Characterization of homologs of the small RNA SgrS reveals diversity in function

SgrS is a small RNA (sRNA) that requires the RNA chaperone Hfq for its function. SgrS is a unique dual-function sRNA with a base pairing function that regulates mRNA targets and an mRNA function that allows production of the 43-amino-acid protein SgrT. SgrS is expressed when non-metabolizable sugars accumulate intracellularly (glucose-phosphate stress) and is required to allow Escherichia coli cells to recover from stress. In this study, homologs of SgrS were used to complement an E. coli sgrS mutant in order elucidate the physiological relevance of differences among homologs. These analyses revealed that the base pairing function of E. coli and Yersinia pestis SgrS homologs is critical for rescue from glucose-phosphate stress. In contrast, base pairing-deficient SgrS homologs from Salmonella typhimurium, Erwinia carotovora and Klebsiella pneumoniae rescue E. coli cells from stress despite their failure to regulate target mRNAs. Compared with E. coli SgrS, S. typhimurium SgrS produces more SgrT and this rescues cell growth even when the base pairing function is inactivated. Genetic evidence suggests that a secondary structure in the E. coli SgrS 5′ region inhibits sgrT translation. This structure is not present in S. typhimurium SgrS, which explains its higher level of SgrT production

Liveness-Based Garbage Collection for Lazy Languages

We consider the problem of reducing the memory required to run lazy first-order functional programs. Our approach is to analyze programs for liveness of heap-allocated data. The result of the analysis is used to preserve only live data---a subset of reachable data---during garbage collection. The result is an increase in the garbage reclaimed and a reduction in the peak memory requirement of programs. While this technique has already been shown to yield benefits for eager first-order languages, the lack of a statically determinable execution order and the presence of closures pose new challenges for lazy languages. These require changes both in the liveness analysis itself and in the design of the garbage collector. To show the effectiveness of our method, we implemented a copying collector that uses the results of the liveness analysis to preserve live objects, both evaluated (i.e., in WHNF) and closures. Our experiments confirm that for programs running with a liveness-based garbage collector, there is a significant decrease in peak memory requirements. In addition, a sizable reduction in the number of collections ensures that in spite of using a more complex garbage collector, the execution times of programs running with liveness and reachability-based collectors remain comparable

A Proof Strategy Language and Proof Script Generation for Isabelle/HOL

We introduce a language, PSL, designed to capture high level proof strategies in Isabelle/HOL. Given a strategy and a proof obligation, PSL's runtime system generates and combines various tactics to explore a large search space with low memory usage. Upon success, PSL generates an efficient proof script, which bypasses a large part of the proof search. We also present PSL's monadic interpreter to show that the underlying idea of PSL is transferable to other ITPs.Comment: This paper has been submitted to CADE2

Combining Static and Dynamic Contract Checking for Curry

Static type systems are usually not sufficient to express all requirements on function calls. Hence, contracts with pre- and postconditions can be used to express more complex constraints on operations. Contracts can be checked at run time to ensure that operations are only invoked with reasonable arguments and return intended results. Although such dynamic contract checking provides more reliable program execution, it requires execution time and could lead to program crashes that might be detected with more advanced methods at compile time. To improve this situation for declarative languages, we present an approach to combine static and dynamic contract checking for the functional logic language Curry. Based on a formal model of contract checking for functional logic programming, we propose an automatic method to verify contracts at compile time. If a contract is successfully verified, dynamic checking of it can be omitted. This method decreases execution time without degrading reliable program execution. In the best case, when all contracts are statically verified, it provides trust in the software since crashes due to contract violations cannot occur during program execution.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854

Uniqueness Typing for Resource Management in Message-Passing Concurrency

We view channels as the main form of resources in a message-passing programming paradigm. These channels need to be carefully managed in settings where resources are scarce. To study this problem, we extend the pi-calculus with primitives for channel allocation and deallocation and allow channels to be reused to communicate values of different types. Inevitably, the added expressiveness increases the possibilities for runtime errors. We define a substructural type system which combines uniqueness typing and affine typing to reject these ill-behaved programs

A semantical approach to equilibria and rationality

Game theoretic equilibria are mathematical expressions of rationality. Rational agents are used to model not only humans and their software representatives, but also organisms, populations, species and genes, interacting with each other and with the environment. Rational behaviors are achieved not only through conscious reasoning, but also through spontaneous stabilization at equilibrium points. Formal theories of rationality are usually guided by informal intuitions, which are acquired by observing some concrete economic, biological, or network processes. Treating such processes as instances of computation, we reconstruct and refine some basic notions of equilibrium and rationality from the some basic structures of computation. It is, of course, well known that equilibria arise as fixed points; the point is that semantics of computation of fixed points seems to be providing novel methods, algebraic and coalgebraic, for reasoning about them.Comment: 18 pages; Proceedings of CALCO 200

Liberal Typing for Functional Logic Programs

We propose a new type system for functional logic programming which is more liberal than the classical Damas-Milner usually adopted, but it is also restrictive enough to ensure type soundness. Starting from Damas-Milner typing of expressions we propose a new notion of well-typed program that adds support for type-indexed functions, existential types, opaque higher-order patterns and generic functions-as shown by an extensive collection of examples that illustrate the possibilities of our proposal. In the negative side, the types of functions must be declared, and therefore types are checked but not inferred. Another consequence is that parametricity is lost, although the impact of this flaw is limited as "free theorems" were already compromised in functional logic programming because of non-determinism

A New Linear Logic for Deadlock-Free Session-Typed Processes

The π -calculus, viewed as a core concurrent programming language, has been used as the target of much research on type systems for concurrency. In this paper we propose a new type system for deadlock-free session-typed π -calculus processes, by integrating two separate lines of work. The first is the propositions-as-types approach by Caires and Pfenning, which provides a linear logic foundation for session types and guarantees deadlock-freedom by forbidding cyclic process connections. The second is Kobayashi’s approach in which types are annotated with priorities so that the type system can check whether or not processes contain genuine cyclic dependencies between communication operations. We combine these two techniques for the first time, and define a new and more expressive variant of classical linear logic with a proof assignment that gives a session type system with Kobayashi-style priorities. This can be seen in three ways: (i) as a new linear logic in which cyclic structures can be derived and a CYCLE -elimination theorem generalises CUT -elimination; (ii) as a logically-based session type system, which is more expressive than Caires and Pfenning’s; (iii) as a logical foundation for Kobayashi’s system, bringing it into the sphere of the propositions-as-types paradigm