Lazy AC-Pattern Matching for Rewriting

We define a lazy pattern-matching mechanism modulo associativity and commutativity. The solutions of a pattern-matching problem are stored in a lazy list composed of a first substitution at the head and a non-evaluated object that encodes the remaining computations. We integrate the lazy AC-matching in a strategy language: rewriting rule and strategy application produce a lazy list of terms.Comment: In Proceedings WRS 2011, arXiv:1204.531

Strategies in PRholog

PRholog is an experimental extension of logic programming with strategic conditional transformation rules, combining Prolog with Rholog calculus. The rules perform nondeterministic transformations on hedges. Queries may have several results that can be explored on backtracking. Strategies provide a control on rule applications in a declarative way. With strategy combinators, the user can construct more complex strategies from simpler ones. Matching with four different kinds of variables provides a flexible mechanism of selecting (sub)terms during execution. We give an overview on programming with strategies in PRholog and demonstrate how rewriting strategies can be expressed

Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition

Child undernutrition is a global health issue associated with a high burden of infectious disease. Undernourished children display an overabundance of intestinal pathogens and pathobionts, and these bacteria induce enteric dysfunction in undernourished mice; however, the cause of their overgrowth remains poorly defined. Here, we show that disease-inducing human isolates of Enterobacteriaceae and Bacteroidales spp. are capable of multi-species symbiotic cross-feeding, resulting in synergistic growth of a mixed community in vitro. Growth synergy occurs uniquely under malnourished conditions limited in protein and iron: in this context, Bacteroidales spp. liberate diet- and mucin-derived sugars and Enterobacteriaceae spp. enhance the bioavailability of iron. Analysis of human microbiota datasets reveals that Bacteroidaceae and Enterobacteriaceae are strongly correlated in undernourished children, but not in adequately nourished children, consistent with a diet-dependent growth synergy in the human gut. Together these data suggest that dietary cross-feeding fuels the overgrowth of pathobionts in undernutrition

Extensional and Intensional Strategies

This paper is a contribution to the theoretical foundations of strategies. We first present a general definition of abstract strategies which is extensional in the sense that a strategy is defined explicitly as a set of derivations of an abstract reduction system. We then move to a more intensional definition supporting the abstract view but more operational in the sense that it describes a means for determining such a set. We characterize the class of extensional strategies that can be defined intensionally. We also give some hints towards a logical characterization of intensional strategies and propose a few challenging perspectives

The graph rewriting calculus: confluence and expressiveness

Introduced at the end of the nineties, the Rewriting Calculus (rho-calculus, for short) is a simple calculus that uniformly integrates term-rewriting and lambda-calculus. The Rhog has been recently introduced as an extension of the rho-calculus, handling structures with cycles and sharing. The calculus over terms is naturally generalized by using unification constraints in addition to the standard rho-calculus matching constraints. This leads to a term-graph representation in an equational style where terms consist of unordered lists of equations. In this paper we show that the (linear) Rhog is confluent. The proof of this result is quite elaborated, due to the non-termination of the system and to the fact that we work on equivalence classes of terms. We also show that the Rhog can be seen as a generalization of first-order term-graph rewriting, in the sense that for any term-graph rewrite step a corresponding sequence of rewritings can be found in the Rhog

AT7519, a Novel Small Molecule Multi-Cyclin Dependent Kinase Inhibitor, Induces Apoptosis in Multiple Myeloma VIA GSK3 beta

Dysregulated cell cycling is a universal hallmark of cancer and is often mediated by abnormal activation of cyclin-dependent kinases (CDKs) and their cyclin partners. Overexpression of individual complexes are reported in multiple myeloma (MM), making them attractive therapeutic targets. In this study, we investigate the preclinical activity of a novel small-molecule multi-CDK inhibitor, AT7519, in MM. We show the anti-MM activity of AT7519 displaying potent cytotoxicity and apoptosis; associated with in vivo tumor growth inhibition and prolonged survival. At the molecular level, AT7519 inhibited RNA polymerase II (RNA pol II) phosphorylation, a CDK9, 7 substrate, associated with decreased RNA synthesis confirmed by [(3)H] Uridine incorporation. In addition, AT7519 inhibited glycogen synthase kinase 3beta (GSK-3beta) phosphorylation; conversely pretreatment with a selective GSK-3 inhibitor and shRNA GSK-3beta knockdown restored MM survival, suggesting the involvement of GSK-3beta in AT7519-induced apoptosis. GSK-3beta activation was independent of RNA pol II dephosphorylation confirmed by alpha-amanitin, a specific RNA pol II inihibitor, showing potent inhibition of RNA pol II phosphorylation without corresponding effects on GSK-3beta phosphorylation. These results offer new insights into the crucial, yet controversial role of GSK-3beta in MM and show significant anti-MM activity of AT7519, providing the rationale for its clinical evaluation in MM

A Domain-Specific Language for Incremental and Modular Design of Large-Scale Verifiably-Safe Flow Networks (Preliminary Report)

We define a domain-specific language (DSL) to inductively assemble flow networks from small networks or modules to produce arbitrarily large ones, with interchangeable functionally-equivalent parts. Our small networks or modules are "small" only as the building blocks in this inductive definition (there is no limit on their size). Associated with our DSL is a type theory, a system of formal annotations to express desirable properties of flow networks together with rules that enforce them as invariants across their interfaces, i.e, the rules guarantee the properties are preserved as we build larger networks from smaller ones. A prerequisite for a type theory is a formal semantics, i.e, a rigorous definition of the entities that qualify as feasible flows through the networks, possibly restricted to satisfy additional efficiency or safety requirements. This can be carried out in one of two ways, as a denotational semantics or as an operational (or reduction) semantics; we choose the first in preference to the second, partly to avoid exponential-growth rewriting in the operational approach. We set up a typing system and prove its soundness for our DSL.Comment: In Proceedings DSL 2011, arXiv:1109.032

To sit or stand? A preliminary, cross sectional study to investigate if there is a difference in glenohumeral subluxation in sitting or standing in people following stroke

Background: Glenohumeral subluxation (GHS) is a common symptom following stroke. Many therapists postulate that GHS may be reduced if the base of support (BOS) is reduced and the centre of mass (COM) is raised as this requires greater postural muscle activity. However, there is little empirical evidence to support this practice. Objective: The aim of this preliminary study was to investigate if the amount of GHS alters from sitting to standing. Study design: A cross sectional, within-subject design in a convenience sample of 15 stroke patients with GHS was utilised. Methods: A prospective design was used with a single blinded tester who assessed GHS using the calliper method in sitting, standing and on return to sitting. Friedman and post hoc Wilcoxon tests showed that GHS was significantly reduced in standing compared to sitting (p <0.05) but this reduction was not maintained on return to sitting (p = 0.25). Conclusions: The results of this study are limited by its small size. However, these results indicate that reducing BOS during rehabilitation may improve GHS after stroke. Whilst the maintenance of benefit is not established, these findings suggest that reducing BOS as part of treatment may help patients with GHS. Further research is now required to replicate these results in a larger sample and to directly examine shoulder muscle activity to investigate which muscles may influence GHS in response to changing BOS. Future work could also aim to determine whether the reduction in GHS was directly attributable to a reduced BOS or the effort associated with moving from sitting to standing