Design and Characterization of a New pVII Combinatorial Phage Display Peptide Library for Protease Substrate Mining Using Factor VII Activating Protease (FSAP) as Model

We describe a novel, easy and efficient combinatorial phage display peptide substrate-mining method to map the substrate specificity of proteases. The peptide library is displayed on the pVII capsid of the M13 bacteriophage, which renders pIII necessary for infectivity and efficient retrieval, in an unmodified state. As capture module, the 3XFLAG was chosen due to its very high binding efficiency to anti-FLAG mAbs and its independency of any post-translational modification. This library was tested with Factor-VII activating protease (WT-FSAP) and its single-nucleotide polymorphism variant Marburg-I (MI)-FSAP. The WT-FSAP results confirmed the previously reported Arg/Lys centered FSAP cleavage site consensus as dominant, as well as reinforcing MI-FSAP as a loss-of-function mutant. Surprisingly, rare substrate clones devoid of basic amino acids were also identified. Indeed one of these peptides was cleaved as free peptide, thus suggesting a broader range of WT-FSAP substrates than previously anticipated.     

The content and composition of sterols and sterol esters in low erucic acid rapeseed (Brassica napus)

The low temperature crystallization technique for the enrichment of “minor” components, such as sterols and sterol esters, from vegetable oils was applied to low erucic acid rapeseed oils. The recovery of free sterols and sterol esters was estimated by use of¹⁴C-cholesterol and¹⁴C-cholesterol oleate. 80% of the free sterols and 45% of the sterol esters were recovered in the liquid fraction, while in two studies total recoveries were 95% and 99%, respectively. This technique showed some selectivity toward the sterol bound fatty acids when compared to direct preparative thin layer chromatography (TLC) of the crude oil. Gas liquid chromatography (GLC) analysis of the free and esterified sterols as TMS-derivatives showed very little selectivity in the enrichment procedure. The fatty acid patterns of the sterol esters demonstrated, however, a preference in the liquid fraction for those sterol esters which have a high linoleic and linolenic acid content. The content of free sterols was 0.3–0.4% and that of sterol esters 0.7–1.2% of the rapeseed oils in both winter and summer types of low erucic acid rapeseed (Brassica napus) when the lipid classes were isolated by direct preparative TLC of the oils. The free sterols in the seven cultivars or breeding lines analyzed were composed of 44–55% sitosterol, 27–36% campesterol, 17–21% brassicasterol, and a trace of cholesterol. The esterified sterols were 47–57% sitosterol, 36–44% campesterol, 6–9% brassicasterol, and traces of cholesterol and Δ5-avenasterol. The fatty acid patterns of these esters were characterized by ca. 30% oleic acid and ca. 50% linoleic acid, whereas these acids constitute 60% and 20%, respectively, of the total fatty acids in the oil. Little or no variation in sterol and sterol ester patterns with locality within Sweden was observed for the one cultivar of summer rapeseed investigated by the low temperature crystallization technique.     

An empirical study of control logic specifications for programmable logic controllers

This paper presents an empirical study of control logic specifications used to document industrial control logic code in manufacturing applications. More than one hundred input/output related property specifications from ten different reusable function blocks were investigated. The main purpose of the study was to provide understanding of how the specifications are expressed by industrial practitioners, in order to develop new tools and methods for specifying control logic software, as well as for evaluating existing ones. In this paper, the studied specifications are used to evaluate linear temporal logic in general and the specification language ST-LTL, tailored for functions blocks, in particular. The study shows that most specifications are expressed as implications, that should always be fulfilled, between input and output conditions. Many of these implications are complex since the input and output conditions may be mixed and involve sequences, timer issues and non-boolean variables. Using ST-LTL it was possible to represent all implications of this study. The few non-implication specifications could be specified in ST-LTL as well after being altered to suit the specification language. The paper demonstrates some advantages of ST-LTL compared to standard linear temporal logic and discusses possible improvements such as support for automatic rewrite of complex specifications.     

Variations in the composition of sterols,tocopherols and lignans in seed oils from fourSesamum species

Seeds from different collections of cultivatedSesamum indicum Linn and three related wild species [specifically,S. alatum Thonn.,S. radiatum Schum & Thonn. andS. angustifolium (Oliv.) Engl.] were studied for their oil contents and fatty acid composition of the total lipids. The oils from wild seeds were characterized by higher percentages of unsaponifiables (4.9, 2.6 and 3.7%, respectively) compared toS. indicum (1.4–1.8%), mainly due to their high contents of lignans. Total sterols accounted forca. 40, 22, 20 and 16% of the unsaponifiables of the four species, respectively. The four species were different in the relative percentages of the three sterol fractions (the desmethyl, monomethyl and dimethyl sterols) and in the percentage composition of each fraction. Campesterol, stigmasterol, sitosterol and Δ⁵-avenasterol were the major desmethyl sterols, whereas obtusifoliol, gramisterol, cycloeucalenol and citrostandienol were the major monomethyl sterols, and α-amyrin, β-amyrin, cycloartenol and 24-methylene cycloartanol were the main dimethyl sterols in all species. Differences were also observed among the four species in sterol patterns of the free sterols compared to the sterol esters.Sesamum alatum contained less tocopherols (210–320 mg/kg oil), andS. radiatum andS. angustifolium contained more tocopherols (ca. 750 and 800 mg/kg oil, respectively) than didS. indicum (490–680 mg/kg oil). The four species were comparable in tocopherol composition, with γ-tocopherol representing 96–99% of the total tocopherols. The four species varied widely in the identity and levels of the different lignans. The percentages of these lignans in the oils ofS. indicum were sesamin (0.55%) and sesamolin (0.50%).Sesamum alatum showed 1.37% of 2-episesalatin and minor amounts of sesamin and sesamolin (0.01% each).Sesamum radiatum was rich in sesamin (2.40%) and contained minor amounts of sesamolin (0.02%), whereS. angustifolium was rich in sesangolin (3.15%) and also contained considerable amounts of sesamin (0.32%) and sesamolin (0.16%).     

Preparation of anchored ceramic coatings on metal substrates: a modified sol-gel technique using colloidal silica sol

A single-step dip-coating technique was developed to produce stable films or washcoats of controlled thickness, surface area and pore-size distribution on alumina whisker-covered metal substrates (both flat plates and monoliths). Dip-coating slurries were prepared by dispersing fine porous powder in a colloidal silica sol. The method provided control over coating thickness and coating properties, such as pore-size distribution and surface area. The coating thickness could be varied between approximately 2 and 40 m by selecting slurry composition and withdrawal speed in the dipping procedure. The pore-size distribution and surface area could be varied by changing type and amount of porous filler material in the dipping slurry. Uniform and bimodal pore-size distributions were obtained using silica and ZSM-5 molecular sieves, respectively, yielding coatings with surface areas between 60 and 400 m²g^–1.     

Implementation of a Modelica compiler using JastAdd attribute grammars

We have implemented a compiler for key parts of Modelica, an object-oriented language supporting equation-based modeling and simulation of complex physical systems. The compiler is extensible, to support experiments with emerging tools for physical models. To achieve extensibility, the implementation is done declaratively in JastAdd, a metacompilation system supporting modern attribute grammar mechanisms such as reference attributes and nonterminal attributes.This paper reports on experiences from this implementation. For name and type analyses, we illustrate how declarative design strategies, originally developed for a Java compiler, could be reused to support Modelica’s advanced features of multiple inheritance and structural subtyping. Furthermore, we present new general design strategies for declarative generation of target ASTs from source ASTs. We illustrate how these strategies are used to resolve a generics-like feature of Modelica called modifications, and to support flattening, a fundamental part of Modelica compilation. To validate that the approach is practical, we have compared the execution speed of our compiler to two existing Modelica compilers.     

Efficient classical simulation of the Deutsch–Jozsa and Simon’s algorithms

A long-standing aim of quantum information research is to understand what gives quantum computers their advantage. This requires separating problems that need genuinely quantum resources from those for which classical resources are enough. Two examples of quantum speed-up are the Deutsch–Jozsa and Simon’s problem, both efficiently solvable on a quantum Turing machine, and both believed to lack efficient classical solutions. Here we present a framework that can simulate both quantum algorithms efficiently, solving the Deutsch–Jozsa problem with probability 1 using only one oracle query, and Simon’s problem using linearly many oracle queries, just as expected of an ideal quantum computer. The presented simulation framework is in turn efficiently simulatable in a classical probabilistic Turing machine. This shows that the Deutsch–Jozsa and Simon’s problem do not require any genuinely quantum resources, and that the quantum algorithms show no speed-up when compared with their corresponding classical simulation. Finally, this gives insight into what properties are needed in the two algorithms and calls for further study of oracle separation between quantum and classical computation.     

Surface wrinkling: the phenomenon causing bees in bitumen

The so called “bee phenomenon” in bitumen has been investigated by means of AFM quantitative nanomechanical property mapping. Bees are a phenomenon that can be observed by topography measurements using AFM. The characteristic “bee” appearance comes from regions with alternating higher and lower bands in the surface topography of bitumen, which are surrounded by a flat area. The proposed mechanism for bee formation is phase separation and differential contraction during cooling from melt temperatures leading to wrinkling due to differences in the elastic modulus of the material phases. Using a laminate wrinkling model, the thickness of the bee laminate was calculated from the wavelengths and Young’s moduli of the bee laminate and the matrix. It was found to vary between 70 and 140 nm for the five bitumen samples that contained significant amounts of wax.