Workload characterization of JVM languages

Originally developed with a single language in mind, the JVM is now targeted by numerous programming languages—its automatic memory management, just‐in‐time compilation, and adaptive optimizations—making it an attractive execution platform. However, the garbage collector, the just‐in‐time compiler, and other optimizations and heuristics were designed primarily with the performance of Java programs in mind. Consequently, many of the languages targeting the JVM, and especially the dynamically typed languages, are suffering from performance problems that cannot be simply solved at the JVM side. In this article, we aim to contribute to the understanding of the character of the workloads imposed on the JVM by both dynamically typed and statically typed JVM languages. To this end, we introduce a new set of dynamic metrics for workload characterization, along with an easy‐to‐use toolchain to collect the metrics. We apply the toolchain to applications written in six JVM languages (Java, Scala, Clojure, Jython, JRuby, and JavaScript) and discuss the findings. Given the recently identified importance of inlining for the performance of Scala programs, we also analyze the inlining behavior of the HotSpot JVM when executing bytecode originating from different JVM languages. As a result, we identify several traits in the non‐Java workloads that represent potential opportunities for optimization. © 2015 The Authors. Software: Practice and Experience Published by John Wiley & Sons Ltd.     

Influence of temperature on the liver circadian clock in the ruin lizard Podarcis sicula

Reptiles represent an interesting animal model to investigate the influence of temperature on molecular circadian clocks. The ruin lizard Podarcis sicula lives in a continental climate and it is subjected to wide range of environmental temperatures during the course of the year. As consequence, ruin lizard daily activity pattern includes either the hibernation or periods of inactivity determined by hypothermia. Here we showed the rhythmic expression of two clock genes, lPer2 and lClock, in the liver of active lizards exposed to summer photo-thermoperiodic conditions. Interestingly, the exposition of lizards to hypothermic conditions, typical of winter season, induced a strong dampening of clock genes mRNA rhythmicity with a coincident decrease of levels. We also examined the qualitative and quantitative distribution of lPER2 and lCLOCK protein in different cellular compartments during the 24-h cycle. In the liver of active lizards both proteins showed a rhythmic expression profile in all cellular compartments. After 3 days at 6 degrees C, some temporal fluctuations of the lCLOCK and lPER2 are still detectable, although, with some marked modifications in respect to the values detected in the liver of active lizards. Besides demonstrating the influence of low temperature on the lizard liver circadian oscillators, present results could provide new essential information for comparative studies on the influence of temperature on the circadian system across vertebrate classes.     

Interplay Between Wetting and Phase Behavior in Binary Polymer Films and Wedges: Monte Carlo Simulations and Mean Field Calculations

Confining a binary mixture, one can profoundly alter its miscibility behavior. The qualitative features of miscibility in confined geometry are ratheruniversal and shared by polymer mixtures as well as small molecules, but the unmixing transition in the bulk and the wetting transition are typically well separated in polymer blends. The interplay between wetting and miscibility of a symmetric polymer mixture via large-scale Monte Carlo simulations in the framework of the bond fluctuation model and via numerical self–consistent field calculations is studied. The film surfaces interact with the monomers via short ranged potentials, and the wetting transition of the semi–infinite system is of first order. It can be accurately located in the simulations by measuring the surface and interface tensions and using Young’s equation. If both surfaces in a film attract the same component, capillary condensation occurs and the critical point is close to the critical point of the bulk. If surfaces attract different components, an interface localization/delocalization occurs which gives rise to phase diagrams with two critical points in the vicinity of the pre-wetting critical point of the semi–infinite system. The crossover between these two types of phase diagrams as a function of the surface field asymmetry is studied. The dependence of the phase diagram on the film thickness Δ for antisymmetric surface fields is investigated. Upon decreasing the film thickness, the two critical points approach the symmetry axis of the phase diagram, and below a certain thickness Δ_tri, there remains only a single critical point at the symmetric composition. This corresponds to a second-order interface localization/delocalization transition even though the wetting transition is of first order. At a specific film thickness, Δ_tri, tricritical behavior is found. The behavior of antisymmetric films is compared with the phase behavior in an antisymmetric double wedge. While the former is the analog of the wetting transition of a planar surface, the latter is related to the filling behavior of a single wedge. Evidence for a second-order interface localization/delocalization transition in an antisymmetric double wedge is presented, and its unconventional critical behavior is related to the predictions of Parry et al. (Phys. Rev. Lett. 83:5535 (1999)) for wedge filling. The critical behavior differs from the Ising universality class and is characterized by strong anisotropic fluctuations.Invited paper presented at the Fifteenth Symposium on Thermophysical Properties, June 022–27, 2003, Boulder, Colorado, U.S.A.     

Limits of economic and strategic rationality for agents and MA systems

AI adoption of the game-theoretic paradigm although motivated and productive, suffers from basic limits for modelling autonomous agents and MA systems. First, we briefly restate game-theory's role for DAI and MAS: the introduction of formal prototypical social situations (“games”); the use of formal and sound notions, a self-interested view of autonomous agents, etc. Then, a number of criticisms, that have an impact on modelling intelligent social/individual action, are examined: the economicist interpretation of rationality; its instrumentalist conception, which leaves implicit the ends of agents' choices; the consequent multiple equilibria allowed by the theory; the context-unboundedness of rationality. Some contributions for a more heterarchic, context-bounded, architecture of rational agent are given, and a goal-based strategy, as distinct from a strictly utilitarian principle of decision-making, is proposed. Troubles of game-theory with multi-agent systems and in particular with modelling “cooperation” are outlined. Finally, some limits inherent in the notion of “incentive engineering” are pointed out.     

A portable CPU-management framework for Java

The Java resource accounting framework, second edition (J-RAF2), is a portable CPU-management framework for Java environments. It is based on fully automated program-transformation techniques applied at the bytecode level and can be used with every standard Java virtual machine. J-RAF2 modifies applications, libraries, and the Java development kit itself to expose details regarding thread execution. This article focuses on the extensible runtime APIs, which are designed to let developers tailor management policies to their needs.     

Vascular endothelial growth factor (VEGF) induces rapid prourokinase (pro-uPA) activation on the surface of endothelial cells

Vascular endothelial growth factor (VEGF) is the pivotal angiogenic growth factor activating endothelial cells to migrate, proliferate, and form capillary tubes. For an ordered endothelial cell migration, tissue invasion, and degradation of the extracellular matrix, proteolytic machinery is indispensable. Such machinery, suitable for localized proteolysis, is provided by the prourokinase-urokinase-plasmin system. Prourokinase (pro-uPA), the initial component of this system, is, however, synthesized in its inactive precursor form and as such bound to its cellular receptor uPAR. Here we identify a mechanism via which VEGF(165) interacting with its receptor VEGFR-2 rapidly induces prourokinase activation that is dependent on a change in integrin affinity, activation of matrix metalloproteinase 2 (MMP-2), and pro-uPA being bound to its surface receptor uPAR. This VEGF-induced pro-uPA activation on endothelial cells is responsible for VEGF-dependent local fibrinolytic activity and might be one of the initial steps in the angiogenic process.     

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K_D=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (K_D=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.     

Effects of thermal processing and iron doping in co-sputtered barium strontium titanate thin films

The effects of the thermal processing and iron doping on RF magnetron co-sputtered barium strontium titanate thin film properties have been investigated. X-ray diffraction and Raman spectroscopy have been used to determine the structural evolution of the films as a function of the annealing temperature and the amount of iron dopant. X-ray photoelectron spectroscopy and electron paramagnetic resonance spectroscopy were employed to gain information about the chemical binding states and the defect structure. The enhancement of the quality factor Q, as well as the decreasing permittivity and tunability due to iron acceptor doping are demonstrated.     

Knowledge Acquisition and Design Using Semantics and Perception: A Case Study for Autonomous Robots

Neural Processing Letters - The pervasive use of artificial intelligence and neural networks in several different research fields has noticeably improved multiple aspects of human life. The...