Tracing and Explaining Execution of CLP(FD) Programs

Previous work in the area of tracing CLP(FD) programs mainly focuses on providing information about control of execution and domain modification. In this paper, we present a trace structure that provides information about additional important aspects. We incorporate explanations in the trace structure, i.e. reasons for why certain solver actions occur. Furthermore, we come up with a format for describing the execution of the filtering algorithms of global constraints. Some new ideas about the design of the trace are also presented. For example, we have modeled our trace as a nested block structure in order to achieve a hierarchical view. Also, new ways about how to represent and identify different entities such as constraints and domain variables are presented.Comment: 16 pages; Alexandre Tessier, editor; WLPE 2002, http://xxx.lanl.gov/abs/cs.SE/020705

Closed sets of non-local correlations

We introduce a fundamental concept -- closed sets of correlations -- for studying non-local correlations. We argue that sets of correlations corresponding to information-theoretic principles, or more generally to consistent physical theories, must be closed under a natural set of operations. Hence, studying the closure of sets of correlations gives insight into which information-theoretic principles are genuinely different, and which are ultimately equivalent. This concept also has implications for understanding why quantum non-locality is limited, and for finding constraints on physical theories beyond quantum mechanics.Comment: 4+2 pages, new introduction and discussio

High-Throughput Hardware Architecture for the SWIFFT / SWIFFTX Hash Functions

Introduced in 1996 and greatly developed over the last few years, Lattice-based cryptography oers a whole set of primitives with nice features, including provable security and asymptotic efficiency. Going from \asymptotic to \real-world efficiency seems important as the set of available primitives increases in size and functionality. In this present paper, we explore the improvements that can be obtained through the use of an FPGA architecture for implementing an ideal-lattice based cryptographic primitive. We chose to target two of the simplest, yet powerful and useful, lattice-based primitives, namely the SWIFFT and SWIFFTX primitives. Apart from being simple, those are also of central use for future primitives as Lyubashevsky\u27s lattice-based signatures. We present a high-throughput FPGA architecture for the SWIFFT and SWIFFTX primitives. One of the main features of this implementation is an efficient implementation of a variant of the Fast Fourier Transform of order 64 on Z257. On a Virtex-5 LX110T FPGA, we are able to hash 0.6GB/s, which shows a ca. 16x speedup compared to SIMD implementations of the literature. We feel that this demonstrates the revelance of FPGA as a target architecture for the implementation of ideal-lattice based primitives

Identification of target antigens of anti-endothelial cell and anti-vascular smooth muscle cell antibodies in patients with giant cell arteritis: a proteomic approach

International audienceABSTRACT: INTRODUCTION: Immunological studies of giant cell arteritis (GCA) suggest that a triggering antigen of unknown nature could generate a specific immune response. We thus decided to detect autoantibodies directed against endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) in the serum of GCA patients and to identify their target antigens. METHODS: Sera from 15 GCA patients were tested in 5 pools of 3 patients' sera and compared to a sera pool from 12 healthy controls (HCs). Serum immunoglobulin G (IgG) reactivity was analysed by 2-D electrophoresis and immunoblotting with antigens from human umbilical vein ECs (HUVECs) and mammary artery VSMCs. Target antigens were identified by mass spectrometry. RESULTS: Serum IgG from GCA patients recognised 162 ± 3 (mean ± SD) and 100 ± 17 (mean ± SD) protein spots from HUVECs and VSMCs, respectively, and that from HCs recognised 79 and 94 protein spots, respectively. In total, 30 spots from HUVECs and 19 from VSMCs were recognised by at least two-thirds and three-fifths, respectively, of the pools of sera from GCA patients and not by sera from HCs. Among identified proteins, we found vinculin, lamin A/C, voltage-dependent anion-selective channel protein 2, annexin V and other proteins involved in cell energy metabolism and key cellular pathways. Ingenuity pathway analysis revealed that most identified target antigens interacted with growth factor receptor-bound protein 2. CONCLUSIONS: IgG antibodies to proteins in the proteome of ECs and VSMCs are present in the sera of GCA patients and recognise cellular targets that play key roles in cell biology and maintenance of homeostasis. Their potential pathogenic role remains to be determined

The surface distributions of the production of the major volatile species, H₂O, CO₂, CO and O₂, from the nucleus of comet 67P/Churyumov-Gerasimenko throughout the Rosetta Mission as measured by the ROSINA double focusing mass spectrometer

The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) suite of instruments operated throughout the over two years of the Rosetta mission operations in the vicinity of comet 67P/Churyumov-Gerasimenko. It measured gas densities and composition throughout the comet's atmosphere, or coma. Here we present two-years' worth of measurements of the relative densities of the four major volatile species in the coma of the comet, H₂O, CO₂, CO and O₂, by one of the ROSINA sub-systems called the Double Focusing Mass Spectrometer (DFMS). The absolute total gas densities were provided by the Comet Pressure Sensor (COPS), another ROSINA sub-system. DFMS is a very high mass resolution and high sensitivity mass spectrometer able to resolve at a tiny fraction of an atomic mass unit. We have analyzed the combined DFMS and COPS measurements using an inversion scheme based on spherical harmonics that solves for the distribution of potential surface activity of each species as the comet rotates, changing solar illumination, over short time intervals and as the comet changes distance from the sun and orientation of its spin axis over long time intervals. We also use the surface boundary conditions derived from the inversion scheme to simulate the whole coma with our fully kinetic Direct Simulation Monte Carlo model and calculate the production rates of the four major species throughout the mission. We compare the derived production rates with revised remote sensing observations by the Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) as well as with published observations from the Microwave Instrument for the Rosetta Orbiter (MIRO). Finally we use the variation of the surface production of the major species to calculate the total mass loss over the mission and, for different estimates of the dust/gas ratio, calculate the variation of surface loss all over the nucleus

Transfer RNA-derived small RNAs in the cancer transcriptome

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing

A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing

A Single Argonaute Gene Participates in Exogenous and Endogenous RNAi and Controls Cellular Functions in the Basal Fungus Mucor circinelloides

The mechanism of RNAi is well described in metazoans where it plays a role in diverse cellular functions. However, although different classes of endogenous small RNAs (esRNAs) have been identified in fungi, their biological roles are poorly described due, in part, to the lack of phenotype of mutants affected in the biogenesis of these esRNAs. Argonaute proteins are one of the key components of the RNAi pathways, in which different members of this protein family participate in the biogenesis of a wide repertoire of esRNAs molecules. Here we identified three argonaute genes of the fungus Mucor circinelloides and investigated their participation in exogenous and endogenous RNAi. We found that only one of the ago genes, ago-1, is involved in RNAi during vegetative growth and is required for both transgene-induced RNA silencing and the accumulation of distinct classes of esRNAs derived from exons (ex-siRNAs). Classes I and II ex-siRNAs bind to Ago-1 to control mRNA accumulation of the target protein coding genes. Class III ex-siRNAs do not specifically bind to Ago-1, but requires this protein for their production, revealing the complexity of the biogenesis pathways of ex-siRNAs. We also show that ago-1 is involved in the response to environmental signals, since vegetative development and autolysis induced by nutritional stress are affected in ago-1(-) M. circinelloides mutants. Our results demonstrate that a single Ago protein participates in the production of different classes of esRNAs that are generated through different pathways. They also highlight the role of ex-siRNAs in the regulation of endogenous genes in fungi and expand the range of biological functions modulated by RNAi