Regular Expression Matching and Operational Semantics

Many programming languages and tools, ranging from grep to the Java String library, contain regular expression matchers. Rather than first translating a regular expression into a deterministic finite automaton, such implementations typically match the regular expression on the fly. Thus they can be seen as virtual machines interpreting the regular expression much as if it were a program with some non-deterministic constructs such as the Kleene star. We formalize this implementation technique for regular expression matching using operational semantics. Specifically, we derive a series of abstract machines, moving from the abstract definition of matching to increasingly realistic machines. First a continuation is added to the operational semantics to describe what remains to be matched after the current expression. Next, we represent the expression as a data structure using pointers, which enables redundant searches to be eliminated via testing for pointer equality. From there, we arrive both at Thompson's lockstep construction and a machine that performs some operations in parallel, suitable for implementation on a large number of cores, such as a GPU. We formalize the parallel machine using process algebra and report some preliminary experiments with an implementation on a graphics processor using CUDA.Comment: In Proceedings SOS 2011, arXiv:1108.279

Robust study design is as important on the social as it is on the ecological side of applied ecological research

1. The effective management of natural systems often requires resource users to change their behaviour. This has led to many applied ecologists using research tools developed by social scientists. This comes with challenges as ecologists often lack relevant disciplinary training. 2. Using an example from the current issue of Journal of Applied Ecology that investigated how conservation interventions influenced conservation outcomes, we discuss the challenges of conducting interdisciplinary science. We illustrate our points using examples from research investigating the role of law enforcement and outreach activities in limiting illegal poaching and the application of the theory of planned behaviour to conservation. 3. Synthesis and applications. Interdisciplinary research requires equal rigour to be applied to ecological and social aspects. Researchers with a natural science background need to access expertise and training in the principles of social science research design and methodology, in order to permit a more balanced interdisciplinary understanding of social–ecological system

Bioactive Food Components and Cancer-Specific Metabonomic Profiles

Cancer cells possess unique metabolic signatures compared to normal cells, including shifts in aerobic glycolysis, glutaminolysis, and de novo biosynthesis of macromolecules. Targeting these changes with agents (drugs and dietary components) has been employed as strategies to reduce the complications associated with tumorigenesis. This paper highlights the ability of several food components to suppress tumor-specific metabolic pathways, including increased expression of glucose transporters, oncogenic tyrosine kinase, tumor-specific M2-type pyruvate kinase, and fatty acid synthase, and the detection of such effects using various metabonomic technologies, including liquid chromatography/mass spectrometry (LC/MS) and stable isotope-labeled MS. Stable isotope-mediated tracing technologies offer exciting opportunities for defining specific target(s) for food components. Exposures, especially during the early transition phase from normal to cancer, are critical for the translation of knowledge about food components into effective prevention strategies. Although appropriate dietary exposures needed to alter cellular metabolism remain inconsistent and/or ill-defined, validated metabonomic biomarkers for dietary components hold promise for establishing effective strategies for cancer prevention

Narrowband spectroscopy by all-optical correlation of broadband pulses

High peak power ultrafast lasers are widely used in nonlinear spectroscopy but often limit its spectral resolution because of the broad frequency bandwidth of ultrashort laser pulses. Improving the resolution by achieving spectrally narrow excitation of, or emission from, the resonant medium by means of multi-photon interferences has been the focus of many recent developments in ultrafast spectroscopy. We demonstrate an alternative approach, in which high resolution is exercised by detecting narrow spectral correlations between broadband excitation and emission optical fields. All-optical correlation analysis, easily incorporated into the traditional spectroscopic setup, enables direct, robust and simultaneous detection of multiple narrow resonances with a single femtosecond pulse.Comment: 5 pages, 4 figures, submitted to PR

Pd-Catalyzed Nucleophilic Fluorination of Aryl Bromides

On the basis of mechanism-driven reaction design, a Pd-catalyzed nucleophilic fluorination of aryl bromides and iodides has been developed. The method exhibits a broad substrate scope, especially with respect to nitrogen-containing heteroaryl bromides, and proceeds with minimal formation of the corresponding reduction products. A facilitated ligand modification process was shown to be critical to the success of the reaction.National Science Foundation (U.S.) (CHE 0946721)Amgen Inc.National Science Foundation (U.S.) (Predoctoral fellowship (2010094243))National Institutes of Health (U.S.) (Award GM46059

Crystalline optical cavity at 4 K with thermal noise limited instability and ultralow drift

Crystalline optical cavities are the foundation of today's state-of-the-art ultrastable lasers. Building on our previous silicon cavity effort, we now achieve the fundamental thermal noise-limited stability for a 6 cm long silicon cavity cooled to 4 Kelvin, reaching $6.5\times10^{-17}$ from 0.8 to 80 seconds. We also report for the first time a clear linear dependence of the cavity frequency drift on the incident optical power. The lowest fractional frequency drift of $-3\times10^{-19}$/s is attained at a transmitted power of 40 nW, with an extrapolated drift approaching zero in the absence of optical power. These demonstrations provide a promising direction to reach a new performance domain for stable lasers, with stability better than $1\times10^{-17}$ and fractional linear drift below $1\times10^{-19}$/s