Cooking the Books: Formalizing JMM Implementation Recipes

The Java Memory Model (JMM) is intended to characterize the meaning of concurrent Java programs. Because of the model\u27s complexity, however, its definition cannot be easily transplanted within an optimizing Java compiler, even though an important rationale for its design was to ensure Java compiler optimizations are not unduly hampered because of the language\u27s concurrency features. In response, Lea\u27s JSR-133 Cookbook for Compiler Writers, an informal guide to realizing the principles underlying the JMM on different (relaxed-memory) platforms was developed. The goal of the cookbook is to give compiler writers a relatively simple, yet reasonably efficient, set of reordering-based recipes that satisfy JMM constraints. In this paper, we present the first formalization of the cookbook, providing a semantic basis upon which the relationship between the recipes defined by the cookbook and the guarantees enforced by the JMM can be rigorously established. Notably, one artifact of our investigation is that the rules defined by the cookbook for compiling Java onto Power are inconsistent with the requirements of the JMM, a surprising result, and one which justifies our belief in the need for formally provable definitions to reason about sophisticated (and racy) concurrency patterns in Java, and their implementation on modern-day relaxed-memory hardware. Our formalization enables simulation arguments between an architecture-independent intermediate representation of the kind suggested by Lea with machine abstractions for Power and x86. Moreover, we provide fixes for cookbook recipes that are inconsistent with the behaviors admitted by the target platform, and prove the correctness of these repairs

Array-A-Lizer: A serial DNA microarray quality analyzer

BACKGROUND: The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments prior to actual data analysis. RESULTS: Array-A-Lizer is a small and convenient stand-alone tool providing the necessary initial analysis of hybridization quality of an unlimited number of microarray experiments. The experiments are analyzed for even hybridization across the slide and between fluorescent dyes in two-color experiments in spotted DNA microarrays. CONCLUSIONS: Array-A-Lizer allows the expedient determination of the quality of multiple DNA microarray experiments allowing for a rapid initial screening of results before progressing to further data analysis. Array-A-Lizer is directed towards speed and ease-of-use allowing both the expert and non-expert microarray researcher to rapidly assess the quality of multiple microarray hybridizations. Array-A-Lizer is available from the Internet as both source code and as a binary installation package

Angular momentum transport in convectively unstable shear flows

Angular momentum transport owing to hydrodynamic turbulent convection is studied using local three dimensional numerical simulations employing the shearing box approximation. We determine the turbulent viscosity from non-rotating runs over a range of values of the shear parameter and use a simple analytical model in order to extract the non-diffusive contribution (Lambda-effect) to the stress in runs where rotation is included. Our results suggest that the turbulent viscosity is of the order of the mixing length estimate and weakly affected by rotation. The Lambda-effect is non-zero and a factor of 2-4 smaller than the turbulent viscosity in the slow rotation regime. We demonstrate that for Keplerian shear, the angular momentum transport can change sign and be outward when the rotation period is greater than the turnover time, i.e. when the Coriolis number is below unity. This result seems to be relatively independent of the value of the Rayleigh number.Comment: 10 pages, 12 figures, published version. Version with higher resolution figures can be found at http://www.helsinki.fi/~kapyla/publ.htm

Inhibition of microRNA function by antimiR oligonucleotides

MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. Moreover, there is now ample evidence that perturbations in the levels of individual or entire families of miRNAs are strongly associated with the pathogenesis of a wide range of human diseases. Indeed, disease-associated miRNAs represent a new class of targets for the development of miRNA-based therapeutic modalities, which may yield patient benefits unobtainable by other therapeutic approaches. The recent explosion in miRNA research has accelerated the development of several computational and experimental approaches for probing miRNA functions in cell culture and in vivo. In this review, we focus on the use of antisense oligonucleotides (antimiRs) in miRNA inhibition for loss-of-function studies. We provide an overview of the currently employed antisense chemistries and their utility in designing antimiR oligonucleotides. Furthermore, we describe the most commonly used in vivo delivery strategies and discuss different approaches for assessment of miRNA inhibition and potential off-target effects. Finally, we summarize recent progress in antimiR mediated pharmacological inhibition of disease-associated miRNAs, which shows great promise in the development of novel miRNA-based therapeutics

Investigating Mesozoic Climate Trends and Sensitivities With a Large Ensemble of Climate Model Simulations

The Mesozoic era (∼252 to 66 million years ago) was a key interval in Earth's evolution toward its modern state, witnessing the breakup of the supercontinent Pangaea and significant biotic innovations like the early evolution of mammals. Plate tectonic dynamics drove a fundamental climatic transition from the early Mesozoic supercontinent toward the Late Cretaceous fragmented continental configuration. Here, key aspects of Mesozoic long-term environmental changes are assessed in a climate model ensemble framework. We analyze so far the most extended ensemble of equilibrium climate states simulated for evolving Mesozoic boundary conditions covering the period from 255 to 60 Ma in 5 Myr timesteps. Global mean temperatures are generally found to be elevated above the present and exhibit a baseline warming trend driven by rising sea levels and increasing solar luminosity. Warm (Triassic and mid-Cretaceous) and cool (Jurassic and end-Cretaceous) anomalies result from pCO2 changes indicated by different reconstructions. Seasonal and zonal temperature contrasts as well as continental aridity show an overall decrease from the Late Triassic-Early Jurassic to the Late Cretaceous. Meridional temperature gradients are reduced at higher global temperatures and less land area in the high latitudes. With systematic sensitivity experiments, the influence of paleogeography, sea level, vegetation patterns, pCO2, solar luminosity, and orbital configuration on these trends is investigated. For example, long-term seasonality trends are driven by paleogeography, but orbital cycles could have had similar-scale effects on shorter timescales. Global mean temperatures, continental humidity, and meridional temperature gradients are, however, also strongly affected by pCO2