Quantum Computer with Mixed States and Four-Valued Logic

In this paper we discuss a model of quantum computer in which a state is an operator of density matrix and gates are general quantum operations, not necessarily unitary. A mixed state (operator of density matrix) of n two-level quantum systems is considered as an element of 4^n-dimensional operator Hilbert space (Liouville space). It allows to use a quantum computer model with four-valued logic. The gates of this model are general superoperators which act on n-ququat state. Ququat is a quantum state in a four-dimensional (operator) Hilbert space. Unitary two-valued logic gates and quantum operations for an n-qubit open system are considered as four-valued logic gates acting on n-ququat. We discuss properties of quantum four-valued logic gates. In the paper we study universality for quantum four-valued logic gates.Comment: 17 page

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.

Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available

Sardine spawning off the European Atlantic coast:Characterization of and spatio-temporal variability in spawning habitat

Data on the occurrence of sardine (Sardina pilchardus) eggs from 42 national ichthyoplankton surveys along the European Atlantic coast were collated in order to describe the spawning habitat and spawning distribution of sardine in recent decades (1985-2005). A modification of existing spawning habitat characterisation techniques and a newly developed method to compare the probability of egg presence across surveys carried out with different sampling gears were used. Results showed that sardine spawning off the Atlantic European coast is mainly restricted to the shelf area, with the main geographical range being between the Strait of Gibraltar (the southern limit of data available for this analysis) and the middle part of the Armorican shelf (latitude around 47.5 degrees North), and along a temperature range of 12-17 degrees C. Spawning grounds within these limits show a nearly continuous geographical distribution, covering a large proportion of the shelf of the Iberian peninsula and adjacent waters, except for: (1) a persistent gap at the north west corner of the Iberian peninsula, (2) a small secondary break at the Spanish-French border in the inner part of the Bay of Biscay and (3) at the south west corner of the peninsula where there is a narrowing of the shelf width. These discontinuities were used to separate spawning into four nuclei and to describe the changes in spawning distribution in the time series. The relative importance of each nucleus and the degree of separation between adjacent nuclei varies between years, with the exception of the permanent gap at the northwest corner of the Iberian peninsula, which is persistent throughout the time series. Year to year changes in the proportion of the potential spawning habitat in which spawning actually occurred, changing from around 60% before the mid 1990s to around 40% thereafter, and did not show any relationship with spawning stock biomass. Evolution of potential habitat occupation over the Armorican shelf shows larger variability than that observed in the Iberian peninsula, with percentages of occupation ranging from around 30% up to nearly 80% of the shelf in recent years (within the limitations of the relatively sparse data for this region). (c) 2007 Elsevier Ltd. All rights reserved.</p