Quark Lagrangian diagonalization versus non-diagonal kinetic terms

Loop corrections induce a dependence on the momentum squared of the coefficients of the Standard Model Lagrangian, making highly non-trivial (or even impossible) the diagonalization of its quadratic part. Fortunately, the introduction of appropriate counterterms solves this puzzle.Comment: 2 pages, 1 figur

Coupling techniques for nonlinear hyperbolic equations. III. The well-balanced approximation of thick interfaces

We continue our analysis of the coupling between nonlinear hyperbolic problems across possibly resonant interfaces. In the first two parts of this series, we introduced a new framework for coupling problems which is based on the so-called thin interface model and uses an augmented formulation and an additional unknown for the interface location; this framework has the advantage of avoiding any explicit modeling of the interface structure. In the present paper, we pursue our investigation of the augmented formulation and we introduce a new coupling framework which is now based on the so-called thick interface model. For scalar nonlinear hyperbolic equations in one space variable, we observe that the Cauchy problem is well-posed. Then, our main achievement in the present paper is the design of a new well-balanced finite volume scheme which is adapted to the thick interface model, together with a proof of its convergence toward the unique entropy solution (for a broad class of nonlinear hyperbolic equations). Due to the presence of a possibly resonant interface, the standard technique based on a total variation estimate does not apply, and DiPerna's uniqueness theorem must be used. Following a method proposed by Coquel and LeFloch, our proof relies on discrete entropy inequalities for the coupling problem and an estimate of the discrete entropy dissipation in the proposed scheme.Comment: 21 page

Inverse Electron-Demand [4 + 2]-Cycloadditions of Ynamides: Access to Novel Pyridine Scaffolds

Functionalized polycyclic aminopyridines are central to the chemical sciences, but their syntheses are still hampered by a number of shortcomings. These nitrogenated heterocycles can be efficiently prepared by an intramolecular inverse electron demand hetero Diels–Alder ( ih DA) cycloaddition of ynamides to pyrimidines. This ihDA/rDA sequence is general in scope and affords expedient access to novel types of aminopyridinyl scaffolds that hold great promise in terms of exit vector patterns

Is there a best Büchi automaton for explicit model checking?

LTL to Büchi automata (BA) translators are traditionally optimized to produce automata with a small number of states or a small number of non-deterministic states. In this paper, we search for properties of Büchi automata that really influence the performance of explicit model checkers. We do that by manual analysis of several automata and by experiments with common LTL-to-BA translators and realistic verification tasks. As a result of these experiences, we gain a better insight into the characteristics of automata that work well with Spin.Překladače LTL na Büchiho automaty jsou obvykle optimalizovány tak, aby produkovaly automaty s co nejmenším počtem stavů, či s co nejmenším počtem nedeterministických stavů. V této publikaci hledáme vlastnosti Büchiho automatů, které skutečně ovlivňují výkon nástrojů pro explicitní metodu ověřování modelu (model checking). A to pomocí manuální analýzy několika automatů a experimenty s běžnými překladače LTL na automaty a realistickými verifikačními úlohami. Výsledkem těchto experimentů je lepší porozumění charakteristik automatů, které jsou dobré pro model checker Spin

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

OrthoDB: the hierarchical catalog of eukaryotic orthologs

The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained delineations between closely related species. We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects and fungi to facilitate further comparative studies. The database is freely available at http://cegg.unige.ch/orthod

Thinking outside the ocean-climate nexus : Towards systems-informed decision making in a rapidly changing world

Despite repeated calls for more inclusive practices, approaches used to address current challenges within the ocean-climate nexus do not sufficiently account for the complexity of the human-social-ecological system. So far, this has prevented efficient and just decision-making and policies. We propose to shift towards systems-informed decision making, which values transdisciplinary system-thinking and cumulative impact assessments, and encourages multi-system collaboration among decision-makers in order to address the recurring technicality of policies and to foster just solutions that account for the needs of varied actors across the sustainable development spectrum

Magnetic fields in noncommutative quantum mechanics

We discuss various descriptions of a quantum particle on noncommutative space in a (possibly non-constant) magnetic field. We have tried to present the basic facts in a unified and synthetic manner, and to clarify the relationship between various approaches and results that are scattered in the literature.Comment: Dedicated to the memory of Julius Wess. Work presented by F. Gieres at the conference `Non-commutative Geometry and Physics' (Orsay, April 2007