MT: A Mathematica package to compute convolutions

We introduce the Mathematica package MT which can be used to compute, both analytically and numerically, convolutions involving harmonic polylogarithms, polynomials or generalized functions. As applications contributions to next-to-next-to-next-to leading order Higgs boson production and the Drell–Yan process are discussed.     

Concerned with the unprivileged: user programs in kernel refinement

It is a great verification challenge to prove properties of complete computer systems on the source code level. The L4.verified project achieved a major step towards this goal by mechanising a proof of functional correctness of the seL4 kernel. They expressed correctness in terms of data refinement with a coarse-grained specification of the kernel’s execution environment. In this paper, we strengthen the original correctness theorem in two ways. First, we convert the previous abstraction relations into projection functions from concrete to abstract states. Second, we revisit the specification of the kernel’s execution environment: we introduce the notion of virtual memory based on the kernel data structures, we distinguish individual user programs that run on top of the kernel and we restrict the memory access of each of these programs to its virtual memory. Through our work, properties like the separation of user programs gain meaning. This paves the way for proving security properties like non-interference of user programs. Furthermore, our extension of L4.verified’s proof facilitates the verification of properties about complete software systems based on the seL4 kernel. Besides the seL4-specific results, we report on our work from an engineering perspective to exemplify general challenges that similar projects are likely to encounter. Moreover, we point out the advantages of using projection functions in L4.verified’s verification approach and for stepwise refinement in general.     

Crystallization and structure solution at 4 A resolution of the recombinant synthase domain of N(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli complexed to a substrate analogue

The recombinant synthase domain of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilateisomerase:indole-3-glycerol-phosphate synthase from Escherichiacoli has been crystallized, and the structure has been solvedat 4 Å resolution. Two closely related crystal forms grownfrom ammonium sulphate diffract to 2 Å resolution. Oneform (space group R32, a = 163 Å, = 29.5°) containsthe unliganded synthase domain; the second crystal form (spacegroup P6₃22, a = 144 Å, c = 158 Å) is co-crystallizedwith the substrate analogue N-(5'-phosphoribit-1-yl)anthranilate.The structure of the synthase–inhibitor complex has beensolved by the molecular replacement method. This achievementrepresents the first successful use of a (ß)_g-barrelmonomer as a trial model. The recombinant synthase domain associatesas a trimer in the crystal, the molecules being related by apseudo-crystallographic triad. The interface contacts betweenthe three domains are mediated by those residues that are alsoinvolved in the domain interface of the bifunctional enzyme.This system provides a model for an interface which is usedin both intermolecular and intramolecular domain contacts.     

Cholesteric and photoreactive polyesters

Several classes of cholesteric and photoreactive homo- and copolyesters were synthesized and characterized. Most of these polyesters were prepared in such a way that a chiral spacer (e.g. isosorbide) was polycondensed with a photoreactive dicarboxylic acid, such as 4-carboxycinnamic acid, benzene- 1,4-bisacrylic acid, 4-(4′-carboxyphthalimido)cinnamic acid. In several cases other dicarboxylic acids, such as naphthalene-2,6-dicarboxylic acid or 4-aminobenzoic acid trimellitimide were cocondensed to favor the formation of a Grandjean texture. When ‘sugar diols’ such as isosorbide or isomannide were used as chiral building blocks, suitable diphenols were required as comonomers to stabilize the LC phase. Most polyesters were capable of forming a selectively reflecting Grandjean texture, which can be fixed by crosslinking using UV light. An alternative synthetic strategy based on chiral, substituted terephthalic acids is discussed.     

Portable bead-based fluorescence detection system for multiplex nucleic acid testing: a case study with Bacillus anthracis

This paper describes the design, functioning and use of a portable detection platform for multiplex nucleic acid testing. The system features a bead-supported DNA hybridization assay performed inside a microfluidic cartridge. Polystyrene particles modified with DNA capture probes are confined in the detection area and exposed to a solution of fluorescently labeled target DNA strands. The cartridge, fabricated from inexpensive thermoplastic polymers, allows for conducting up to eight assays in parallel. The detection instrument is equipped with a pneumatic module and a manifold lid serving as an interface to mediate fluid displacement on the cartridge. The fluorescence signal deriving from each assay is recorded by a semi-confocal fluorescence reader embedded in the detection platform. The compact design of the instrument and its level of integration make it possible to obtain an analytical result in less than 15 min, while only few manual steps need to be performed in between. A proof-of-concept demonstration involving Cy3-labeled, PCR-amplified genomic DNA confirms the ability to detect Bacillus anthracis in a multiplexed single-assay format using lef and capC genes. Limits of quantification are on the order of 1 × 10⁹ copies/μL for lef targets.     

Combinatorial micro electrochemistry: Part 1. Automated micro electrosynthesis of iminoquinol ether and [1,2,4]triazolo[4,3-a]pyridinium perchlorate collections in the wells of microtiter plates

A computer-controlled instrument, based on scanning electrochemical microscope technology, is employed in the miniaturized combinatorial electrosynthesis of localized compound collections. Libraries of iminoquinol ethers and triazolo-pyridinium ions are generated in the wells of microtiter plates by potentiostatic electrolysis. Several experimental protocols are described and implemented. Progress of the electrolyses is monitored by microelectrode steady-state voltammetry and product formation is screened by HPLC/MS.     

Task orientation and user‐oriented dialog design

Work psychologists have introduced a concept, in which dialog design is a part of task design. A set of criteria of user‐oriented dialog design is presented here. These criteria are consistently integrated into a control concept. Empirical investigations on some of these criteria are then described. In an experiment to prove the criterion transparency, a desktop interface (high transparency) and a conventional menu selection interface (low transparency) were compared. The main result is the clear superiority of the user interface with direct manipulation over the conventional user interface with menu selection. Support is another of the criteria of user‐oriented dialog design that was empirically investigated. The advantages of goal‐ and task‐oriented help messages are also described here. To make the criterion flexibility and the criterion user‐definability practicable, the implementation of a dialog handler for user‐tailorable systems is introduced. The criterion participation was investigated in field studies. It will be shown that in projects with active participation the costs were exceeded to a lesser degree than in projects with passive participation and to a much lesser degree than in projects without participation.     

Segmentation-based tracking by support fusion

In this paper we present a novel fusion framework to combine the diverse outputs of arbitrary trackers, which are typically not directly combinable, allowing for significantly increasing the tracking quality. Our main idea is first to transform individual tracking outputs such as motion inliers, bounding boxes, or specific target image features to a shared pixel-based representation and then to run a fusion step on this representation. The fusion process additionally provides a segmentation, which, in turn, further allows for a dynamic weighting of the specific trackers’ contributions. In particular, we demonstrate our fusion concept by combining three diverse heterogeneous tracking approaches that significantly differ in methodology as well as in their reported outputs. In the experiments we show that the proposed fusion strategy can successfully handle highly complex non-rigid object scenarios where the individual trackers and state-of-the-art (non-rigid object and fusion based) trackers fail. We demonstrate high performance on a large number of challenging sequences, where we clearly outperform the individual trackers as well as state-of-the-art tracking approaches.     

Fine-Grain Interoperability of Scientific Workflows in Distributed Computing Infrastructures

Today there exist a wide variety of scientific workflow management systems, each designed to fulfill the needs of a certain scientific community. Unfortunately, once a workflow application has been designed in one particular system it becomes very hard to share it with users working with different systems. Portability of workflows and interoperability between current systems barely exists. In this work, we present the fine-grained interoperability solution proposed in the SHIWA European project that brings together four representative European workflow systems: ASKALON, MOTEUR, WS-PGRADE, and Triana. The proposed interoperability is realised at two levels of abstraction: abstract and concrete. At the abstract level, we propose a generic Interoperable Workflow Intermediate Representation (IWIR) that can be used as a common bridge for translating workflows between different languages independent of the underlying distributed computing infrastructure. At the concrete level, we propose a bundling technique that aggregates the abstract IWIR representation and concrete task representations to enable workflow instantiation, execution and scheduling. We illustrate case studies using two real-workflow applications designed in a native environment and then translated and executed by a foreign workflow system in a foreign distributed computing infrastructure.