Formal Methods for Communication Services

We survey formal methods as they are applied to the development of communication services. We report on industrial and academic projects, consider different communication architectures and work related to the feature interaction problem. Based on our survey, the results reported in the literature and most importantly, on extensive discussions with industry, we investigate important industrial concerns and criticisms about the use of formal methods for the development of communication services. We report on a collaborative project between the Swiss Federal Institute of Technology in Lausanne, Swisscom, Alcatel and Thomson in which these industrial concerns have been taken into account from the very beginning. The results of this project are currently being integrated into an industrial software development platform

TINA Service Validation: The ErnesTINA Project

While extensive work has been carried out with the goal of validating the TINA architecture and the TINA documents, little has been done yet for the validation of TINA services. This is the main focus of the ErnesTINA project. In the ErnesTINA project, we propose an integrated approach to facilitate the validation of TINA services by verifying at run-time that the service implementation has not violated and is not violating certain predefined properties. In this paper, we present the specification of the properties, the run-time observation of the distributed environment, the validation of the properties and finally the implementation of the concepts in a prototype

Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice

<p>Abstract</p> <p>Background</p> <p>In a transgenic mouse model of Alzheimer disease (AD), cleavage of the amyloid precursor protein (APP) by the α-secretase ADAM10 prevented amyloid plaque formation, and alleviated cognitive deficits. Furthermore, ADAM10 overexpression increased the cortical synaptogenesis. These results suggest that upregulation of ADAM10 in the brain has beneficial effects on AD pathology.</p> <p>Results</p> <p>To assess the influence of ADAM10 on the gene expression profile in the brain, we performed a microarray analysis using RNA isolated from brains of five months old mice overexpressing either the α-secretase ADAM10, or a dominant-negative mutant (dn) of this enzyme. As compared to non-transgenic wild-type mice, in ADAM10 transgenic mice 355 genes, and in dnADAM10 mice 143 genes were found to be differentially expressed. A higher number of genes was differentially regulated in double-transgenic mouse strains additionally expressing the human APP_[V717I]mutant.</p> <p>Overexpression of proteolytically active ADAM10 affected several physiological pathways, such as cell communication, nervous system development, neuron projection as well as synaptic transmission. Although ADAM10 has been implicated in Notch and β-catenin signaling, no significant changes in the respective target genes were observed in adult ADAM10 transgenic mice.</p> <p>Real-time RT-PCR confirmed a downregulation of genes coding for the inflammation-associated proteins S100a8 and S100a9 induced by moderate ADAM10 overexpression. Overexpression of the dominant-negative form dnADAM10 led to a significant increase in the expression of the fatty acid-binding protein Fabp7, which also has been found in higher amounts in brains of Down syndrome patients.</p> <p>Conclusion</p> <p>In general, there was only a moderate alteration of gene expression in ADAM10 overexpressing mice. Genes coding for pro-inflammatory or pro-apoptotic proteins were not over-represented among differentially regulated genes. Even a decrease of inflammation markers was observed. These results are further supportive for the strategy to treat AD by increasing the α-secretase activity.</p

Binary Reactive Adsorbate on a Random Catalytic Substrate

We study the equilibrium properties of a model for a binary mixture of catalytically-reactive monomers adsorbed on a two-dimensional substrate decorated by randomly placed catalytic bonds. The interacting $A$ and $B$ monomer species undergo continuous exchanges with particle reservoirs and react ($A + B \to \emptyset$) as soon as a pair of unlike particles appears on sites connected by a catalytic bond. For the case of annealed disorder in the placement of the catalytic bonds this model can be mapped onto a classical spin model with spin values $S = -1,0,+1$, with effective couplings dependent on the temperature and on the mean density $q$ of catalytic bonds. This allows us to exploit the mean-field theory developed for the latter to determine the phase diagram as a function of $q$ in the (symmetric) case in which the chemical potentials of the particle reservoirs, as well as the $A-A$ and $B-B$ interactions are equal.Comment: 12 pages, 4 figure

Testing Temporal Logic Properties in Distributed Systems

The concept of event-based behavioral abstraction (EBBA) is shown to facilitate the Design For Testability (DFT) if the set of events is well-chosen. We provide a predefined set of events which, together with linear-time temporal logic, can be used for expressing behavioral properties in object-oriented distributed systems. This allows automizing several steps in the testing process: instrumenting the source code, constructing test-oracles and generating an observer. Taking an industrial example as basis, we discuss how our proposal can be integrated into the software design- and testing process

Toxic cyanobacteria in Svalbard: chemical diversity of microcystins detected using a liquid chromatography mass spectrometry precursor ion screening method

Cyanobacteria synthesize a large variety of secondary metabolites including toxins. Microcystins (MCs) with hepato- and neurotoxic potential are well studied in bloom-forming planktonic species of temperate and tropical regions. Cyanobacterial biofilms thriving in the polar regions have recently emerged as a rich source for cyanobacterial secondary metabolites including previously undescribed congeners of microcystin. However, detection and detailed identification of these compounds is difficult due to unusual sample matrices and structural congeners produced. We here report a time-efficient liquid chromatography-mass spectrometry (LC-MS) precursor ion screening method that facilitates microcystin detection and identification. We applied this method to detect six different MC congeners in 8 out of 26 microbial mat samples of the Svalbard Archipelago in the Arctic. The congeners, of which [Asp3, ADMAdda5, Dhb7] MC-LR was most abundant, were similar to those reported in other polar habitats. Microcystins were also determined using an Adda-specific enzyme-linked immunosorbent assay (Adda-ELISA). Nostoc sp. was identified as a putative toxin producer using molecular methods that targeted 16S rRNA genes and genes involved in microcystin production. The mcy genes detected showed highest similarities to other Arctic or Antarctic sequences. The LC-MS precursor ion screening method could be useful for microcystin detection in unusual matrices such as benthic biofilms or liche

Modelling and Testing Object-Oriented Distributed Systems with Linear-time Temporal Logic

Numerous proposals for applying temporal logic to the specification and verification of object-oriented systems have appeared in the past several years. Although various temporal models have been proposed for the requirements analysis of object-oriented distributed systems, there is no similar amount of work for the design- and implementation phase. We present a formal model for the design- and implementation stage which reflects practical requirements and is yet sufficiently general to be applied to a wide range of systems. In our model, which relies on event-based behavioral abstraction, we use linear-time temporal logic as the underlying formalism for the specification of behavioral constraints. We show that although temporal logic is a powerful tool for behavior specifications, it does not have the expressive power required for non-trivial object systems. Specifically, in an object-system it is often essential to express procedural dependencies rather than simple temporal relationships for which we introduce two novel operators. In a case study we demonstrate the practical relevance and applicability of our model

Pole-to-Pole Connections : Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change

Acknowledgments JK acknowledges the Carl Zeiss foundation for PhD funding, the Marie-Curie COFUND-BEIPD PostDoc fellowship for PostDoc funding, FNRS travel funding and the logistical and financial support by UNIS. JK and FK acknowledge the Natural Environment Research Council (NERC) Antarctic Funding Initiative AFI-CGS-70 (collaborative gearing scheme) and logistic support from the British Antarctic Survey (BAS) for field work in Antarctica. JK and CZ acknowledge the Excellence Initiative at the University of Tübingen funded by the German Federal Ministry of Education and Research and the German Research Foundation (DFG). FH, AV, and PB received funding from MetaHIT (HEALTH-F4-2007-201052), Microbios (ERC-AdG-502 669830) and the European Molecular Biology Laboratory (EMBL). We thank members of the Bork group at EMBL for helpful discussions. We acknowledge the EMBL Genomics Core Facility for sequencing support and Y. P. Yuan and the EMBL Information Technology Core Facility for support with high-performance computing and EMBL for financial support. PC is supported by NERC core funding to the BAS “Biodiversity, Evolution and Adaptation” Team. MB was funded by Helge Ax:son Johnsons Stiftelse and PUT1317. DRD acknowledges the DFG funded project DI698/18-1 Dietrich and the Marie Curie International Research Staff Exchange Scheme Fellowship (PIRSES-GA-2011-295223). Operations in the Canadian High Arctic were supported by the Natural Sciences and Engineering Research Council of Canada (NSERC), ArcticNet and the Polar Continental Shelf Program (PCSP). We are also grateful to the TOTAL Foundation (Paris) and the UK NERC (WP 4.3 of Oceans 2025 core funding to FCK at the Scottish Association for Marine Science) for funding the expedition to Baffin Island and within this context Olivier Dargent and Dr. Pieter van West for sample collection, and the Spanish Ministry of Science and Technology through project LIMNOPOLAR (POL200606635 and CGL2005-06549-C02-01/ANT to AQ as well as CGL2005-06549-C02-02/ANT to AC, the last of these co-financed by European FEDER funds). We are grateful for funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland), funded by the Scottish Funding Council (HR09011) and contributing institutions. Supplementary Material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fevo.2017.00137/full#supplementary-materialPeer reviewedPublisher PD

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype