are available online.Comment: In Proceedings PLACES 2016, arXiv:1606.0540

Regulation of Sindbis virus RNA replication: uncleaved P123 and nsP4 function in minus-strand RNA synthesis, whereas cleaved products from P123 are required for efficient plus-strand RNA synthesis

Nonstructural proteins of Sindbis virus, nsPl, nsP2, nsP3, and nsP4, as well as intermediate polyproteins, are produced from two precursor polyproteins, Pl23 and Pl234, by a proteolytic enzyme encoded in the C-terminal half of nsP2. We studied the requirements for and the functions of the intermediate and mature processing products for Sindbis virus RNA synthesis by using site-directed mutants which have a defect(s) in processing the 1/2, 2/3, or 3/4 cleavage sites either singly or in various combinations. A mutant defective in cleaving both the 1/2 and 2/3 sites, which makes only uncleavable Pl23 and mature nsP4 as final products, produced 10-3 as much virus as did the wild-type virus after 10 hat 30°C and was nonviable at 40°C. A mutant defective in processing the 2/3 site, which makes nsPl, nsP4, and P23 as well as precursor Pl23, grew 10-1 as efficiently as wild-type virus at 30°C and 10-3 as efficiently at 40°C. Early minus-strand RNA synthesis by these mutants was as efficient as that by wild-type virus, whereas plus-strand RNA synthesis was substantially decreased compared with that by wild-type virus. A mutant defective in processing the 3/4 site was nonviable at either 30 or 40°C. The 3/4 site mutant could be complemented by the mutant unable to cleave either the 1/2 or 2/3 site, which can provide mature nsP4. We interpret these results to signify that (i) mature nsP4 is required for RNA replication, (ii) nsP4 and uncleaved Pl23 function in minus-strand RNA synthesis, and (iii) cleavage of Pl23 is required for efficient plus-strand RNA synthesis. We propose that Sindbis virus RNA replication is regulated by differential proteolysis of Pl23. Early in infection, nsP4 and uncleaved Pl23 form transient minus-strand RNA replication complexes which vanish upon cleavage of Pl23. Later in infection, an elevated level of viral proteinase activity eliminates de novo synthesis of Pl23, and no further synthesis of minus-strand RNA is possible. In contrast, nsP4 and cleavage products from Pl23 form plus-strand RNA replication complexes which are stable and remain active throughout the infection cycle

Dynamic Determinacy Race Detection for Task-Parallel Programs with Promises

Much of the past work on dynamic data-race and determinacy-race detection algorithms for task parallelism has focused on structured parallelism with fork-join constructs and, more recently, with future constructs. This paper addresses the problem of dynamic detection of data-races and determinacy-races in task-parallel programs with promises, which are more general than fork-join constructs and futures. The motivation for our work is twofold. First, promises have now become a mainstream synchronization construct, with their inclusion in multiple languages, including C++, JavaScript, and Java. Second, past work on dynamic data-race and determinacy-race detection for task-parallel programs does not apply to programs with promises, thereby identifying a vital need for this work. This paper makes multiple contributions. First, we introduce a featherweight programming language that captures the semantics of task-parallel programs with promises and provides a basis for formally defining determinacy using our semantics. This definition subsumes functional determinacy (same output for same input) and structural determinacy (same computation graph for same input). The main theoretical result shows that the absence of data races is sufficient to guarantee determinacy with both properties. We are unaware of any prior work that established this result for task-parallel programs with promises. Next, we introduce a new Dynamic Race Detector for Promises that we call DRDP. DRDP is the first known race detection algorithm that executes a task-parallel program sequentially without requiring the serial-projection property; this is a critical requirement since programs with promises do not satisfy the serial-projection property in general. Finally, the paper includes experimental results obtained from an implementation of DRDP. The results show that, with some important optimizations introduced in our work, the space and time overheads of DRDP are comparable to those of more restrictive race detection algorithms from past work. To the best of our knowledge, DRDP is the first determinacy race detector for task-parallel programs with promises

Superconductivity suppression of Ba0.5K0.5Fe2-2xM2xAs2 single crystals by substitution of transition-metal (M = Mn, Ru, Co, Ni, Cu, and Zn)

We investigated the doping effects of magnetic and nonmagnetic impurities on the single-crystalline p-type Ba0.5K0.5Fe2-2xM2xAs2 (M = Mn, Ru, Co, Ni, Cu and Zn) superconductors. The superconductivity indicates robustly against impurity of Ru, while weakly against the impurities of Mn, Co, Ni, Cu, and Zn. However, the present Tc suppression rate of both magnetic and nonmagnetic impurities remains much lower than what was expected for the s\pm-wave model. The temperature dependence of resistivity data is observed an obvious low-T upturn for the crystals doped with high-level impurity, which is due to the occurrence of localization. Thus, the relatively weak Tc suppression effect from Mn, Co, Ni, Cu, and Zn are considered as a result of localization rather than pair-breaking effect in s\pm-wave model.Comment: 8 pages, 9 figures, to be published in Phys. Rev.

Thermal Expansion in BaRuO3 Perovskites – an unusual case of bond strengthening at high temperatures

The temperature dependence of the structures of three polytypes of BaRuO3 have been investigated between room temperature and 1000 °C using high resolution Synchrotron X-ray diffraction. The structural studies reveal a systematic decrease in the Ru-Ru distance as the pressure required to prepare the polytype increases. The O-O distance across the shared face increases as the Ru-Ru separation decreases. The 9R and 4H polytypes undergo unexceptional changes with increasing temperature. In 6H-BaRuO3 there is an apparent increase in the Ru-Ru interaction around 650 °C and concurrent reduction in the O-O distance indicating an anomalous strengthening of the Ru-Ru interactions upon heating.Australian Synchrotron Australian Research Counci

Properties of non-structural protein 1 of Semliki Forest virus and its interference with virus replication

Semliki Forest virus (SFV) non-structural protein 1 (nsP1) is a major component of the virus replicase complex. It has previously been studied in cells infected with virus or using transient or stable expression systems. To extend these studies, tetracycline-inducible stable cell lines expressing SFV nsP1 or its palmitoylation-negative mutant (nsP16D) were constructed. The levels of protein expression and the subcellular localization of nsP1 in induced cells were similar to those in virus-infected cells. The nsP1 expressed by stable, inducible cell lines or by SFV-infected HEK293 T-REx cells was a stable protein with a half-life of approximately 5 h. In contrast to SFV infection, induction of nsP1 expression had no detectable effect on cellular transcription, translation or viability. Induction of expression of nsP1 or nsP16D interfered with multiplication of SFV, typically resulting in a 5–10-fold reduction in virus yields. This reduction was not due to a decrease in the number of infected cells, indicating that nsP1 expression does not block virus entry or initiation of replication. Expression of nsP1 interfered with virus genomic RNA synthesis and delayed accumulation of viral subgenomic RNA translation products. Expression of nsP1 with a mutation in the palmitoylation site reduced synthesis of genomic and subgenomic RNAs and their products of translation, and this effect did not resolve with time. These results are in agreement with data published previously, suggesting a role for nsP1 in genomic RNA synthesis

NaIrO3 - A pentavalent post-perovskite

Sodium iridium(V) oxide, NaIrO3, was synthesized by a high pressure solid state method and recovered to ambient conditions. It is found to be isostructural with CaIrO3, the much-studied structural analogue of the high-pressure post-perovskite phase of MgSiO3. Among the oxide post-perovskites, NaIrO3 is the first example with a pentavalent cation. The structure consists of layers of corner- and edge-sharing IrO6 octahedra separated by layers of NaO8 bicapped trigonal prisms. NaIrO3 shows no magnetic ordering and resistivity measurements show non-metallic behavior. The crystal structure, electrical and magnetic properties are discussed and compared to known post-perovskites and pentavalent perovskite metal oxides.Comment: 22 pages, 5 figures. Submitted to Journal of Solid State Chemistr

Comparison of Anti-Inflammatory Analgesics for Mechanical Stress-induced Inflammation in a Human Synovial Sarcoma Cell Line

Osteoarthritis is a complicated clinical condition affected by age, mechanical stress, cartilage hypertrophy, cytokines, and genetic predisposition. In this study, we compared the effects of various anti-inflammatory analgesics on mechanical stress-induced inflammation in a synovial sarcoma cell line （SW982 cells）. SW982 cells exposed to mechanical stress by shaking with hydroxyapatite-simulating bone chips were treated with acetaminophen, ketoprofen, triamcinolone acetonide, celecoxib, or neurotrophin for 48hr. The expression of integrin α5β1 receptor, observed in fibroblasts and synovium, was evaluated. Levels of the transcription factor, nuclear factor-κB, the inflammatory cytokine, tumor necrosis factor-α, the proteolytic enzyme, matrix metalloproteinase-3, and prostaglandin E2, which is associated with pain and arachidonate cascade product levels, were measured by ELISA. The expression of integrin α5β1 was significantly increased by mechanical stress. Activation of nuclear factor-κB by mechanical stress was significantly suppressed by celecoxib only. Mechanical stress-induced increases in tumor necrosis factor-α and matrix metalloproteinase-3 levels were significantly suppressed by acetaminophen, triamcinolone acetonide, and neurotrophin. The mechanical stress-induced increase in prostaglandin E2 levels was significantly suppressed by acetaminophen, ketoprofen, and celecoxib. SW982 exposed to mechanical stress is proposed as a model for arthritis, and indeed, the expression of integrin α5β1, a membrane receptor protein that binds to fibronectin and the extracellular matrix, and is involved in cell proliferation, differentiation, and neovascularization in osteoarthritis, was significantly upregulated. Following evaluation using this model, acetaminophen was found to possess anti-inflammatory, analgesic, and joint-destruction suppression properties. This drug may, therefore, have applications in the treatment of mechanical stress-induced inflammation