On the complexity of SNP block partitioning under the perfect phylogeny model

Recent technologies for typing single nucleotide polymorphisms (SNPs) across a population are producing genome-wide genotype data for tens of thousands of SNP sites. The emergence of such large data sets underscores the importance of algorithms for large-scale haplotyping. Common haplotyping approaches first partition the SNPs into blocks of high linkage-disequilibrium, and then infer haplotypes for each block separately. We investigate an integrated haplotyping approach where a partition of the SNPs into a minimum number of non-contiguous subsets is sought, such that each subset can be haplotyped under the perfect phylogeny model. We show that finding an optimum partition is -hard even if we are guaranteed that two subsets suffice. On the positive side, we show that a variant of the problem, in which each subset is required to admit a perfect path phylogeny haplotyping, is solvable in polynomial time.     

What is a Logic Translation?

We study logic translations from an abstract perspective, without any commitment to the structure of sentences and the nature of logical entailment, which also means that we cover both proof- theoretic and model-theoretic entailment. We show how logic translations induce notions of logical expressiveness, consistency strength and sublogic, leading to an explanation of paradoxes that have been described in the literature. Connectives and quantifiers, although not present in the definition of logic and logic translation, can be recovered by their abstract properties and are preserved and reflected by translations under suitable conditions. In memoriam Joseph Goguen     

Radiation damage to alkyl chain monolayers on semiconductor substrates investigated by electron spectroscopy

Monolayers of alkyl chains, attached through direct Si-C bonds to Si(111), via phosphonates to GaAs(100) surfaces, or deposited as alkyl-silane monolayers on SiO2, are investigated by ultraviolet and inverse photoemission spectroscopy and X-ray absorption spectroscopy. Exposure to ultraviolet radiation from a He discharge lamp, or to a beam of energetic electrons, leads to significant damage, presumably associated with radiation- or electron-induced H-abstraction leading to carbon-carbon double-bond formation in the alkyl monolayer. The damage results in an overall distortion of the valence spectrum, in the appearance of (occupied) states above the highest occupied molecular orbital of the alkyl molecule, and in a characteristic (unoccupied state) pi resonance at the edge of the carbon absorption peak. These distortions present a serious challenge for the interpretation of the electronic structure of the monolayer system. We show that extrapolation to zero damage at short exposure times eliminates extrinsic features and allows a meaningful extraction of the density of state of the pristine monolayer from spectroscopy measurements.     

Preparation of indoles from alpha-aminonitriles: A short synthesis of FGIN-1-27

Alpha-Aminonitriles derived from 2-aminocinnamic acid esters and amides can be cyclized under basic conditions to furnish substituted indole-3-acetic acid derivatives in quantitative yield. The reaction provides a simple access to a class of biologically active compounds.     

Carnap,Goguen, and the Hyperontologies: Logical Pluralism and Heterogeneous Structuring in Ontology Design

This paper addresses questions of universality related to ontological engineering, namely aims at substantiating (negative) answers to the following three basic questions: (i) Is there a ‘universal ontology’?, (ii) Is there a ‘universal formal ontology language’?, and (iii) Is there a universally applicable ‘mode of reasoning’ for formal ontologies? To support our answers in a principled way, we present a general framework for the design of formal ontologies resting on two main principles: firstly, we endorse Rudolf Carnap’s principle of logical tolerance by giving central stage to the concept of logical heterogeneity, i.e. the use of a plurality of logical languages within one ontology design. Secondly, to structure and combine heterogeneous ontologies in a semantically well-founded way, we base our work on abstract model theory in the form of institutional semantics, as forcefully put forward by Joseph Goguen and Rod Burstall. In particular, we employ the structuring mechanisms of the heterogeneous algebraic specification language HetCasl for defining a general concept of heterogeneous, distributed, highly modular and structured ontologies, called hyperontologies. Moreover, we distinguish, on a structural and semantic level, several different kinds of combining and aligning heterogeneous ontologies, namely integration, connection, and refinement. We show how the notion of heterogeneous refinement can be used to provide both a general notion of sub-ontology as well as a notion of heterogeneous equivalence of ontologies, and finally sketch how different modes of reasoning over ontologies are related to these different structuring aspects.     

Biomimetic oxidation of plant protecting agents

The suitability of two in vitro oxidation systems as chemical models for the biological degradation of plant protecting agents has been investigated. As representative herbicides diclofop, fenoxaprop, isoproturon, linuron and monolinuron have been oxidised by two systems, the Fentons' reagent and the ascorbic acid oxidation system (AAOS) and the results compared to those of the known metabolic pathways of these compounds. The herbicides have been oxidised by Fentons' reagent (hydroxy radicals). The main products were isolated by preparative scale HPLC and identified with (1)H-NMR and MS. Some of the products have been identified by comparing their retention times and UV/Vis-spectra to those of standard compounds. Several products known from biological degradation are also found after chemical oxidation, however, notable differences between the two pathways have been observed, for instance in the case of diclofop. Oxidation by the AAOS leads to comparable results. Reaction rates for the oxidation with the AAOS have been studied and compared with data known from degradation studies of the herbicides in soil. Compounds which are slowly degraded in soil are oxidised more slowly in the biomimetic process than those with a fast degradation in soil.     

Quantitative determination of four nitrofuran metabolites in meat by isotope dilution liquid chromatography-electrospray ionisation-tandem mass spectrometry

A confirmatory method based on isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been developed for the low-level determination of residues of four nitrofuran veterinary drugs in meat, e.g., furazolidone, furaltadone, nitrofurantoin, and nitrofurazone. The procedure entails an acid-catalysed release of protein-bound metabolites, followed by their in situ conversion into the 2-nitrobenzaldehyde (NBA) imine-type derivatives. Liquid-liquid extraction and clean-up on a polymeric solid phase extraction cartridge are then performed before LC-MS/MS analysis by positive electrospray ionisation (ESI) applying multiple reaction monitoring of three transition reactions for each compound. Reliable quantitation is obtained by using one deuterated analogue per analyte (d4-NBA derivative) as internal standard (IS). Validation of the method in chicken meat was conducted following the European Union (EU) criteria for the analysis of veterinary drug residues in foods. The decision limits (CCalpha) were 0.11-0.21 microg/kg, and the detection capabilities (CCbeta) 0.19-0.36 microg/kg, thus below the minimum required performance limit (MRPL) set at 1 microg/kg by the EU. The method is robust and suitable for routine quality control operations, and more than 200 sample injections were performed without excessive pollution of the mass spectrometer or loss of LC column performance.     

Structural characterization of organic multilayers on silicon(111) formed by immobilization of molecular films on functionalized Si-C linked monolayers

Silicon(111)-H surfaces were derivatized with omega-functionalized alkenes in UV-mediated and thermal hydrosilylation reactions to give Si-C linked monolayers. Additional molecular layers of organic compounds were coupled either directly or via linker molecules to the functionalized alkyl monolayers. In the first instance, amino-terminated monolayers were prepared from a tert-butoxycarbonyl-protected omega-aminoalkene followed by removal of the protecting group. Various thiols were coupled to the monolayer using a heterobifunctional linker, which introduced maleimide groups onto the surface. In the second system, N-hydroxysuccinimide (NHS) ester-terminated monolayers were formed by reaction of Si-H with N-succinimidyl undecenoate. The reactivity of the NHS ester groups was confirmed by further modification of the monolayer. The stepwise assembly of these multilayer structures was characterized by X-ray reflectometry and X-ray photoelectron spectroscopy.