Continuation-Passing C: compiling threads to events through continuations

In this paper, we introduce Continuation Passing C (CPC), a programming language for concurrent systems in which native and cooperative threads are unified and presented to the programmer as a single abstraction. The CPC compiler uses a compilation technique, based on the CPS transform, that yields efficient code and an extremely lightweight representation for contexts. We provide a proof of the correctness of our compilation scheme. We show in particular that lambda-lifting, a common compilation technique for functional languages, is also correct in an imperative language like C, under some conditions enforced by the CPC compiler. The current CPC compiler is mature enough to write substantial programs such as Hekate, a highly concurrent BitTorrent seeder. Our benchmark results show that CPC is as efficient, while using significantly less space, as the most efficient thread libraries available.Comment: Higher-Order and Symbolic Computation (2012). arXiv admin note: substantial text overlap with arXiv:1202.324

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

A Semantic Analysis of C++ Templates

Abstract. Templates are a powerful but poorly understood feature of the C++ language. Their syntax resembles the parameterized classes of other languages (e.g., of Java). But because C++ supports template spe-cialization, their semantics is quite different from that of parameterized classes. Template specialization provides a Turing-complete sub-language within C++ that executes at compile-time. Programmers put this power to many uses. For example, templates are a popular tool for writing program generators. The C++ Standard defines the semantics of templates using natural lan-guage, so it is prone to misinterpretation. The meta-theoretic properties of C++ templates have not been studied, so the semantics of templates has not been systematically checked for errors. In this paper we present the first formal account of C++ templates including some of the more complex aspects, such as template partial specialization. We validate our semantics by proving type safety and verify the proof with the Isabelle proof assistant. Our formalization reveals two interesting issues in the C++ Standard: the first is a problem with member instantiation and the second concerns the generation of unnecessary template specializations.

A new method for dependent parsing

Abstract. Dependent grammars extend context-free grammars by allowing semantic values to be bound to variables and used to constrain parsing. Dependent grammars can cleanly specify common features that cannot be handled by context-free grammars, such as length fields in data formats and significant indentation in programming languages. Few parser generators support dependent parsing, however. To address this we have developed a new method for implementing dependent parsers by extending existing parsing algorithms. Our method proposes a point-free language of dependent grammars, which we believe closely corresponds to existing context-free parsing algorithms, and gives a novel transformation from conventional dependent grammars to point-free ones. To validate our technique, we have specified the semantics of both source and target dependent grammar languages, and proven our transformation sound and complete with respect to those semantics. Furthermore, we have empirically validated the suitability of our point-free language by adapting four parsing engines to support it: an Earley parsing engine; a GLR parsing engine; memoizing, arrow-style parser combinators; and PEG parser combinators.

Radial dGEMRIC in developmental dysplasia of the hip and in femoroacetabular impingement: preliminary results

To assess the pattern of cartilage damage in symptomatic cases of developmental dysplasia of the hip (DDH) and of femoroacetabular impingement (FAI) with a novel three-dimensional (3D) delayed Gadolinium enhanced magnetic resonance imaging of cartilage (dGEMRIC) technique